TIME	EVENT DESCRIPTION	LOCATION
UNIVERSE
1,000,000,000,000 YBN	1) We are a tiny part of a universe made of an infinite amount of space, matter and time.
995,000,000,000 YBN	11) There is no time I can identify as the start of the universe, the universe has no beginning and no end; perhaps the same photons that have always been in the universe continue to move in the space that has always been.
990,000,000,000 YBN	2) There is more space than matter.
980,000,000,000 YBN	3) All of the matter is made of particles of light humans have named "photons". Photons are the base unit of all matter from the tiniest particles to the largest galaxies.1 The basic order of matter from smaller to largest is photons, electrons, positrons, muons, protons, neutrons, atoms, molecules, living objects, planets, stars, globular clusters, galaxies, galaxtic clusters.2 FOOTNOTES 1. ^ Ted Huntington. 2. ^ Ted Huntington.
960,000,000,001 YBN	5) Photons generally move 300 million meters every second in a line, but as pieces of matter, can be slightly slowed from the force of gravity, and stop for an instant when they collide.1 Photons move 300 million meters every second in a line but as pieces of matter their velocity changes slightly because of gravity, and theoretically photons bounce off each other, at which time they come to a complete stop relative to the rest of the universe for an instant before bouncing and accelerating away from each other in the opposite direction.2 FOOTNOTES 1. ^ Ted Huntington 2. ^ Ted Huntington
950,000,000,000 YBN	6) Matter is attracted to other matter and so photons form structures such as protons, atoms, molecules, molecule groups (like all of life of earth), planets, stars, galaxies, and clusters of galaxies. Gravity is responsible for photons forming Hydrogen, Hydrogen forming nebulas, nebulas forming stars, and stars forming galaxies.
940,000,000,000 YBN	7) All of the hundreds of billions of galaxies we can see are only a tiny part of the universe. 1 Most of the galaxies in the universe we will never see because they are too far away for even 1 particle of light from them to be going in the exact direction of our tiny location, or are captured by atoms between here and there. 2 One estimate has 70e21 (sextillion) stars in only the universe we can see. That is 10 times more stars than grains of sand on all the earth. 3 FOOTNOTES 1. ^ Carl Sagan, "Cosmos", Carl Sagan Productions, KCET Los Angeles, (1980). (estimate of how many galaxies) 2. ^ Ted Huntington 3. ^ http://edition.cnn.com/2003/TECH/space/07/22/stars.survey/
935,000,000,000 YBN	4) The patterns in the universe are clear. Photons form gas clouds of Hydrogen and Helium, these gas clouds, called nebuli condense to form galaxies of stars. The stars emit photons back out into the rest of the universe, where they collect and form clouds again. Around each star are many planets and pieces of matter. On many of those planets intelligent life evolves. This life moves their stars out of spiral galaxies to form globular clusters, and ultimately to transform spiral galaxies into elliptical galaxies that travel the universe looking for more matter to fuel their movement. It may very well be that stars at this scale are photons, spiral galaxies charged particles, globular galaxies neutral particles, and galactic clusters atoms at a much larger scale in an infinite macro and micro scale.1 FOOTNOTES 1. ^ Ted Huntington
930,000,000,000 YBN	8) That the frequency of photons from the most distant galaxies we can see have a lower frequency may be due to the effects of gravitation and/or particle collision in the large distance between source and observer.1 EXPERIMENT: does sound frequency actually get lower over large distances?2 FOOTNOTES 1. ^ Ted Huntington. 2. ^ Ted Huntington.
920,000,000,000 YBN	9) Quasars may be very distant regular galaxies.
910,000,000,000 YBN	10) Globular clusters and elliptical galaxies may be made by intelligent life, and spiral galaxies formed without the direct help of living objects. The star types are almost all long lived yellow stars, and there is little or no Hydrogen or Helium "dust" as there are in spiral galaxies. The stars in elliptical galaxies are light weeks apart, much closer together than our star which is 4 light years to the closest star system. Life orbiting any star of a spiral galaxy probably would leave the plane of the galaxy by going up or down.
890,000,000,000 YBN	12) How photons form atoms may still be unknown. Perhaps simply from gravitational attraction, or maybe there need to be large groups of photons to limit available spaces for photons to move in (for example in stars, or galactic centers, and or supernovas.
880,000,000,000 YBN	13) The Milky Way Galaxy forms, perhaps from a gas cloud that formed by capturing matter in the form of light from other stars, from the remains of a previously destroyed galaxy, or some combination of the two.
870,000,000,000 YBN	14) Photons take on a variety of shapes at different scales from the smallest forms in light, up to atoms, molecules, molecule groups (like living objects), planets, stars, galaxies, galactic clusters and the visible universe is the largest formation of photons we can see.
5,500,000,000 YBN 5	16) The yellow star earth will eventually orbit forms, perhaps in a nebula, when matter in the nebula starts accumulating and rotating as a result of gravity, or from the remains of an exploded star that condensed again under the influence of gravity. My opinion is that stars contain molten iron in their center, similar to the earth. {check with supernova remnants} The density of the star the earth rotates is similar to that of a liquid. The most popular theory to explain how stars give off so many photons is that these photons exit as a result of Hydrogen atomically fusing into Helium, and I want to add my opinion that potentially the pressure of gravity simply separates atoms of Hydrogen and helium into their source photons. Perhaps the reaction is similar to the center of the earth where red hot liquid iron emits photons. We obviously do not explain that red hot molten metal as being the result of nuclear fusion, but yet it is clearly not oxygen combustion. Clearly there are many photons exiting stars every second, and each star is losing large amounts of matter in the form of photons. In addition, the most popular theory explains that most atoms heavier than Hydrogen and no heavier than Iron are made in stars, and atoms larger than iron can only be made in supernovae. 1 The current view theorizes that the iron is made just before the supernova, in the gravitational collapse, but I find a liquid iron core being there for the lifetime of every star as a more logical explanation. 2 3 4 FOOTNOTES 1. ^ Ted Huntington 2. ^ http://zebu.uoregon.edu/~imamura/208/mar1/nucleo.html (with image of onion skin layers) 3. ^ Ted Huntington 4. ^ another person declares star inside to be similar to planets: iron, oxygen, nickel, etc. do not support standard solar model. star_inside_iron.pdf 5. ^ Ted Huntington, guess
5,000,000,000 YBN	22) Heavier atoms in the star system move closer to the center and lighter atoms are sent farther out.
4,600,000,000 YBN	17) Planets form around star. Terrestrial planets are red hot, have surface of melted rock, all lighter atoms float to the surface of the molten planets. All the H2O from the first earth oceans and lakes is in the atmosphere in gas form.
4,600,000,000 YBN	30) Moon of earth is formed by 1 of 3 ways: 1) spherical planet collides with earth, moon forms from remaining matter in ring around earth. 2) spherical planet is caught in earth orbit 3) moon of earth forms naturally from original matter of star system in orbit around earth. The Moon orbiting 5 degrees from the axis of the Earth's orbit implies that the Moon was captured, although 5% is not a particularly large difference from the plane of the Earth's rotation.1 That the Moon orbits in the same direction as the Earth is evidence in favor of the Moon forming around the Earth.2 FOOTNOTES 1. ^ Ted Huntington. 2. ^ Ted Huntington.
4,571,000,000 YBN 3 4	31) Oldest meteorite yet found on earth 4,571 million years old.1 2 FOOTNOTES 1. ^ http://www.sciencemag.org/cgi/content/full/288/5472/1819?maxtoshow=&HITS=10&hits =10&RESULTFORMAT=&fulltext=zag+morocco&searchid=1129920472874_9236&stored_search =&FIRSTINDEX=0#RF2 2. ^ http://news.bbc.co.uk/1/hi/sci/tech/783048.stm 3. ^ http://www.sciencemag.org/cgi/content/full/288/5472/1819?maxtoshow=&HITS=10&hits =10&RESULTFORMAT=&fulltext=zag+morocco&searchid=1129920472874_9236&stored_search =&FIRSTINDEX=0#RF2 (4.7 +- .2 billion years) 4. ^ sci has 4.7 +- .2 by where did 4.571 come from?
4,566,000,000 YBN	32) Allende Meteorite 4,566 million years old.
4,530,000,000 YBN	33) Oldest Moon rock returned from Apollo missions (4.53 billions old).
4,500,000,000 YBN	24) Oldest meteor and moon (although no earth) rocks date from this time 4.5 billion years before now.
LIFE
4,500,000,000 YBN	50) Start Precambrian Eon, Hadean Era.1 2 FOOTNOTES 1. ^ The geological Society of America ucmp.berkeley.edu 2. ^ Richard Cowen, "History of Life", (Malden, MA: Blackwell, 2005).
4,450,000,000 YBN	21) Planet earth cools, molten rock cools into thin crust, H2O condenses from the atmosphere by raining, filling the lowest parts of land to make the first earth oceans, lakes, and rivers.1 FOOTNOTES 1. ^ part about rain and streams going to bottom of land: http://www.ersdac.or.jp/Others/geoessay_htm/geoessay_e/geo_text_09_e.htm
4,404,000,000 YBN	34) Oldest "terrestrial" (not from meteorite) zircon yet found on earth, 4.404 billion years old, from Gneiss in West Australia, is evidence that the crust and liquid water were on the surface of earth 4.4 billion years before now.1 FOOTNOTES 1. ^ http://www.nature.com/nature/links/010111/010111-1.html
4,400,000,000 YBN	18) Amino acids, phosphates, and sugars, the components of living objects are created on earth. These molecules are made in the oceans, fresh water, and or atmosphere of earth (or other planets) by lightning, photons with ultraviolet frequency from the star, or ocean floor volcanos.
4,395,000,000 YBN	19) How nucleic acids (polymers made of nucleotides), proteins (polymers made of amino acids), carbohydrates (polymers made of sugars) and lipids (glycerol attached to fatty acids) evolved is not clearly known. Some proteins and nucleic acids have been formed in labs by using clay which can dehydrate and which provides long linear crystal structures to build proteins and nucleic acids on. Amino acids join together to form polypeptides when an H2O molecule is formed from a Hydrogen (H) on 1 amino acid and a hydroxyl (OH) on the second. Are all proteins, carbohydrates, lipids and DNA the products of living objects? Is RNA the only molecule of these that was made without the help of living objects? The most popular theory now has RNA (and potentially lipids) evolving first before any living objects. There is still a large amount of experiment, exploration and education that needs to be done to understand the origins of living objects on planet earth. My opinion is that as soon as there was liquid water on the earth, 4.4 billion years before now, as zircon crystals show, the construction of living objects started on earth.
4,390,000,000 YBN	25) RNA duplication evolves. Perhaps RNA molecules, called "ribozymes" evolved which can make copies of RNA, by connecting free floating nucleotides that match a nucleotide on the same or a different RNA, without any proteins. But until such ribozyme RNA molecules are found, the only molecule known to copy nucleic acids are proteins called polymerases. If such ribozymes exist, then one of the first coded instructions on the RNA molecule that was the ancestor of every living species, must have been the code to make this ribozyme. These early RNA molecules may have been protected by liposomes (spheres of lipids). This process of RNA (and then later DNA) duplication is the most basic aspect of life on earth, and for all the diversity, the one common element of all life is this constant process of DNA duplication, which will later evolve to include cell division. This starts the unbroken thread of copying and division that connects the earliest ancestor, some RNA molecule, to all life on earth that has ever lived.
4,385,000,000 YBN	167) Protein assembly evolves with the creation of various Transfer RNA (tRNA) molecules. Random mutations in the copying (and perhaps even in the natural formation) of RNA molecules probably created a number of the necessary tRNAs (transfer RNA, an RNA molecule responsible for matching free floating amino acid molecules to 3 nucleotide sequences on other RNA molecules). This would be a precellular protein assembly system, where tRNA (transfer RNA) molecules can build polypeptide chains of amino acids by linking directly to other RNA strands. Part of each tRNA molecule bonds with a specific amino acid, and a 3 nucleotide sequence from a different part of the tRNA molecule bonds with the opposite matching 3 nucleotide sequence on an (m)RNA molecule. Since there are tRNA molecules for each amino acid (although some tRNAs can attach to more than one amino acid?), there must have been a slow accumulation of various tRNA molecules for each of the 20 amino acids used in constructing polypeptides in cells living now. Perhaps after the evolution of the first tRNA, the first polypeptides were chains of all the same one amino acid. With the evolution of a second tRNA polypeptides would have more variety because now two amino acids would be available to build polypeptides. This polypeptide assembly system may exist freely in water, or within a liposome1 . This sytem builds many more proteins than would be built without such a system. The mRNA with the code to make copier RNA, now also contains the code to produce various tRNA molecules. These molecules function as a unit, and proto-cell, with the rest of the mRNA initially containing random codes for random proteins. For the first time, RNA code represents a template for other RNA molecules, but also a template for building proteins with the help of tRNA molecules. There is some question of where the origin of the first cell took place, near volcanos on the ocean floor, or in fresh water lakes and tidal pools near volcanos on land, because unprotected nucleic acids cannot exist for much time in the ocean because of Sodium and Chlorine. What were the first amino acids connected as proteins? Were the first proteins all made with the same amino acid?
4,380,000,000 YBN	168) Ribosomal RNA (rRNA) evolves. Ribosomal RNA moves down mRNA molecules functioning as a platform for bringing the mRNA and tRNA molecules together to assemble polypeptides (proteins). This rRNA serves as an early ribosome; objects that serve as sites for building polypeptides and are found in every cell. As time continues the ribosome will grow to include two more RNA molecules, some protein molecules, and a second half that will make polypeptide construction more efficient. The rRNA serves the purpose of bringing amino acids close enough to bond with each other to form polypeptides. As an rRNA moves down an mRNA, tRNA molecules bond with the mRNA and on the opposite side of the tRNA, a matching amino acid (separates? from the tRNA and) attaches to a growing polypeptide chain. Now the mRNA that is the ancestral/progenitor of all of life, contains the code for the copier RNA, tRNAs, and the rRNA molecule. These nucleic acids function as a unit, and proto-cell.
4,375,000,000 YBN	211) The first protein of real importance is built, an RNA polymerase. A molecule that can more efficiently copy RNA. The first protein of real importance is evolved by RNA and assembled by the early ribosome, an RNA polymerase. A molecule that can more efficiently copy RNA.
4,370,000,000 YBN	41) A ribonucleotide reductase protein is built by the early ribosome protein making protocell. This protein changes ribonucleotides into deoxyribonucleotides. This allows the first DNA molecule on earth to be assembled. Ribonucleotide reductase may be the molecule that allowed DNA to be the template for the line of cells that survived to now.
4,365,000,000 YBN	212) A DNA polymerase protein evolves to copy DNA by assembling DNA nucleotides from other DNA molecules.
4,360,000,000 YBN	166) An RNA molecule evolves that causes the early ribosome to create reverse transcriptase, a protein that can assemble DNA molecules from an RNA molecule template. With this advance, a DNA molecule can be constructed that has all of the code that was stored on the long evolved RNA molecule. DNA now serves as a more stable template for making mRNA, each tRNA, rRNA, and the RNA and DNA polymerases. RNA polymerase proteins build RNA molecules using the new DNA template, that still perform their original polypeptide building function together with the tRNA and rRNA molecules, but are labeled "mRNA" (Messenger RNA) because they move from DNA to ribosome. Why DNA serves as the template for all cells and not mRNA is not fully understood, but DNA is a more stable molecule than the single stranded RNA. Perhaps the 2 legs of DNA serve some other important reasons, for example, two legs may allow two processes to happen at one time.
4,355,000,000 YBN	20) The first cell membrane evolves around DNA, made of proteins. This membrane holds water inside a cell. This is the first cell. rRNA comparison shows that this is most likely a eubacterium.1 DNA produces instructions for cytoplasm, the cytoplasm is assembled from proteins made by the ribosome. For the first time, DNA and ribosomes are building cell structure. The templates for each tRNA, rRNA, mRNA and DNA polymerase proteins are already coded in a central strand of DNA. DNA protected by cytoplasm is more likely to survive and copy. This cell is heterotrophic and has no metabolism to produce ATP. Amino acids, nucleotides, H2O, and other molecules enter and exit the cytoplasm only because of a difference in concentration from inside and outside the cell (passive transport) and represent the beginnings of the first digestive system. This either happens in fresh water lakes or in salty oceans, perhaps near lava vents on or under the ocean floor. As this line of DNA continues to make copies of itself, all copies now have cytoplasm. The DNA is composed mainly of instructions to assemble the nucleic acids and proteins needed to build ribosomes, polymerases and cytoplasm. This cell structure forms the basis of all future cells of every living object on earth. These first cells are anaerobic (do not require free oxygen) and heterotrophic, meaning that they do not make their own food: amino acids, nucleotides, phosphates, and sugars. These bacteria depend on these molecules and photons in the form of heat to reproduce and grow. A system of division must evolve which attaches the original and newly synthesized copy of DNA to the cytoplasm, so that as the cell grows, the two copies of DNA can be separated and the first membraned cells can divide into two cells. This is the beginning of the "binary fission" method of cell division. Division of the cell begins with the division of the DNA membrane-attachment site and separates by the growth of new cytoplasm. DNA has 2 functions, 1) to be copied by the polymerase protein, 2) to serve as a code for assembling proteins. Two important evolutionary steps evolve: DNA duplication in cytoplasm, and cell (DNA with cytoplasm) division. The process of DNA duplication is probably similar if not the same process using the same proteins that were used to duplicate DNA without cytoplasm.
4,350,000,001 YBN	26) Perhaps DNA that is connected in a circle allows the DNA polymerase to make continuous copies of the cell. In theory prokaryote cells do not deteroiate from the effect of aging, but they do endure mutations (from photons with ultraviolet frequency, for example), however, there are many other ways prokaryotes can be destroyed (loss of water, physically damaged by nonliving objects, eaten by other organisms, and other mechanisms).
4,345,000,000 YBN	195) Proteins that actively transport molecules into and out of the cytoplasm (facilitative diffusion) evolve.1 FOOTNOTES 1. ^ http://www.cat.cc.md.us/~gkaiser/biotutorials/eustruct/cmeu.html
4,340,000,000 YBN	23) The first viruses are made either from bacteria, or are initially bacteria. These cells depend on the DNA duplicating and protein producing systems of other cells to reproduce themselves. Over time, more effective, and efficient virus designs will survive.1 FOOTNOTES 1. ^ http://cellbio.utmb.edu/cellbio/rer2.htm
4,335,000,000 YBN	28) Glycolysis evolves in the cytoplasm. Cells can now make ATP from glucose and eventually other monosaccharides, the end product is pyruvate. The glycolysis equation is: C6H12O6 (glucose) + 2 NAD+ + 2 ADP + 2 P -----> 2 pyruvic acid, (CH3(C=O)COOH + 2 ATP + 2 NADH + 2 H+
4,330,000,000 YBN	44) Fermentation evolves in the cytoplasm. Cells (all anaerobic) can now make more ATP and convert pyruvate (the final product of glycolysis) to lactate (an ionized form of lactic acid).1 FOOTNOTES 1. ^ http://216.239.63.104/search?q=cache:3s2stckAJoMJ:www.nmc.edu/~ftank/115f04/Ch%2 5209%2520Notes.pdf+cellular+respiration+oldest&hl=en
4,325,000,000 YBN	213) A second kind of fermentation evolves in the cytoplasm. Cells (all anaerobic) can now convert pyruvate (the final product of glycolysis) to ethanol.1 FOOTNOTES 1. ^ http://216.239.63.104/search?q=cache:3s2stckAJoMJ:www.nmc.edu/~ftank/115f04/Ch%2 5209%2520Notes.pdf+cellular+respiration+oldest&hl=en
4,320,000,000 YBN 1	183) Cells evolve that make proteins that can assemble lipids. FOOTNOTES 1. ^ find biomarker evidence
4,315,000,000 YBN	196) Cells that use both proteins and metabolism (ATP) to transport molecules into and out of the cytoplasm (active transport) evolve.1 FOOTNOTES 1. ^ http://www.cat.cc.md.us/~gkaiser/biotutorials/eustruct/cmeu.html
4,310,000,000 YBN	40) One of the first useful proteins to be created with an early precellular protein production system must have been a protein (like RNA polymerase) that can make copies of RNA from mRNA molecules. This protein may have outperformed a ribozyme that was performing the copying function. Eventually mRNA that coded for tRNA molecules and mRNA that coded for rRNA molecules merged to form a template. Now the entire protein production system (the mRNA itself, tRNAs, rRNAs, and the RNA polymerase) could be copied many times by the RNA polymerase protein. This is before cytoplasm or any cell wall has evolved. RNA and DNA copying happens in water, the first cell has not evolved yet.
4,310,000,000 YBN	76) Pili, plasmids and conjugation evolves in prokaryotes. Now some prokaryotes can exchange circular pieces of DNA (plasmids), through tubes (pili). Conjugation may be the process that led to sex (cellular fusion) and also the transition from a circle of DNA to chromosomes in eukaryotes, since some protists (cilliates and some algae) reproduce sexually by conjugation.1 Ar chaeal flagellins are related to members of the type IV pilin/transport superfamily widespread in bacteria. In addition to pili and conjugation, proteins evolve that can assist in splitting DNA and also proteins that assist in merging two strands of DNA together, since some times the DNA in split and the new plasmid is connected and the DNA circle is sown back together.2 FOOTNOTES 1. ^ conjugation in protists, flagella in eukaryotes: Michael Sleigh, "Protozoa and Other Protists", (London; New York: Edward Arnold, 1989). 2. ^ prokaryote pili and archaea flagella related: http://www.queens-pfd.ca/people/index.cfm?meds=profile&profile=12
4,307,000,000 YBN	292) Prokaryote flagella evolve.1 Perhaps pili evolved into flagella, flagella into pili, or the two systems are unrelated.2 Proteins in Archaebacteria flagella are related to pili in bacteria. This may be the beginning of motility. Now for the first time, cells are not completely controlled by surrounding matter, but can make limited choices about their location. FOOTNOTES 1. ^ conjugation in protists, flagella in eukaryotes: Michael Sleigh, "Protozoa and Other Protists", (London; New York: Edward Arnold, 1989). 2. ^ prokaryote pili and archaea flagella related: http://www.queens-pfd.ca/people/index.cfm?meds=profile&profile=12
4,305,000,000 YBN	64) Operons, sequences of DNA that allow certain proteins coded by DNA to not be built, evolve. Proteins bind with these DNA sequences to stop RNA polymerase from building mRNA molecules which would be translated into proteins. Operons allow a bacterium to produce certain proteins only when necessary. Bacteria before now can only build a constant stream of all proteins encoded in their DNA.1 2 FOOTNOTES 1. ^ http://info.bio.cmu.edu/Courses/03441/TermPapers/99TermPapers/GenEvo/operon.html 2. ^ http://web.indstate.edu/thcme/mwking/gene-regulation.html#table
4,304,500,000 YBN	322) Nitrogen fixation evolves in eubacteria. Without bacteria that convert N2 into nitrogen compounds, the supply of nitrogen necessary for much of life would be seriously limited and would drastically slow evolution on earth. Nitrogen fixation is the process by which nitrogen is taken from its relatively inert molecular form (N2) in the atmosphere and converted into nitrogen compounds useful for other chemical processes (such as, notably, ammonia, nitrate and nitrogen dioxide).1 Nitrogen fixation is performed naturally by a number of different prokaryotes, including bacteria, and actinobacteria certain types of anaerobic bacteria. Many higher plants, and some animals (termites), have formed associations with these microorganisms.2 The best-known are legumes (such as clover, beans, alfalfa and peanuts,) which contain symbiotic bacteria called rhizobia within nodules in their root systems, producing nitrogen compounds that help the plant to grow and compete with other plants. When the plant dies, the nitrogen helps to fertilize the soil. The great majority of legumes have this association, but a few genera (e.g., Styphnolobium) do not. 3 FOOTNOTES 1. ^ "Nitrogen fixation". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Nitrogen_fixation 2. ^ "Nitrogen fixation". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Nitrogen_fixation 3. ^ "Nitrogen fixation". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Nitrogen_fixation
4,304,000,000 YBN	287) Multicellularity in the form of filment growth evolves in prokaryotes. Cyanobacteria grow in filaments. Unlike eukaryotes, there is no communication between cells in prokaryote filments.
4,302,000,000 YBN 2	316) Cell differentiation in prokaryotes evolve. Heterocysts evolve in cyanobacteria. Heterocysts are specialized nitrogen-fixing cells formed by some filamentous cyanobacteria during nitrogen starvation. What cell differentiation is first is unknown, perhaps cells that form spores, or cysts, or perhaps cell differentiation that is observes in cyanobacterial filamentous cells. Heterocysts are specialized nitrogen-fixing cells formed by some filamentous cyanobacteria, such as Nostoc punctiforme and Anabaena sperica, during nitrogen starvation. They fix nitrogen from dinitrogen (N2) in the air using the enzyme nitrogenase, in order to provide the cells in the filament with nitrogen for biosynthesis. Nitrogenase is inactivated by oxygen, so the heterocyst must create a microanaerobic environment. The heterocysts' unique structure and physiology requires a global change in gene expression. For example, heterocysts: * produce three additional cell walls, including one of glycolipid that forms a hydrophobic barrier to oxygen * produce nitrogenase and other proteins involved in nitrogen fixation * degrade photosystem II, which produces oxygen * up regulate glycolytic enzymes, which use up oxygen and provide energy for nitrogenase * produce proteins that scavenge any remaining oxygen Cyanobacteria usually obtain a fixed carbon (carbohydrate) by photosynthesis. The lack of photosystem II prevents heterocysts from photosynthesising, so the vegetative cells provide them with carbohydrates, which is thought to be sucrose. The fixed carbon and nitrogen sources are exchanged though channels between the cells in the filament. Heterocysts maintain photosystem I, allowing them to generate ATP by cyclic photophosphorylation. Single heterocysts develop about every 9-15 cells, producing a one-dimensional pattern along the filament. The interval between heterocysts remains approximately constant even though the cells in the filament are dividing. The bacterial filament can be seen as a multicellular organism with two distinct yet interdependent cell types. Such behaviour is highly unusual in prokaryotes and may have been the first example of multicellular patterning in evolution. Once a heterocyst has formed, it cannot revert to a vegetative cell, so this differentiation can be seen as a form of apoptosis. Certain heterocyst-forming bacteria can differentiate into spore-like cells called akinetes or motile cells called hormogonia, making them the most phenotyptically versatile of all prokaryotes. The mechanism of controlling heterocysts is thought to involve the diffusion of an inhibitor of differentiation called PatS. Heterocyst formation is inhibited in the presence of a fixed nitrogen source, such as ammonium or nitrate. The bacteria may also enter a symbiotic relationship with certain plants. In such a relationship, the bacteria do not respond to the availability of nitrogen, but to signals produced by the plant. Up to 60% of the cells can become heterocysts, providing fixed nitrogen to the plant in return for fixed carbon. The cyanobacteria that form heterocysts are divided into the orders Nostocales and Stigonematales, which form simple and branching filaments respectively. Together they form a monophyletic group, with very low genetic variability.1 FOOTNOTES 1. ^ "Heterocyst". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Heterocyst 2. ^ Ted Huntington, a tital guess my friends
4,300,000,000 YBN	58) First autotrophic cells, cells that can produce some if not all of their own food (amino acids, nucleotides, sugars, phophates, lipids, and carbohydrates), but require phosphorus, nitrogen, CO2, water and light in the form of heat.1 There are only 2 kinds of autotrophy: Lithotrophy and Photosynthesis. These are lithotrophic cells that change inorganic (abiotic) molecules into organic molecules. These cells are archaebacteria, called methanogens that perform the reaction: 4H2 + CO2 -> CH4 + 2H2O. They convert CO2 into Methane. Methane is better than CO2 for trapping heat, and could have contributed to heating the earth. FOOTNOTES 1. ^ Richard Cowen, "History of Life", (Malden, MA: Blackwell, 2005).
4,295,000,000 YBN	49) First photosynthetic cells. These cells only have Photosystem I. Photosynthesis Photosystem I evolves in early anaerobic prokaryote cells. One of two photosythesis systems, photosystem I uses a pigment chlorophyll A, absorbs photons in 700 nm wave lengths best, breaking the bond betwenn H2 and S. They are anaerobic and perform the reaction: H2S (Hydrogen Sulfide) + CO2 + light -> CH2O (Formaldehyde) + 2S. Only 5 phyla of eubacteria can photosynthesize.1 FOOTNOTES 1. ^ Battistuzzi, Feijao, Hedges, "A Genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land", BMC Evolutionary Biology, (2004).
4,290,000,000 YBN	43) Photosynthesis Photosystem II evolves in early prokaryote cells. Photosystem 2 absorbs photons best at 680nm wavelengths, a higher frequency of light than Photosystem I. These cells can break the strong Hydrogen bonds between Hydrogen and Oxygen in water molecules (more abundant than Sulphur). This system emits free Oxygen.1 The simple equation of photosynthesis is: 6 H2O + 6 CO2 + photons = C6H12O6 (glucose) + 6O2. The detailed steps of photosynthesis are called the "Calvin Cycle". Prokaryote cells can now produce their own glucose to store and be converted to ATP by glycolysis and fermentation later. This sytem is the main system responsible for producing the Oxygen now in the air of earth. Of the 5 phyla of eubacteria that can photosynthesize, only 1, cyanobacteria, produces oxygen.
4,280,000,000 YBN 1	57) Cellular Respiration (also called the "Citric Acid Cycle", and the "Krebs Cycle") evolves, probably in cyanobacteria, as a substitute for fermentaton, by using oxygen to break down the products of glycolysis, pyruvic acid, to CO2 and H2O, producing 18 more ATP molecules.1 This is the first aerobic cell, a cell that has an oxygen based metabolism. This cell uses oxygen to convert glucose (and eventually other sugars and fats) into CO2, H2O and ATP. For example, cells that oxidize glucose perform the reaction: C6H12O6 + 6 O2 + 38 ADP + 38 phosphate -> 6 CO2 + 6 H2O + 38 ATP This reaction (with glycolysis) can produce up to 36 ATP molecules. Cellular respiration is the opposite (although the specific reactions differ) of photosynthesis which starts with H2O and CO2 and produces glucose. Steps are: Glycolysis preparatory phase Glycolysis pay-off phase Oxidative carboxylation Krebs cycle FOOTNOTES 1. ^ "Aerobic organism". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Aerobic_organism
4,260,000,000 YBN	27) DNA (or RNA) produces instructions for a cell wall. The cell wall only protects bacteria and does not filter any molecules as the cytoplasm does. is first gram-negative cell wall? 1. Only contain a few layers of peptidoglycan -- the building block for strong, rigid cell walls 2. Contain an outer membrane, external to the peptidoglycan, called the lipopolysaccharide 3. The space between the layers of peptidoglycan and the secondary cell membrane is called periplasmatic space 4. The S-layer is directly attached to the outer membrane, rather than the peptidoglycan 5. Any flagella, if present, have 4 supporting rings instead of two 6. No teichoic acids are present"
4,250,000,000 YBN	29) There are many proteins and secondary processes in cells that are not fully understood yet.
4,250,000,000 YBN	42) More prokaryote cell fossils need to be found, more DNA needs to be sequenced, and more bacteria found and grown to fully understand when bacteria parts evolved. For example: flagella plasmids pili and "conjugation" the trade of pieces of plasmid DNA (this may be the earliest form of sex {or syngamy}) changing into spores When gram-stain positive cell walls evolved. When the various shapes evolved: spherical (coccus,cocci) rod (bacillus,bacilli) spiral (spirilla) other: short rods (coccobacilli). commas (vibrii). squares (rare) stars (rare) irregular (rare) Which specific bacteria of the Archaea (if any) were first, which of the Eubacteria and Cyanobacteria came next. When the "Nitrogen Cycle" or "Nitrogen Fixing" evolved. Few cells can separate N2 into N, (needed for nucleic acids?1 ). The waste product urea is converted by one bacteria to ammonia, a second bacteria converts the ammonia to N2. FOOTNOTES 1. ^ Ted Huntington.
4,250,000,000 YBN 1 2 3 4 5 6 7	77) There are many widely varying estimates of when the first Eubacteria and Archaea evolved. Eubacteria and Archaea (also called Archaebacteria) are the two major lines of Prokaryotes. Prokaryotes are the most primitive living objects ever found. In contrast to the later evolved Eukaryotes, Prokaryotes have a circle of DNA located in their cytoplasm (not chromosomes) and have no nucleus. At least one genetic comparison shows Eubacteria and Archaea evolving now.1 2 3 4 5 6 7 After the full genomes of all living species are known, and understood we will have more certainty about the history of evolution. Many genetic trees are based on DNA genes (sequences of DNA that define nucleic acids or proteins). In particular the genes for ribosomal RNA are thought to be very conserved over time, although perhaps genes for reproduction, or cytoplasm, for example may later prove to be more conserved over time. Only when the full genomes of all living species are known, and understood will we have strong certainty about the history of evolution. Many genetic trees are based on DNA genes (sequences of DNA that define nucleic acids or proteins), in particular ribosomal RNA which is thought to be highly conserved over the eons of time. Ribosomal RNA may be the best record of evolutionary history, but perhaps other genes, for example, those involved with reproduction, or cytoplasm will prove to be more conserved or better estimates of evolutionary history. For example, I think the method of reproduction would be the most conserved, since that process is the most necessary for survival, changes to those genes may stop continued existence, where changes to rrna may not be as serious. In addition, the vast diversity and change in reproductive method over time, should tell us that similar large scale changes could have happened for rrna, cytoplasm, and indeed any part of a cell. These early Archaea and Eubacteria are "thermophile" bacteria, bacteria that are found and grow best in hot water (80+ degrees Celsius). That genetic evidence puts these prokaryotes as the oldest living prokaryotes is evidence that the first prokaryotes on earth may have lived in hot water, perhaps near thermal springs or near ocean floor volcanos. Perhaps the water on the early earth was hot when these first prokaryotes evolved. Archaea are similar to other prokaryotes in most aspects of cell structure and metabolism. However, their genetic transcription and translation are very similar to those of eukaryotes. FOOTNOTES 1. ^ http://www.nature.com/nrg/journal/v3/n11/full/nrg929_fs.html 2. ^ Russell F. Doolittle, Da-Fei Feng, Simon Tsang, Glen Cho, Elizabeth Little, "Determining Divergence Times of the Major Kingdoms of Living Organisms with a Protein Clock", Science, (1996). 2142-1873my (2142-1873my) 3. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). 2300my (2300my) 4. ^ Battistuzzi, Feijao, Hedges, "A Genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land", BMC Evolutionary Biology, (2004). 4100my (has arche b4 eu) (4100my) 5. ^ Osawa, S., Honjo, "Archaebacteria vs Metabacteria : Phylogenetic tree of organisms indicated by comparison of 5S ribosomal RNA sequences.", (Tokyo: Springer, Tokyo/ Berlin eds.:"Evolution of Life", pp. 325-336,, 1991). 1800my (1800my) 6. ^ S. Blair Hedges, "The Origin and Evolution of Model Organisms", Nature Reviews Genetics 3, 838-849 (2002); doi:10.1038/nrg929, (2002). 4000my (4000my) 7. ^ S. Blair Hedges and Sudhir Kumar, "Genomic clocks and evolutionary timescales", Trends in Genetics Volume 19, Issue 4 , April 2003, Pages 200-206, (2003). 3970my (3970my)
4,112,000,000 YBN 1	180) The Archaea Phylum, Euryarchaeotes evolve.1 2 3 Genetic comparison shows the Archaea Phylum, Euryarchaeotes evolving now. The Euryarchaeota are a major group of Archaea. They include the methanogens, which produce methane and are often found in intestines, the halobacteria, which survive extreme concentrations of salt, and some extremely thermophilic aerobes and anaerobes. They are separated from the other archaeans based mainly on rRNA sequences.4 Euryarchaeota may contain the most ancient DNA of any living object on earth. PHYLUM Euryarchaeota CLASS Archaeoglobi CLASS Halobacteria CLASS Methanobacteria CLASS Methanococci CLASS Methanomicrobia CLASS Methanopyri CLASS Methanosarcinae CLASS Thermococci CLASS Thermoplasmata FOOTNOTES 1. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004).
4,112,000,000 YBN 1	181) The Archaea Phylum, Crenarchaeotes evolves.1 2 3 Genetic comparison shows Archaea Phylum, Crenarchaeotes evolving now. The phylum Crenarchaeota, commonly referred to as the crenarchaea, in the domain Archaea, contains many extremely thermophilic and psychrophilic organisms. They were originally separated from the other archaeons based on rRNA sequences, since then physiological features, such as lack of histones have supported this division. Until recently all cultured crenarchaea have been thermophilic or hyperthermophilic organisms, some of which have the ability to grow up to 113 degrees C. These organisms stain gram negative and are morphologically diverse having rod, cocci, filamentous and unusually shaped cells.4 PHYLUM Crenarchaeotes ORDER Caldisphaerales ORDER Cenarchaeales ORDER Desulfurococcales ORDER Sulfolobales ORDER Thermoproteales FOOTNOTES 1. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004).
4,030,000,000 YBN	35) Metamorphic rock, a Gneiss near Acasta and Great Slave Lake in the North West territories of Canada dates from this time, 4030 million years before now.1 2 3 4 FOOTNOTES 1. ^ http://pubs.usgs.gov/gip/geotime/age.html 2. ^ http://www.geol.umd.edu/~tholtz/G102/102arch1.htm 3. ^ http://chigaku.ed.gifu-u.ac.jp/chigakuhp/dem/tec/history/isua.html 4. ^ http://www.mediaworkshop.org/techcamp/groupc/geology/geohome.htm
3,977,000,000 YBN 4	193) Eubacteria "Hyperthermophiles" (Aquifex, Thermotoga, etc.) evolve now.1 2 Genetic comparison shows that Eubacteria "Hyperthermophiles" (Aquifex, Thermotoga, etc.) evolve now. This may be the living object with the most primitive DNA found on earth (depending on the age of the archaea). This group of eubacteria includes the Phyla "Aquificae", "Thermodesulfobacteria", and "Thermotogae". The Aquificae phylum is a diverse collection of bacteria that live in harsh environmental settings. They have been found in hot springs, sulfur pools, and thermal ocean vents. Members of the genus Aquifex, for example, are productive in water between 85 to 95 °C. They are the dominant members of most terrestrial neutral to alkaline hot springs above 60 degrees celsius. They are autotrophs, and are the primary carbon fixers in these environments. They are true bacteria (domain eubacteria) as opposed to the other inhabitants of extreme environments, the Archaea. Thermotoga are thermophile or hyperthermophile bacteria whose cell is wrapped in an outer "toga" membrane. They metabolize carbohydrates. Species have varying amounts of salt and oxygen tolerance. Thermotoga subterranea strain SL1 was found in a 70°C deep continental oil reservoir in the East Paris Basin, France. It is anaerobic and reduces cystine and thiosulfate to hydrogen sulfide.3 FOOTNOTES 1. ^ Battistuzzi, Feijao, Hedges, "A Genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land", BMC Evolutionary Biology, (2004). 2. ^ Brocks, Buick, "A reconstruction of Archean biological diversity based on", Geochimica et cosmochimica acta, (2003). 3. ^ "Aquifex". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Aquifex 4. ^ Battistuzzi, Feijao, Hedges, "A Genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land", BMC Evolutionary Biology, (2004).
3,850,000,000 YBN	36) The oldest sediment on earth is also the oldest Banded Iron Formation, on Akilia Island in Western Greenland. The oldest evidence for life on earth was found in this rock by measuring the ratio of carbon 12 to carbon 13 in grains of apatite (calcium phosphate) from this rock. Life uses the lighter Carbon-12 isotope and not Carbon-13 and so the ratio of carbon-12 to carbon-13 is different from a nonliving source (calcium carbonate or limestone).1 2 FOOTNOTES 1. ^ Mojzsis, et al. nature nov 7, 1996 http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v384/n6604/index .html, 2:102, 2. ^ http://jersey.uoregon.edu/~mstrick/RogueComCollege/RCC_Lectures/Banded_Iron.html
3,850,000,000 YBN	45) This marks the beginning of the Banded Iron Formation Rocks. These rocks are sedimentary. They are made of iron rich chert (silicates, like SiO2). These rocks have alternative bands of orange or yellow and black. In the red parts the iron is oxydized (contains iron oxides, either hematite {Fe2O3 = rust} or magnetite {Fe3O4]}).1 2 3 4 5 These bands may have formed because photosynthetic bacteria (in stromatolites found in shallow ocean shores, and purple bacteria floating in water) produce oxygen from CO2 during photosynthesis. When the level of oxygen in the water became too high, many bacteria died, and this cycle created the BIF. But BIF also may form naturally when photons in uv frequencies split H2O into H2 and O2. So perhaps the BIF bands represent cycles of more or less uv light reaching the earth. Perhaps the alternating phenomenon is similar to eukaryotic algal blooms. In any event, this free oxygen bonded with the many tons of iron dissolved in the water to form insoluable iron oxide which then fell to the ocean floor to form the orange layers of Banded Iron Formation. How these alternating bands are made is not clear and has not yet been duplicated in a lab. This cycle of alternating orange and black bands will continue for 2 billion years until 1,800 million years before now. This is the beginning of oxygen production on earth, the atmosphere of earth still has only small amounts of oxygen at this time. It is amazing that people are still not certain what was the cause of the oxygen, and the cycles that deposited the banded Iron Formation.
3,850,000,000 YBN	189) Fossils from Isua Banded iron formation, SW Greenland.1 2 FOOTNOTES 1. ^ Hans D. Pflug, "Earliest organic evolution. Essay to the memory of Bartholomew Nagy",Precambrian Research Volume 106, Issues 1-2, 1 February 2001, Pages 79-91. http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VBP-42G6M5T-7 &_user=4422&_coverDate=02%2F01%2F2001&_fmt=full&_orig=browse&_cdi=5932&view=c&_a cct=C000059600&_version=1&_urlVersion=0&_userid=4422&md5=d61bf36f008d6b2cba3ba5d bd5a628d7&ref=full#bib9 2. ^ Schopf, J.W., 1993. Microfossils from the early Archean Apex chert: New evidence of the antiquity of life. Science 260, pp. 640-646. Abstract-GEOBASE Abstract-MEDLINE
3,800,000,000 YBN	51) End Hadean Era, start Archean Era.1 2 FOOTNOTES 1. ^ The geological Society of America ucmp.berkeley.edu 2. ^ Richard Cowen, "History of Life", (Malden, MA: Blackwell, 2005).
3,800,000,000 YBN 3	185) Isoprene compounds from Isua, Greenland Banded Iron Formation sediment are evidence of the existence of Archaea.1 2 FOOTNOTES 1. ^ http://www.ucmp.berkeley.edu/archaea/archaeafr.html 2. ^ Jürgen Hahn & Pat Haug. 1986. Traces of Archaebacteria in ancient sediments. System. Appl. Microbiol. 7: 178-183. (Archaebacteria '85 Proceedings). 3. ^ http://www.ucmp.berkeley.edu/archaea/archaeafr.html
3,760,000,000 YBN 2	186) Sulfur isotope ratios (34S/32S) and Hydrocarbon molecules (alkanes) detected in 3760 billion year old Isua Banded Iron Formation, indicate the possibility of photosynthetic sulfate reducing bacteria (Archaea, for example Sulpholobus) and Cyanobacteria living at that time.1 FOOTNOTES 1. ^ Systematic and Applied Microbiology, Vol 7, pp 178-183 1986 2. ^ Systematic and Applied Microbiology, Vol 7, pp 180-189 1986
3,700,000,000 YBN 2	184) Amount of Uranium isotope measured in Isua, Greenland Banded Iron Formation evidence of prokaryote Oxygen photosynthesis.1 FOOTNOTES 1. ^ Earth and Planetary Science Letters Volume 217, Issues 3-4 , 15 January 2004, Pages 237-244U-rich "Archaean sea-floor sediments from Greenland - indications of >3700 Ma oxygenic photosynthesis" Minik T. Rosing and Robert Frei 2. ^ Earth and Planetary Science Letters Volume 217, Issues 3-4 , 15 January 2004, Pages 237-244U-rich "Archaean sea-floor sediments from Greenland - indications of >3700 Ma oxygenic photosynthesis" Minik T. Rosing and Robert Frei
3,700,000,000 YBN 2	215) C13/C12 ratio of 3700+ MYO sediment in Australia shown to be consistent with planktonic photosynthesizing organisms.1 FOOTNOTES 1. ^ 13C-Depleted Carbon Microparticles in >3700-Ma Sea-Floor Sedimentary Rocks from West Greenland http://www.sciencemag.org/cgi/content/full/283/5402/674 Science 29 January 1999: Vol. 283. no. 5402, pp. 674 - 676 DOI: 10.1126/science.283.5402.674 2. ^ 13C-Depleted Carbon Microparticles in >3700-Ma Sea-Floor Sedimentary Rocks from West Greenland http://www.sciencemag.org/cgi/content/full/283/5402/674 Science 29 January 1999: Vol. 283. no. 5402, pp. 674 - 676 DOI: 10.1126/science.283.5402.674
3,566,000,000 YBN 3	78) Genetic comparison shows Archaebacteria (Archaea) Phylum, Korarchaeotes evolving now.1 2 FOOTNOTES 1. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). 2. ^ Battistuzzi, Feijao, Hedges, "A Genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land", BMC Evolutionary Biology, (2004). 3. ^ Battistuzzi, Feijao, Hedges, "A Genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land", BMC Evolutionary Biology, (2004). and image 1 MORE INFO [1] also see nature v417 n6886
3,500,000,000 YBN	37) The oldest fossil evidence of life yet found. Stromatolites made by photosynthetic bacteria found in both Warrawoona, Western Australia, and Fig Tree Group, South Africa.1 2 FOOTNOTES 1. ^ nature feb 6, 1986 2. ^ nature apr 3, 1980
3,500,000,000 YBN	39) Oldest fossils of an organism, thought to be cyanobacteria, found in 3,500 Million Year old chert from South Africa and 3,465 Million year old Apex chert of north-western Australia.1 2 3 4 5 Oldest fossils of an organism, thought to be cyanobacteria, found in 3,500 Million Year old chert from South Africa and 3,465 Million year old Apex chert of the Pilbara Supergroup, Warrawoona Group, northwestern Western Australia. Some people argue that these are not fossils of bacteria but abiotic material. Most genetic timelines put the origin of cyanobacteria much later around 2,700mybn. Cyanobacteria evolved multicellularity where cellular differentiation occurs.6 7 FOOTNOTES 1. ^ warrawoona Nature416, 73 - 76 (07 Mar 2002) Letters to Nature http://www.nature.com/nature/journal/v416/n6876/full/416073a_fs.html 2. ^ swaziland Nature 314, 530-532 (11 Apr 1985) Letters to Editor "Filamentous microfossils from the 3,500-Myr-old Onverwacht Group, Barberton Mountain Land, South Africa" 3. ^ argues that these are not fossils: http://www.nature.com/nature/journal/v420/n6915/full/420476b.html "we contend that the Raman spectra of Schopf et al.1 indicate that these are disordered carbonaceous materials of indeterminate origin. We maintain that Raman spectroscopy cannot be used to identify microfossils unambiguously, although it is a useful technique for pinpointing promising microscopic entities for further investigation." 4. ^ http://www.nature.com/news/2002/020304/full/020304-6.html "Gloves are coming off in ancient bacteria bust-up." 2002 5. ^ http://www.nature.com/nature/journal/v416/n6876/full/416076a.html braiser et al. "Questioning the evidence for Earth's oldest fossils" 6. ^ BIO415 (Author? University?) Multicelluarity.pdf (t3: multicellularity of cyanobacteria) 7. ^ t3: http://www.mansfield.ohio-state.edu/~sabedon/biol3018.htm multiceullarity. "Some cyanobacteria species exist in a truly, though primitive, multicellular form in which cellular differentiation occurs."
3,500,000,000 YBN 3 4	289) Some people think the origin of eukaryotes happened here at 3.5 bybn.1 2 FOOTNOTES 1. ^ Michael Sleigh, "Protozoa and Other Protists", (London; New York: Edward Arnold, 1989). 2. ^ Carl R. Woese, "Bacterial Evolution", Microbiological Reviews, June 1877, p. 221-271. woese1987b.pdf 3. ^ Michael Sleigh, "Protozoa and Other Protists", (London; New York: Edward Arnold, 1989). 4. ^ Carl R. Woese, "Bacterial Evolution", Microbiological Reviews, June 1877, p. 221-271. woese1987b.pdf
3,470,000,000 YBN 2	182) Sulphate fossil molecular marker evidence of moderate thermophile sulphur reducing prokaryotes from North Pole, Australia.1 FOOTNOTES 1. ^ http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v410/n6824/full/ 410077a0_fs.html 2. ^ http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v410/n6824/full/ 410077a0_fs.html
3,470,000,000 YBN 2	216) Evidence of sulphate reduction by bacteria.1 FOOTNOTES 1. ^ http://www.nature.com/nature/journal/v410/n6824/full/410077a0.html 2. ^ http://www.nature.com/nature/journal/v410/n6824/full/410077a0.html
3,430,000,000 YBN 1	833) Stromatolites made by photosynthetic bacteria found in Pilbara Craton, Australia. Strelley Pool Chert FOOTNOTES 1. ^ http://www.nature.com/nature/journal/v441/n7094/full/nature04764.html
3,416,000,000 YBN 2	218) Fossil and molecular evidence of photosynthetic, probably anoxygenic, bacteria that lived in mats in the ocean date to this time.1 FOOTNOTES 1. ^ http://www.nature.com/nature/journal/v431/n7008/full/nature02888.html 2. ^ http://www.nature.com/nature/journal/v431/n7008/full/nature02888.html
3,400,000,000 YBN	190) Fossils from Kromberg Formation, Swaziland System, South Africa.1 FOOTNOTES 1. ^ http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VBP-42G6M5T-7&_user=4 422&_coverDate=02%2F01%2F2001&_fmt=full&_orig=browse&_cdi=5932&view=c&_acct=C000 059600&_version=1&_urlVersion=0&_userid=4422&md5=d61bf36f008d6b2cba3ba5dbd5a628d 7&ref=full#bib9 MORE INFO [1] maybe evidence: Nagy, B. and Nagy, L.A., 1969. Early Precambrian microstructures: possibly the oldest fossils on Earth?. Nature 223, pp. 1226-1229.?
3,260,000,000 YBN 1	71) Budding evolves in prokayotes. Different from binary division, where a cell is split in half, in budding, a new complete cell is made in the original cell, and the new cell bursts through the cell wall, the original cell wall must then be repaired. Budding is the only other method of reproduction known in prokaryotes besides binary fission. The only major difference between prokaryote budding and binary division are that one or more new cells are completely formed inside the original cell, where in binary division part of the original cell wall is used to make the new cell. In budding, a complete new cell is synthesized from a DNA template, where in binary division only the DNA is duplicated and more cytoplasm and cell wall is synthesized. So, budding preserves organelles made by the main DNA template that cannot duplicate themselves and would not get duplicated or synthesized in binary division, for example, flagella. Although it is very unlikely, the possibility does exist that prokaryote budding evolved from a eukaryote that lost it's nucleus. FOOTNOTES 1. ^ Record ID 191. "Universe, life, Science Future". Ted Huntington. (based on my own estimate based on fossils from id191) (3.4)
3,250,000,000 YBN	191) Fossils from Swartkoppie chert, South Africa are oldest evidence of procaryotes that reproduce by budding and not binary fission.1 FOOTNOTES 1. ^ http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VBP-42G6M5T-7&_user=4 422&_coverDate=02%2F01%2F2001&_fmt=full&_orig=browse&_cdi=5932&view=c&_acct=C000 059600&_version=1&_urlVersion=0&_userid=4422&md5=d61bf36f008d6b2cba3ba5dbd5a628d 7&ref=full#bib9 MORE INFO [1] (maybe evidence): ZENTRALBLATT FUR BAKTERIOLOGIE MIKROBIOLOGIE UND HYGIENE I ABTEILUNG Pflug, H.D., 1982. Early diversification of life in the Archean. Zbl. Bakt. Hyg. I.Abt. Orig. C3, pp. 53-64.?
3,235,000,000 YBN	68) Thermophilic prokaryote fossils found in 3235 million year old deep-sea volcanogenic massive sulphide deposits from the Pilbara Craton of Australia may be oldest Archaea fossils.1 FOOTNOTES 1. ^ Nature 405, 676 - 679 (08 June 2000); doi:10.1038/35015063 Filamentous microfossils in a 3,235-million-year-old volcanogenic massive sulphide deposit BIRGER RASMUSSEN
2,923,000,000 YBN 1	178) Eubacteria Phylum Firmicutes (low G+C {Guanine and Cytosine count} Gram positive) evolve.1 2 3 Genetic comparison shows Eubacteria Phylum Firmicutes (low G+C {Guanine and Cytosine count} Gram positive) evolving here. Firmicutes include the Classes: Bacillus (anthrax), Listeria, Mollicutes, and Stephylococcus. Firmicutes may be the first rod shaped bacteria, and first bacteria to have a gram positive cell wall. The peptidoglycan layer is thicker in Gram-positive bacteria (20 to 80 nm) than in Gram-negative bacteria (7 to 8 nm) Firmicultes form endospores, and is the only phlyum of bacteria that evolved the ability to build endospores. The Firmicutes are a division of bacteria, most of which have Gram-positive stains. A few, the Mollicutes or mycoplasmas, lack cell walls altogether and so do not respond to Gram staining, but still lack the second membrane found in other Gram-negative forms. Originally the Firmicutes were taken to include all Gram-positive bacteria, but more recently they tend to be restricted to a core group of related forms, called the low G+C group in contrast to the Actinobacteria. They have round cells, called cocci (singular coccus), or rod-shaped forms. Many Firmicutes produce endospores, which are resistant to desiccation and can survive extreme conditions. They are found in various environments, and some notable pathogens. Those in one family, the heliobacteria, produce energy through photosynthesis. Firmicutes include: CLASS Bacilli (rod shaped) ORDER Bacillales (anthrax) ORDER Lactobacillales CLASS Clostridia ORDER Clostridiales ORDER Halanaerobiales ORDER Thermoanaerobacteriales CLASS Mollicutes ORDER Mycoplasmatales ORDER Entomoplasmatales ORDER Anaeroplasmatales ORDER Acholeplasmatales FOOTNOTES 1. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). MORE INFO [1] http://en.wikipedia.org/wiki/Peptidoglycan [2] firmicutes only bacteria to make endospores http://en.wikipedia.org/wiki/Endospore [3] http://en.wikipedia.org/wiki/Firmicutes
2,920,000,000 YBN 1	288) Eubacteria firmicutes evolve the abililty to form endpospores.1 An endospore is any spore that is produced within an organism (usually a bacterium). Most bacterium produce only one spore, as this is not a reproduction process. This is in contrast to exospores, which are rather produced by growth or budding. The primary function of most endospores is to ensure the survival of a colony through periods of environmental stress. Endospores are therefore resistant to desiccation, temperature, starvation, ultraviolet and gamma radiation, and chemical disinfectants. One of the great questions of this time is: "what is the process behind cell differentiation and cell growth?" How is each stage initiated and stopped? There are a number of theories. One theory presumes the entire DNA strand is accessible at all times. In this view operons are used sequentially, while many proteins are supressed, some operons are active, which results in one set of proteins developing the cell, at some point, the first group of operons are inhibited and a different operon (or set of operons) is turned on, signalling a new set of proteins to be built which effects the growth and shape of the cell. An abundance of a first stage protein might initiate the second stage. A second theory is that DNA is read like a computer program with some proteins moving along the DNA strand, one part at a time. In this way, one portion of the DNA may reflect one life stage, while the next portion represents the next (and perhaps very different) life stage. The endospore-forming bacteria belong to the Firmicutes. FOOTNOTES 1. ^ "Endospore". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Endospore
2,800,000,000 YBN 1	177) Genetic comparison shows the ancestor of all Proteobacteria (Rickettsia {mitochondria}, gonorrhoea, Salmonella, E coli) evolving now.1 2 3 4 Proteobact eria include 5 Classes: CLASS Alpha Proteobacteria (Rickettsia Prowazekii {mitochondria/typhus}) CLASS Beta Proteobacteria (Neisseria gonorrhoeae {gonorrhoea}) CLASS Gamma Proteobacteria (Salmonella and Escherichia coli.) CLASS Delta Proteobacteria CLASS Epsilon Proteobacteria The Proteobacteria are a major group of bacteria. They include a wide variety of pathogens, such as Escherichia, Salmonella, Vibrio, Helicobacter, and many other notable genera. Others are free-living, and include many of the bacteria responsible for nitrogen fixation. The group is defined primarily in terms of ribosomal RNA (rRNA) sequences, and is named for the Greek god Proteus, who could change his shape, because of the great diversity of forms found in it. All Proteobacteria are Gram-negative, with an outer membrane mainly composed of lipopolysaccharides. Many move about using flagella, but some are non-motile or rely on bacterial gliding. The last include the myxobacteria, a unique group of bacteria that can aggregate to form multicellular fruiting bodies. There is also a wide variety in the types of metabolism. Most members are facultatively or obligately anaerobic and heterotrophic, but there are numerous exceptions. A variety of genera, which are not closely related, can photosynthesize. These are called purple bacteria, referring to their mostly reddish pigmentation. The delta-proteobacteria Myxobacteria is capable of colonial multicellularity and some view as possibly being the bacteria that formed the cytoplasm in eukaryotes. CLASS Alpha Proteobacteria (Rickettsia Prowazekii {mitochondria/typhus}) CLASS Beta Proteobacteria (Neisseria gonorrhoeae {gonorrhoea}) CLASS Gamma Proteobacteria (Salmonella, Escherichia coli., fireblight {Erwinia amylovora}, one form of dysentery {Shigella dysenteriae}, Legionaires' disease {Legionella pneumophilia}, Haemophilus influenzae {first free living organism to have entire genome sequenced}, Pseudomonas, the largest known bacteria {Thiomargarita namibiensis}, Cholera {Vibrio cholerae}) The number of individual E. coli bacteria in the feces that one human passes in one day averages between 100 billion and 10 trillion. CLASS Delta Proteobacteria (Bdellovibrio {parasite on other bacteria}, Geobacter {can oxydize uranium, may be used as battery that runs on waste}, myxobacteria {form multicellular bodies that make spores, have large genome} CLASS Epsilon Proteobacteria (Helicobacter {spiral bacteria}) FOOTNOTES 1. ^ Battistuzzi, Feijao, Hedges, "A Genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land", BMC Evolutionary Biology, (2004). MORE INFO [1] multicellularity. http://www.mansfield.ohio-state.edu/~sabedon/biol3018.htm multicellularity. Multicellularity.pdf http://en.wikipedia.org/wiki/Escherichia_coli http://en.wikipedia.org/wiki/Proteobacteria
2,784,000,000 YBN 1	176) Genetic comparison shows Eubacteria Phylum, Planctomycetes (Planctobacteria) evolving now.1 Planctomycetes are a possible ancestor of all eukaryotes because the circle of DNA can sometimes be enclosed in a double membrane. Planctomycetes is a small phylum with only 4 Genera, require oxygen for growth (obligately aerobic), are found in fresh and salt water. They reproduce by budding. They have holdfast (stalk) at the nonreproductive end that helps them to attach to each other during budding. The life cycle involves alternation between sessile cells and flagellated swarmer cells. The sessile cells bud to form the flagellated swarmer cells which swim for a while before settling down to attach and begin reproduction. It is also possible, although unlikely, that planctomycetes are descended from a very early eukaryote that lost the nucleus but retained the cytoplasmic DNA, since budding may have evolved as a method to duplicate a eukaryote cell from the nucleus. (ok this is out there...maybe t3) The organisms belonging to this group lack murein in their cell wall Murein is an important heteropolymer present in most bacterial cell walls that serves as a protective component in the cell wall skeleton. Instead their walls are made up of glycoprotein rich in glutamate. Planctomycetes have internal structures that are more complex than would be typically expected in prokaryotes. While they don't have a nucleus in the eukaryotic sense, the nuclear material can sometimes be enclosed in a double membrane. In addition to this nucleoid, there are two other membrane-separated compartments; the pirrellulosome or riboplasm, which contains the ribosome and related proteins, and the ribosome-free paryphoplasm. FOOTNOTES 1. ^ Battistuzzi, Feijao, Hedges, "A Genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land", BMC Evolutionary Biology, (2004). MORE INFO [1] s10 http://ijs.sgmjournals.org/cgi/reprint/50/6/1965 [2] http://genomebiology.com/2002/3/6/research/0031 [3] http://en.wikipedia.org/wiki/Planctomycetes
2,784,000,000 YBN 1	179) Genetic comparison shows Eubacteria Phylum, Actinobacteria (high G+C, Gram positive) evolving now.1 2 3 4 5 Actinobacteria have 5 Orders: ORDER Acidimicrobiales ORDER Actinobacteriales ORDER Coriobacteriales ORDER Rubrobacteriales ORDER Sphaerobacteriales Actinobacteria include the causes of tuberculosis (Mycobacteria tuberculosis) and leprosy (Mycobacteria leprae). The Actinobacteria or Actinomycetes are a group of Gram-positive bacteria. Most are found in the soil, and they include some of the most common soil life, playing an important role in decomposition of organic materials, such as cellulose and chitin. This replenishes the supply of nutrients in the soil and is an important part of humus formation. Other Actinobacteria inhabit plants and animals, including a few pathogens, such as Mycobacterium. Some Actinobacteria form braching filaments, which somewhat resemble the mycelia of the unrelated fungi, among which they were originally classified under the older name Actinomycetes. Most members are aerobic, but a few, such as Actinomyces israelii, can grow under anaerobic conditions. Unlike the Firmicutes, the other main group of Gram-positive bacteria, they have DNA with a high GC-content {guanine-cytosine content} and some Actinomycetes species produce external spores. Mycobacterium bovis (the bacterium responsible for bovine TB) in particular has been estimated to be responsible, for the period of the first half of the 20th century, for more losses among farm animals than all other infectious diseases combined. Infection occurs if the bacterium is ingested. Actinobacteria are unsurpassed in their ability to produce many compounds that have pharmaceutically useful properties. In 1940 Selman Waksman discovered that the soil bacteria he was studying made actinomycin, a discovery which granted him a Nobel Prize. Since then hundreds of naturally occurring antibiotics have been discovered in these terrestrial microorganisms, especially from the genus Streptomyces. When M.leprae was discovered by G.A. Hansen in 1873, it was the first bacterium to be identified as causing disease in man. Although Leprosy is contagious, it is not widespread because 95% of the population have immune systems able to cope with the bacteria. FOOTNOTES 1. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004).
2,775,000,000 YBN 1	174) Genetic comparison shows Eubacteria Phylum, Spirochaetes (Syphilis, Lyme disease) evolving now.1 Includes leptospirosis (leptospira), Lyme disease (Borrelia burgdorferi), and Syphilis (Treponema pallidum). Spirochaetes only have one order: ORDER Spirochaetales This is when the first spiral shaped bacteria evolve. The spirochaetes (or spirochetes) are a phylum of distinctive bacteria, which have long, helically coiled cells. They are distinguished by the presence of flagella running lengthwise between the cell membrane and cell wall, called axial filaments. These cause a twisting motion which allows the spirochaete to move about. Most spirochaetes are free-living and anaerobic, but there are numerous exceptions. Spirochaetes only have one order: ORDER Spirochaetales and 3 families. FOOTNOTES 1. ^ Battistuzzi, Feijao, Hedges, "A Genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land", BMC Evolutionary Biology, (2004). MORE INFO [1] Tree of Life. http://tolweb.org/tree/ [2] Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004).
2,775,000,000 YBN 4 5	175) Genetic comparison shows Eubacteria Phyla Bacteroidetes and Chlorobi (green sulphur bacteria) evolving now.1 2 PHYLUM Bacteroidetes CLASS Bacteroides ORDER Bacteroidales CLASS Flavobacteria ORDER Flavobacteriales CLASS Sphingobacteria ORDER Sphingobacteriales PHLYUM Chlorobi (Green sulphur) CLASS Chlorobia ORDER Chlorobiales3 The phylum Bacteroidetes is composed of three large groups of bacteria. By far, more is written about and known about the Bacteroides class, than the other two, the Flavobacteria and the Sphingobacteria classes. They are related by the similarity in the composition of the small 16S subunit of their ribosomes. Members of the bacteroides class are human commensals (they benefit but humans receive no effect) and sometimes pathogens. Members of the other two classes are rarely pathogenic to humans. Chlorobi are the "green sulphur bacteria", are a family of phototrophic (photosynthesizing) bacteria. Green sulfur bacteria are generally nonmotile (one species has a flagellum), and come in spheres, rods, and spirals. Their environment must be oxygen-free, and they need light to grow. They engage in photosynthesis, using bacteriochlorophylls c, d, and e in vesicles called chlorosomes attached to the membrane. They use sulfide ions as electron donor, and in the process the sulfide gets oxidized, producing globules of elemental sulfur outside the cell, which may then be further oxidized. (By contrast, the photosynthesis in plants uses water as electron donor and produces oxygen.) A species of green sulfur bacteria has been found living near a black smoker off the coast of Mexico at a depth of 2,500 meters beneath the surface of the Pacific Ocean. At this depth, the bacteria, designated GSB1, lives off the dim glow of the thermal vent since no sunlight can penetrate to that depth. FOOTNOTES 1. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). 2. ^ Battistuzzi, Feijao, Hedges, "A Genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land", BMC Evolutionary Biology, (2004).. ^ 3. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=563 4. ^ estimate from Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). 5. ^ estimate from Battistuzzi, Feijao, Hedges, "A Genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land", BMC Evolutionary Biology, (2004). MORE INFO [1] Tree of Life [2] http://en.wikipedia.org/wiki/Bacteroidetes [3] http://en.wikipedia.org/wiki/Chlorobi
2,775,000,000 YBN 1	217) Genetic comparison shows Eubacteria Phyla Chlamydiae and Verrucomicrobia evolving now.1 Chlamydiae includes (clamydia, trachoma {Chlamydia trachomatis}, a form of pneumonia {Chlamydophila pneumoniae}, psittacosis {Chlamydophila psittaci}. CLASS Chlamydiae ORDER Chlamydiales PHYLA Verrucomicrobia ORDER Verrucomicrobiales The Chlamydiae are a group of bacteria, all of which are intracellular parasites of eukaryotic cells. Most described species infect mammals and birds, but some have been found in other hosts, such as amoebae. Chlamydiae have a life-cycle involving two distinct forms. Infection takes place by means of elementary bodies (EB), which are metabolically inactive. These are taken up within a cellular vacuole, where they grow into larger reticulate bodies (RB), which reproduce. Ultimately new elementary bodies are produced and expelled from the cell. Verrucomicrobia is a recently described phylum of bacteria. This phylum contains only a few described species (Verrucomicrobia spinosum, is an example, the phylum is named after this). The species identified have been isolated from fresh water and soil environments and human feces. A number of as-yet uncultivated species have been identified in association with eukaryotic hosts including extrusive explosive ectosymbionts of protists and endosymbionts of nematodes residing in their gametes. Evidence suggests that verrucomicrobia are abundant within the environment, and important (especially to soil cultures). This phylum is considered to have two sister phyla Chlamydiae and Lentisphaera. There are three main species of chlamydiae that infect humans: * Chlamydia trachomatis, which causes the eye-disease trachoma and the sexually transmitted infection chlamydia; * Chlamydophila pneumoniae, which causes a form of pneumonia; * Chlamydophila psittaci, which causes psittacosis. FOOTNOTES 1. ^ Battistuzzi, Feijao, Hedges, "A Genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land", BMC Evolutionary Biology, (2004). MORE INFO [1] Tree of Life. http://tolweb.org/tree/ [2] Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). [3] http://en.wikipedia.org/wiki/Chlamydiae [4] http://en.wikipedia.org/wiki/Verrucomicrobia
2,760,000,000 YBN 1	80) Endocytosis, a process where the cell membrane folds around some molecules to form a spherical vesicle which enters the cytoplasm, and exocytosis, the opposite process, where a vesicle combines with a call membrane to empty molecules outside a cell both evolve in an early eukaryote cell. Eukaryote cells can now swallow bacteria (phagocytosis) and liquid (pinocytosis). The cells can then (heterotrophically) use the molecules injested (for example a bacterium) for copying and to make ATP. This is the first time one cell can eat a different living cell. How similar endocytosis is to conjugation is unknown at this time. FOOTNOTES 1. ^ guess based on Cav-Smith saving endo before cytoskeleton
2,750,000,000 YBN 1	207) Cytoskeleton evolves in eukaryote cytoplasm.1 2 3 One theory is that the cytoskeleton formed from the eukaryote flagella (cilia, undulipodia) tubules. Cytoskeleto n is a single body with the endoplasmic reticulum and nuclear membrane? FOOTNOTES 1. ^ Cavalier-Smith, annals of Botony 2005 vol95 issue 1
2,725,000,000 YBN 12	60) First eukaryotic cell evolves.1 2 3 4 5 6 7 8 9 10 This cell has a nucleus, with either single strands or a circle of DNA inside. This is a single anaerobic cell. This is the first protist. This cell evolves either by: 1) two or more bacteria joined, one with flagella (perhaps a eubacteria) formed the nucleus, a second formed the cytoplasm outside the nucleus, eventually the code to build the entire cell including the instructions to build the symbiotic captured bacteria was included in the new nucleus, 2) the nucleus formed as part of the cytoplasm lattice, perhaps the outer wall folded in on itself creating a double membrane, or a membrane grew around the DNA (for example like planctobacteria) which provided more protection for the DNA from the movement and digestive activities of cytoplasm now without a rigid cell wall, 3) a bacteria with flagella that grew cytoplasm and a secondary cell wall outside the original cell wall, 4) a virus, 5) a DNA strand from conjugation with a different prokaryote stored in a vesicle. There are key features that are different from eukaryotes and prokaryotes: 1) Eukaryotes have a nucleus, prokaryotes do not. 2) DNA in eukaryotes is in the form of chromosomes, in prokaryotes the DNA is in a circle. 3) Eukaryotes can do endocytosis, fold their cell membrane around some external object and injest the object, prokaryotes can not. 4) Eukaryotes have a membrane lattice of proteins, actin and myacin, prokaryotes do not. 5) Eukaryotes have an endoplasmic reticulum and golgi body. 6) Eukaryotes reproduce asexually by dual binary division (both nucleus and cell divide by binary division), budding, or mitosis, prokaryotes reproduce by budding or binary division. If the nucleus is an engulfed prokaryote, this cell inherits the processes of nuclear DNA duplication and nucleus division (karyokinesis) from prokaryote binary division. Initially, both the nucleus and cell divide by binary division. Support for the nucleus forming from a prokaryote is that chromosomes in parabasalia and dinoflagellates remain permanently anchored to the nuclear membrane (envelope?) by the kinetochores, the same way prokaryote DNA anchors to the cell membrane (wall?) during cell division. A theory of an archaebacteria (perhaps an eocyte) forming the first eukaryote nucleus and a gram-negative eubacteria forming the cytoplasm of the first eukaryote is supported by genetic evidence. This cell reproduces asexually by either binary fission (both nucleus and cytoplasm) or budding, or sexually by conjugation or both cell and nuclei fully merging. If this cell has chromosomes, this is the first (haploid) organism with chromosomes. Perhaps a sperm-like flagellated prokaryote merged with an ovum-like prokaryote from the same or a different species, perhaps by the ovum opening a pilus and the sperm-like cell entering the pilus, and once inside opening a pilus through which the DNA from the two cells could merge. Many diplomonads look like sperm cells stuck in an ovum, with the still flagellated sperm forming the nucleus, and some diplomonads, for example, the oxymonad, Saccinobaculus reproduce sexually. An important evolutionary step had to evolve here, and that is the evolution of the prokaryote binary division system: 1) duplicating DNA in the cytoplasm, 2) separating the two copies of DNA, and 3) the division of cytoplasm into two cells to an adapted process of eukaryote cell division: 1) duplicating DNA in the nucleus, 2) separating the DNA in the nucleus, 3) dividing the nucleus into two nuclei, 4) separating the two nuclei, and then 5) dividing the cytoplasm into two cells. It appears in early eukaryote nuclei (as seen in closed mitosis, where the nuclear membrane persistes through mitosis) that the nuclei divide by a process similar to binary division (as opposed to budding), which adds to the support for the first nucleus being a prokaryote and continuing to divide by binary division. Most people accept that the centrioles from which grow the microtubule spindles that pull apart chromosomes in mitosis, evolved from the base pairs which originally were, and on some species still are, connected to a cilium. Perhaps there are some eukaryote nuclei that duplicate by budding, although this has never been found to my knowledge. If ever found, that would imply that budding evolved before the first eukaryote, but could have possibly evolved after by simply dropping the instructions to copy anything other than the nucleus. Binary cell division in the most basic form only synthesizes more cytoplasm and cell wall, where budding reproduces the entire body plan of a cell (or nucleus in this case). evidence for prokaryote=eukaryote nucleus 1) flagella connected to nucleus of metamonads. a) flagella hints that nucleus prokaryote may have been a male gamete (and the cytoplasm the female gamete). b) flagella are presumably outside the double membrane, indicates that came after capture? Maybe flagella penetrate double membrane...perhaps were initialy inside or partially inside and outside. 2) nucleus division does not need to be recreated, can be basically the same inherited prokaryote cell division (perhaps with minor adjustments), only within a cell membrane. 3) conjugation already existed as a form of exchanging DNA before the first eukaryote, it is possible that a complete bacterium could be taken in through a pilus. Some eukaryotes like spyrogrya still reproduce sexually through conjugation. 4) DNA was splitting and merging with conjugation in prokaryotes before eukaryotes. 5) division of nucleus and cytoplasm is different, just like mitochondria, when the cytoplasm divides is signalled by molecules (as far as I know), and a nucleus may divide without the cytoplasm dividing (immediately or perhaps ever) in some protists. (Clearly many metamonads have multiple nuclei). It's interesting that some metamonads have muliple nuclei (mastigonts), because when they reproduce it is all integrated, each nuceli is rebuilt (as far as I know). Maybe that shows how simple throwing together nuclei and cytoplasm is for DNA for put together and reproduce. 6) two layer membrane around nucleus, is evidence of a prokaryote being captured in a vacuole. 7) happened for mitochondria, chloroplasts, (and later red algae and green algae), that is support for a prokaryote similar to rikettsia, or cyanobacteria being engulfed and forming nucleus. 8) "all eukaryotic HSP70 homologs share in common with the Gram-negative group of eubacteria a number of sequence features that are not present in any archaebacterium or Gram-positive bacterium, indicating their evolution from this group of organisms." 9) Most genes related to the nucleus are related to archaebacteria, while those relating to the cytoplasm are related to eubacteria. Perhaps there was a long period of time where the future eukaryote nucleus was only an organelle, reproducing initially like mitochondria and chloroplasts do, by themselves, but initiated by the nuclear duplication and cytoplasmic division (check). Somehow the binary division process of the cytoplasm DNA and the binary division process of the nucleus-organelle had to merge into one process. Either the spindle chromosome method (mitosis) evolved before or after the nucleus-organelle has taken over the cytoplasm building function. As time continued, the process of spindle separation evolved for the nucleus-organelle. As time continued, the building of the nucleus-organelle was taken over by the cytoplasmic DNA, still reproducing by binary fission. I could see how budding would be a natural evolution for a cell nucleus that starts as an organelle, is reproduced by cytoplasm DNA and then the DNA is tranfered back into the nucleus-organelle. The nucelus-organelle would then recreate the entire cell inside the nucleus (including the cytoplasm DNA presumably), and presumably it would burst out and continue to copy that way. Perhaps budding prokaryotes were budding eukaryotes that still had their cytoplasm DNA that actually lost their nucleus-organelle. Then budding perhaps evolved into mitosis. I think that mitosis is more similar to binary division than budding is. It seems clear that the nucleus-organelle copied itself. Potentially the same proteins that initiate DNA duplication and cell division for the cytoplasm DNA simulteously initiate DNA duplication and cell (nucleus-organelle) division in the nucleus-organelle. So the nucleus-organelle may have been exactly like a mitochondrion for many years. Although there are uncertainties, this first eukaryote is thought to be a member of the broad group of single celled eukaryotes called "flagellates". It is theorized that later will evolve the unicellular "ameobozoid" and "ciliate" groups. (this is a little vague and I am not sure it really covers algae, and the other alveolates, but it does reduce the complexity of protists11 ) FOOTNOTES 1. ^ Nature 396, 109 - 110 (12 November 1998); doi:10.1038/24030 Rickettsia, typhus and the mitochondrial connection MICHAEL W. GRAY 2. ^ Richard Cowen, "History of Life", (Malden, MA: Blackwell, 2005). 3. ^ Nature 392, 15 - 16 (05 March 1998); doi:10.1038/32033 A paradigm gets shifty W. FORD DOOLITTLE 4. ^ (h2 symbiosis) The chimeric eukaryote: Origin of the nucleus from the karyomastigont in amitochondriate protists Lynn Margulis*, Michael F. Dolan* , and Ricardo Guerrero file:/root/web/euk_nucleo6954.pdf 5. ^ "Planctomycetes a phylum of emerging interest for microbial evolution and ecology John A. Fuerst" planctomycetes_a1.pdf and fuerst1.pdf 6. ^ Nature 392, 37 - 41 (05 March 1998); doi:10.1038/32096 The hydrogen hypothesis for the first eukaryote WILLIAM MARTIN* AND MIKLÓS MÜLLER† 7. ^ Nature 431, 152 - 155 (09 September 2004); doi:10.1038/nature02848 The ring of life provides evidence for a genome fusion origin of eukaryotes MARIA C. RIVERA1,3,4 AND JAMES A. LAKE1,2,4 8. ^ Science, Vol 305, Issue 5685, 766-768 , 6 August 2004 EVOLUTIONARY BIOLOGY: The Birth of the Nucleus Elizabeth Pennisi 9. ^ Richard Cowen, "History of Life", (Malden, MA: Blackwell, 2005).0) origin of nuclear membrane/envelope, is anaerobic eukorig1 thru eukorig7 10. ^ S Blair Hedges, Hsiong Chen, Sudhir Kumar, Daniel YC Wang, Amanda S Thompson and Hidemi Wa, "A genomic timescale for the origin of eukaryotes", BMC Evolutionary Biology 2001, 1:4 doi:10.1186/1471-2148-1-4, (2001). 11. ^ Ted Huntington. 12. ^ S Blair Hedges, Hsiong Chen, Sudhir Kumar, Daniel YC Wang, Amanda S Thompson and Hidemi Wa, "A genomic timescale for the origin of eukaryotes", BMC Evolutionary Biology 2001, 1:4 doi:10.1186/1471-2148-1-4, (2001).
2,725,000,000 YBN 6	65) DNA in the nucleus changes from a single circular chromosome to linear chromosomes.1 2 3 4 Possibly the prokaryote ancestor of the first eukaryote had linear chromosomes since some prokaryotes (although very few) are known to have linear chromosomes instead of or in addition to a single circular chromosome. Perhaps a DNA strand entered a cell by conjugation, the circle of DNA was cut to insert the new DNA (plasmid), but the new DNA strand was not sewn back into the original strand of DNA creating two strands of DNA which eventually evolved into the first 2 chromosomes. Perhaps the first eukaryote nucleus was a virus, many of which have linear chromosomes. This includes the evolution of histones, proteins which are packed in between nucleotides in each chromosome. Presumably DNA duplication (sythesis) of chromosomes (in the nucleus) is initially identical to DNA duplication of DNA strands or circular DNA. Some prokaryotes do not have just one circle of DNA.5 Brucella melitensis has 2 circlular chromosomes. Agrobacterium tumefaciens has a circular and a linear chromosome. Streptomyces griseus can have one linear chromosome. Borrelia burgdorferi contains a linear chromosome and a number of variable circular and linear plasmids. Most eukaryote orgenelles have a single circular chromosome except for the mitochondria of most cnidarians and some other forms which have linear chromosomes. FOOTNOTES 1. ^ not all prokaryotes has circle of DNA: http://arjournals.annualreviews.org/doi/full/10.1146/annurev.ecolsys.28.1. 391;jsessionid=npo4ogeI2anbnHbeKO 2. ^ Jumas-Bilak E, Maugard C, Michaux-Charachon S, Allardet-Servent A, Perrin A, et al. 1995. Study of the organization of the genomes of Escherichia coli, Brucella melitensis and Agrobacterium tumefaciens by insertion of a unique restriction site. Microbiology 141:2425-32 (Medline) 3. ^ Lezhava A, Kameoka D, Sugino H, Goshi K, Shinkawa H, et al. 1997. Chromosomal deletions in Streptomyces griseus that remove the afsA locus. Mol. Gen. Genet. 253:478-83 4. ^ Marconi RT, Casjens S, Munderloh UG, Samuels DS. 1996. Analysis of linear plasmid dimers in Borrelia burgdorferi sensu lato isolates: implications concerning the potential mechanisms of linear plasmid replication. J. Bact. 178:3357-61 5. ^ not all prokaryotes has circle of DNA: http://arjournals.annualreviews.org/doi/full/10.1146/annurev.ecolsys.28.1. 391;jsessionid=npo4ogeI2anbnHbeKO 6. ^ Ted Huntington, my guess due to absence of published info
2,720,000,000 YBN	208) A eukaryote flagellum (cilium, undulipodium) evolves on early single cell eukaryotes. The eukaryote cilia (flagella, undulipodia) may evolve from a prokaryote flagella connected to the nucleus, from the cytoskeleten, or a symbiotic prokaryote. Cilia and eukaryote flagella are structurally the same, but have minor functional differences. Cilia are a special class of eukaryote flagella. The eukarote flagellum is different from prokayote flagellum. The prokaryote flagallum is a solid structures, made of the protein flagellin, which protrudes through the plasma membrane. The eukaryote flagellum (and cilium) contains a "9 plus 2 array", 9 microtubules in a circle with 2 microtubules in the center. Some people think that the eukaryote flagella and cilia should be called "undulipodia". In some species the spindles used in mitosis connect to the bases of the eukaryote cilia (undulipodia), which leads some people to think that the spindles of mitosis may have evolved from the eukaryote cilia. Some people think that the eukaryote cilium (flagellum, undulipodia) was a spirochete (prokaryote) that formed a symbiotic relationship with a eukaryote host, whose DNA was transfered to the host nucleus. Other possibilities are that the eukaryote flagellum evolved from prokaryote flagellum, or simply evolved over time through natural selection. The eukaryote flagellum protein "tubulin" is thought to be related to a bacterial replication/cytoskeletal protein "FtsZ" found in some archaebacteria (archaea). What method of reproduction this first nucleated cell used is a great mystery. Among the choices are binary division, budding, or mitosis. My own feeling is that budding or dual binary division (both nucleus and cytoplasm) was how this cell initially copied. The eukaryote flagellum (cilium, undulipodium) is the same inherited and found on sperm cells.
2,720,000,000 YBN	291) For the first time, a cell is not constantly synthesizing DNA and then having a division period (as is the case for all known prokaryotes), but this cell has a period in between cell division and DNA synthesis where DNA synthesis is not performed. Later some cells develop a stage after synthesis and before cell division.1 For the first time, a cell is not constantly synthesizing DNA (S) and then having a division period (D) (as is the case for all known prokaryotes), but this cell has a period in between cell division and DNA synthesis where DNA synthesis is not performed (G1) . Later some cells develop a stage after synthesis and before cell division (G2).
2,719,000,000 YBN 1	302) If the first eukaryote nucleus was a prokaryote, synchronized duplication and division of organelle-nucleus and cytoplasm of early eukaryote cell evolves. Before this, eukaryote cell division usually results in one cell with no organelle-nuclei and a second cell with 2 organelle-nuclei. Perhaps the organelle-nuclei attach to the outer cell membrane in the same way the cytoplasmic DNA do, which allows new cytoplasm growth to separate the two organelle-nucleus in addition to the cytoplasmic DNA.1 2 Or perhaps the first system of organized nuclei separation originated with the organelle-nucleus flagella microtubules grewing into the cytoskeleton, and organized system spindles and mitosis. If the nuclear membrane was formed around the DNA within a prokaryote, then binary division had to adapt to separate the duplicated DNA within the proto-nucleus (not within the entire cell) which may have been very simple to evolve. If the cytoplasm grew outside the cell wall of a prokaryote, binary division would have to adapt to separate that external cytoplasm. FOOTNOTES 1. ^ Michael Sleigh, "Protozoa and Other Protists", (London; New York: Edward Arnold, 1989).
2,715,000,000 YBN	72) Mitosis, asexual copying of a haploid (single set of chomosomes) eukaryote nucleus, evolves in eukaryotes. Before mitosis, there is a synthesis stage where DNA in the form of chromosomes are duplicated in the nucleus before the nucleus and cell divide.1 2 explain basic process of mitosis: prophase, metaphase, anaphase, telophase Presumably no prokaryotes have ever reproduced through mitosis. Only eukaryotes reproduce asexually using mitosis. Most people accept that some protists were sexual and later lost that ability. But the majority view now is that the first eukaryotes were asexual, and that some protists still living now have never had sexual ability. Because mitosis is complex and similar in detail in all species that do mitosis, people think that mitosis only evolved once, and was inherited by all species that do mitosis. The major differences between this new method of copying, mitosis and the older method, binary fission (add budding?) are: 1) In mitosis, microtubule spindles attach to the kinetochore (the protein structure in eukaryotes which assembles on the centromere and links the chromosome to microtubule polymers from the mitotic spindle during mitosis) and pull apart the two DNA copies, where in binary fission the DNA (single chromosome) attaches to a part of the cytoplasm which pulls apart the two cells. 2) Chromosomes (linear pieces of DNA), not a circle of DNA is being copied. People speculate that early mitosis had spindles outside the nucleus, with chromosomes fastened to the nuclear membrane, as can still be seen in parabasalia and dinoflagellates, which appear to have primitive nuclei. In more ancient species the nuclear membrane persists through mitosis (closed mitosis), but in more recent species, like metazoa, land plants, and many kinds of protists, the nuclear membrane disintegrates before mitosis and is rebuilt after (open mitosis). Most people think that extranuclear spindles (spindles that originate outside of the nucleus) and closed mitosis evolved first. Only later did pleuromitosis (spindles rotate 90 degrees, nucleus can be semi-open, or closed) and then orthomitosis (spindles are on both sides of nucleus and separate chromosomes in a straight line, nucleus can be open, semi-open or closed) evolve in later eukaryotes. It is interesting to think about how how binary fission (or potentially budding) of prokaryote cells with no nucleus evolved into mitosis and the use of spindles. Mitosis, budding, and binary fission are the only asexual methods of reproduction known. Perhaps mitosis evolved first only copying the nucleus then later evolved to make not only a new nucleus but also a new cell around that nucleus.
2,711,000,000 YBN	303) Cytoplasmic cell fusion and division evolves. Two eukaryote cells can merge into one cell with 2 nuclei and then divide back into single 1 nucleus cells. Possibly two cells that fuse cytoplasms but not nuclei, may still retain the system of cytoplasmic DNA and organelle-nucleus attachment to cell membrane (wall?), but on each half of the new cell, therefore making dual haploid mitosis (potentially of both cytoplasmic DNA and organelle-nucleus in synchronized duplication) a simple evolutionary next step.
2,710,000,000 YBN 1 2	73) Sex (cell and genetic fusion, syngamy, gametogamy) evolves in protists. Haploid (1 set of chromosomes) eukaryote cells merge and then their nuclei merge (karyogamy) to form the first diploid (2 sets of chromosomes) cells (the first zygote).1 2 This fusion of 2 haploid cells results in the first diploid single-celled organism, which then immediately divides (both nucleus and cytoplasm by single-division meiosis) back to two haploid cells. Possibly first, only cytoplasmic merging happened with nuclear merging (karyogamy) and nuclear division (karyokinesis) evolving later. Now, two cells with different DNA can mix providing more chance of variety/mutation. Two chromosome sets provides a backup copy of important genes (sequences that code for proteins, or nucleic acids) that might be lost with only a set of single chromosomes. The life cycle of future organisms will now have two phases, a gamophase (from n to 2n (until syngamy3 )), and zygophase (from 2n to n (until meiosis4 )). Gamoid cells are not haploid in polyploid organisms. Potentially sexual cell and genetic fusion is what made the first eukaryote cell, and sex in protists may be directly descended from conjugation in prokaryotes, in other words not evolved from a different method independently of conjugation, because some metamonads, for example Saccinobaculus reproduce sexually, and look very much like a prokaryote sperm cell which formed the nucleus captured in an ovum cell. For sexual species there are 3 basic life cycles: 1) Haploid (Haplontic) life cycle: zygotic meiosis. Life as haploid cells, cell division immediately after creation of zygote from fusion. (All fungi, Some green algae, Many protozoa) 2) Diploid (Diplontic) life cycle: gametic meiosis. Instead of immediate cell division, zygote reproduces by mitosis. Haploid gametes never copy by mitosis. (animals, some brown algae) 3) Haplodiploid (Haplodiplontic, Diplohaplontic, Diplobiontic) life cycle: sporic meiosis. Diploid cell (sporocyte) meiosis results in 2 haploid sporophytes (gamonts), not 2 haploid gametes. These haploid cells then differentiate? or mitosis? to form haploid gametes. Haplodiplontic organisms have alternation of generations, one generation involves diploid spore-producing single or multicellular sporophytes (makes spores) and the other generation involves haploid single or multicellular gamete-producing multicellular gametophytes (makes gametes). Pants and many algae have this haplodiplontic life cycle. These first sexual cells are haplontic, with zygotic meiosis; they reproduce asexually through mitosis as haploid cells, fusing to a diploid cell without mitosis, then dividing back into haploid cells. An important evolutionary step evolves here in that now two cells can completely merge into one cell. This merge not only includes their nuclei, but also their cytoplasm (althought the DNA do not merge). Before now, as far as has ever been observed, no two cells have ever completely merged, although, through conjugation some prokaryotes have been observed to exchange DNA. This marks the beginning of the "haplonic lifestyle" with "zygotic meosis", where the organism is haploid until cell fusion which is immediately followed by (one-step) meiosis of the zygote, after which the haploid cells continues to reproduce through mitosis. Possibly the first sexual organism merged through a form of "autogamy" (both haploid gametes originate from the same individual, the opposite of "allogamy" where the gametes originate from different individuals). Some species reproduce by a form of autogamy (intracellular autogamy), where nuclei (also called pronuclei) divide and then merge within the same cell before the entire cell divides. Some metamonads (earliest still living eukaryotes), like Oxymonas and Saccinobaculus can reproduce asexually by mitosis, but also can reproduce sexually using this form of autogamy. This may be evidence that some prokaryote could also merge two entire cells (if the eukaryote nucleus was a prokaryote). Perhaps prokaryotes evolved full cellular fusion before the first eukaryote. If that is true, then this initial form of nuclei dividing and merging (intracellular autogamy) may have existed for some time before full eukaryote cell merging and synchronized eukayote nucleus and cytoplasm division evolved. It is difficult to see what selective advantage autogamy could possibly have since no new DNA is ever introduced into the next generation of organism, as opposed to "allogamy", where DNA from different individuals is merged, and which has a clear selective advantage. So perhaps autogamy evolved after allogamy, although to me it appears that allogamy is more complex than autogamy, and autogamy would be a perfect starting step to develop the needed proteins and processes for the more complicated allogamy (autogamy only involves the duplication and merging of two nuclei, where allogamy involves the merging of the cell walls, and cytoplasm in addition to the two nuclei.) This is the beginning of the label "gamete" for haploid cells that can merge to form a diploid zygote. In addition, the label "gametocyte" or "gamont" is any polyploid cell that divides (meiosis) into haploid gamete cells which can merge to form a zygote. Perhaps there is a relationship between prokaryote spore formation and the phenomenon of diploid zygotes forming a thick cell wall. Perhaps the first sex (full cell nucleus and cytoplasm fusion) was interchangeably isogamous (both gametes are identical and interchangable), with only one gender, in other words, the first sex on earth was homosexual. Then later heterogamous gametes evolved, where there were two distinct haploid gamete cells, usually a large female cell and a smaller flagellated male cell. Sex also allows organisms to choose reproductive partners that are more likely to make new organisms that are more likely to survive. An alternative theory is that a failed mitosis could result in a diploid nucleus. What advantage might autogamy of intercellular nuclei have, the added chance of mistakes in the merging of two nuclei? In addition, why would such a system (intracellular autogamy) persist if there was no selective advantage? Why wouldn't oxymonas or saccinobacculus reduce totally to asexual mitosis and or allogamous sexual reproduction and either never make use of or lose intracellular autogamous sexual reproduction completely? This is the first eukaryote cell to have a life cycle that involves two different kinds of cells. FOOTNOTES 1. ^ Sir Gavin De Beer, "Atlas of Evolution", (London: Nelson, 1964). 2. ^ estimate based on diplomonads having sex repro, and origin of euk being (is now)
2,710,000,000 YBN	206) Meiosis (one-step meiosis, one DNA duplication and a cell division of a diploid cell into 2 haploid cells) evolves.1 2 detail one-step meiosis: The is no DNA crossover or chiasma formation in one-division meiosis, apparently because either duplication of chromosomes or separation of chromatids does not occurred. As far as I know, mitosis and one-step meiosis are the same with the only exceptions that 1) in meiosis two haploid cells join before cell division, and 2) in mitosis the DNA is duplicated before cell division, but in meiosis the DNA is not duplicated before cell division. Meiosis can be one step (one DNA duplication and then one cell division) or two step (two DNA duplications and then two divisions). Probably one step meosis evolved first and two step meiosis later. Meiosis can only function on cells with two or more sets of chromosomes. The Protists Pyrsonympha and Dinenympha has up to a four step meiosis. Because meiosis is similar and complex in detail in all species that do meiosis, people think that meiosis only evolved once, and was inherited by all species that do meiosis.
2,706,000,000 YBN	299) Duplication of diploid DNA (after 2 haploid cells fuse) evolves. This is required for diploid mitosis. Duplication of diploid DNA may be very similar to duplication of haploid DNA. Initially perhaps the diploid DNA duplicated, but still divided in one-division meiosis.
2,705,000,000 YBN	210) Mitosis of diploid cells evolves. This begins the "diplontic" life cycle (with gametic meiosis), where diploid cells (a zygote) can copy asexually through mitosis after merging. This organism, when haploid, cannot do mitosis (presumably haploid gamete mitosis will evolve much later in brown algae), and this is still true in all descendents (including humans) of this single celled organism. The proteins and mechanism of mitosis of diploid cells is probably very similar to mitosis of haploid cells. The most primitive organisms still alive that are diplontic are the metamonads (e.g. Oxymonads: Notila, Hypermastigotes: Urinympha, Macrospironympha, Rhynchonympha).
2,704,000,000 YBN	296) The origin of gender evolves: sex (cell and nucleus fusion) between two isogamous (same size) gametes but which have 2 different (+ and -) forms (genders).1 Perhaps the invention of two different genders originated when a flagellated cell (or nucleus) divided by binary division and only one half of the two new cells retained the flagellum. Then to differentiate the two cells even more, but still keep the same DNA template, different proteins could be weighted on one half of the cell during division to activate various operons in one gender but not the other once the two DNA pairs are separated. Perhaps sex where the gametes are the same size but cannot merge themselves should be called "specific" or "gendered" isogamy, and where any two same sized gametes can merge called "nonspecific" or "nongendered" isogamy.
2,703,000,000 YBN	297) Sex (cell and nucleus fusion) between two different size gamete cells (heterogamy or anisogamy) evolves in protists.1 Some species are heterogamous but two of the same sized (gender) gametes can fuse to form a zygote.
2,702,000,000 YBN	298) Sex (cell and nucleus fusion) between one flagellated gamete and an unflagellated gamete (oogamy, a form of heterogamy) evolves in protists.1 This system is the system humans inherited.
2,700,000,000 YBN	62) Oldest steranes (formed from sterols, molecules made by mitochondria in eukaryotes) found in northwestern Australia.1 2 FOOTNOTES 1. ^ Richard Cowen, "History of Life", (Malden, MA: Blackwell, 2005). 2. ^ Science, Vol 285, Issue 5430, 1033-1036 , 13 August 1999 Archean Molecular Fossils and the Early Rise of Eukaryotes Jochen J. Brocks, 1,2* Graham A. Logan, 2 Roger Buick, 1 Roger E. Summons 2
2,700,000,000 YBN	192) Fossils from the Bulawaya stromatolite, Zimbabwe.1 FOOTNOTES 1. ^ http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VBP-42G6M5T-7&_user=4 422&_coverDate=02%2F01%2F2001&_fmt=full&_orig=browse&_cdi=5932&view=c&_acct=C000 059600&_version=1&_urlVersion=0&_userid=4422&md5=d61bf36f008d6b2cba3ba5dbd5a628d 7&ref=full#bib9 Nagy, L.A. and Zumberge, J.E., 1976. Fossil microorganisms from the approximately 2800-2500 million-year-old Bulawaya stromatolites: Application of ultramicrochemical analyses. Proc. Natl. Acad. Sci. Wash. 73, pp. 2973-2976.
2,700,000,000 YBN	214) Biomarkers characteristic of cyanobacteria, 2alpha -methylhopanes, indicate that oxygenic photosynthesis evolved well before the atmosphere became oxidizing.1 FOOTNOTES 1. ^ Science, Vol 285, Issue 5430, 1033-1036 , 13 August 1999, Archean Molecular Fossils and the Early Rise of Eukaryotes Jochen J. Brocks, 1,2* Graham A. Logan, 2 Roger Buick, 1 Roger E. Summons 2
2,692,000,000 YBN	300) Diploid cell fusion (Gamontogamy) evolves.1 2 3 4 Only a few species exhibit this property (e.g. the Oxymonad Notilla, Diatoms, Dasicladales {Acetabularia}, in many foraminiferans, and in gregarines). Gamontogamy may have evolved into two-step meiosis. The vast majority of eukaryotes living now that reproduce sexually fuse haploid cells. All "gametes" are haploid cells that can merge, diploid cells that can merge are gamonts. Gamonts (Meiocytes) are cells that produce gametes. In theory this should be very similar if not exactly like haploid cell fusion, so perhaps this is not a major evolutionary step.
2,690,000,000 YBN	295) Meiosis (two step meiosis, two cell divisions with no stage in between which result in one diplid cell dividing into four haploid cells) evolves.1 Mei osis and mitosis are similar in being process of nucleus and cell division, but are different. Differences between meiosis and mitosis: 1) At least one crossover per homologous pair happens in 2 step meiosis but crossover usually does not happen in mitosis. 2) Two step meiosis involves cell divisions that happen one after the other, where mitosis only happens after one DNA duplication (there are never 2 mitoses together without a DNA duplication between them to my knowledge). The cell division in two step meiosis that involves a separation of sister chromatids (not homologous chromosome pairs) is basically identical to mitosis. For two step meiosis, this is the second nucleus and cell division. Later multistep meiosis evolves, where there may be as many as 4 divisions (for example in the protists Pyrsonympha and Dinenympha).
2,650,000,000 YBN 2	170) First bacteria live on land.1 FOOTNOTES 1. ^ Battistuzzi, Feijao, Hedges, "A Genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land", BMC Evolutionary Biology, (2004). 2. ^ Battistuzzi, Feijao, Hedges, "A Genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land", BMC Evolutionary Biology, (2004). (2600-2700my)
2,558,000,000 YBN 1	171) Phylum Deinococcus-Thermus (Thermus Aquaticus {used in PCR}, Deinococcus radiodurans {can survive long exposure to radiation}) evolve now.1 PHYLUM Deinococcus-Thermus CLASS Deinococci ORDER Deinococcales ORDER Thermales The Deinococcus-Thermus are a small group of bacteria comprised of cocci highly resistant to environmental hazards. There are two main groups. The Deinococcales include a single genus, Deinococcus, with several species that are resistant to radiation; they have become famous for their ability to eat nuclear waste and other toxic materials, survive in the vacuum of space and survive extremes of heat and cold. The Thermales include several genera resistant to heat. Thermus aquaticus was important in the development of the polymerase chain reaction where repeated cycles of heating DNA to near boiling make it advantageous to use a thermo-stable DNA polymerase enzyme. These bacteria have thick cell walls that give them gram-positive stains, but they include a second membrane and so are closer in structure to those of gram-negative bacteria. FOOTNOTES 1. ^ Battistuzzi, Feijao, Hedges, "A Genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land", BMC Evolutionary Biology, (2004). MORE INFO [1] Tree of Life. http://tolweb.org/tree/ [2] Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004).
2,558,000,000 YBN 1 2	172) Genetic comparison shows Eubacteria phylum, Cyanobacteria (ancestor of all eukaryote chloroplasts {plastids}) evolving now. There is a conflict between the interpretation of the geological and the genetic evidence as to if oxygen photosynthesis and cyanobacteria evolved earlier around 3800mybn or here at 2500mybn.1 2 Cyanobacteria get their energy from photosythesis. Cyanobacteria include unicellular, colonial, and filamentous forms. Some filamentous cyanophytes form differentiated cells, called heterocysts, that are specialized for nitrogen fixation, and resting or spore cells called akinetes. Each individual cell typically has a thick, gelatinous cell wall, which stains gram-negative. The cyanophytes lack flagella, but may move about by gliding along surfaces. Most are found in fresh water, while others are marine, occur in damp soil, or even temporarily moistened rocks in deserts. A few are endosymbionts in lichens, plants, various protists, or sponges and provide energy for the host. Chloroplasts found in eukaryotes (algae and higher plants) most likely represent reduced endosymbiotic cyanobacteria. This endosymbiotic theory is supported by various structural and genetic similarities. Primary chloroplasts are found among the green plants, where they contain chlorophyll b, and among the red algae and glaucophytes, where they contain phycobilins. It now appears that these chloroplasts probably had a single origin. Other algae likely took their chloroplasts from these forms by secondary endosymbiosis or ingestion. tenative: CLASS Chroobacteria CLASS Hormogoneae CLASS Gloeobacteria Some live in the fur of sloths, providing a form of camouflage. FOOTNOTES 1. ^ Battistuzzi, Feijao, Hedges, "A Genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land", BMC Evolutionary Biology, (2004). 2. ^ S. Blair Hedges and Sudhir Kumar, "Genomic clocks and evolutionary timescales", Trends in Genetics Volume 19, Issue 4 , April 2003, Pages 200-206, (2003). MORE INFO [1] Tree of Life. http://tolweb.org/tree/ [2] Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). [3] Journal of Molecular Evolution Publisher: Springer-Verlag New York ISSN: 0022-2844 (Paper) 1432-1432 (Online) Issue: Volume 42, Number 2 Date: February 1996 Pages: 194 - 200 [4] Phylogenetic Relationships of Nonaxenic Filamentous Cyanobacterial Strains Based on 16S rRNA Sequence Analysis jme_42_2_1996.pdf [5] http://en.wikipedia.org/wiki/Cyanobacteria
2,558,000,000 YBN 3	315) Phylum Chloroflexi, (Green Non-Sulphur) evolve now.1 PHYLUM Chloroflexi CLASS Chloroflexi CLASS Thermomicrobia2 The Chloroflexi are a group of bacteria that produce ATP through photosynthesis. They make up the bulk of the green non-sulfur bacteria, though some are classified separately in the Phylum Thermomicrobia. They are named for their green pigment, usually found in photosynthetic bodies called chlorosomes. Chloroflexi are typically filamentous, and can move about through bacterial gliding. They are facultatively aerobic, but do not produce oxygen during photosynthesis, and have a different method of carbon fixation than other photosynthetic bacteria. Phylogenetic trees indicate that they had a separate origin. FOOTNOTES 1. ^ Battistuzzi, Feijao, Hedges, "A Genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land", BMC Evolutionary Biology, (2004). 2. ^ "Chloroflexi". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Chloroflexi 3. ^ Battistuzzi, Feijao, Hedges, "A Genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land", BMC Evolutionary Biology, (2004). MORE INFO [1] Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). [2] Tree of Life http://tolweb.org/tree/
2,500,000,000 YBN	52) End Archean Era, Start Proterozoic Era.1 2 FOOTNOTES 1. ^ The geological Society of America ucmp.berkeley.edu 2. ^ Richard Cowen, "History of Life", (Malden, MA: Blackwell, 2005).
2,500,000,000 YBN	56) Banded Iron Formations start to appear in many places.1 2 FOOTNOTES 1. ^ Richard Cowen, "History of Life", (Malden, MA: Blackwell, 2005). 2. ^ greenspirit.uk
2,400,000,000 YBN	59) Very large ice age that lasts 200 million years starts now.1 FOOTNOTES 1. ^ Richard Cowen, "History of Life", (Malden, MA: Blackwell, 2005).
2,335,000,000 YBN 1	290) The nucleolus, a sphere in the nucleus that makes ribosomes, evolves.1 In some eukaryotes (thought to be more ancient), the nucleolus just divides during mitosis, but in other eukaryotes the mitosis is dissolved and rebuilt after nuclear division. In euglenids, kinetoplastids, dinoflagellates, some amoebae and some coccidians, the nucleolus remains visible throughout mitosis and divides into two, but in the majority of groups the nucleolus dissapears and reforms at telophase. That the nucleolus can divide by itself suggests that it was once a free living cell. FOOTNOTES 1. ^ Michael Sleigh, "Protozoa and Other Protists", (London; New York: Edward Arnold, 1989).: p48 nucleolus divides
2,330,000,000 YBN	198) Rough and smooth endoplasmic reticulum evolves in eukaryote cell. Rough and smooth endoplasmic reticulum evolves in eukaryote cell. The rough ER manufactures and transports proteins destined for membranes and secretion. It synthesizes membrane, organellar, and excreted proteins. Minutes after proteins are synthesized most of them leave to the Golgi apparatus within vesicles. The rough ER also modifies, folds, and controls the quality of proteins. The smooth ER has functions in several metabolic processes. It takes part in the synthesis of various lipids (e.g., for building membranes such as phospholipids), fatty acids and steroids (e.g., hormones), and also plays an important role in carbohydrate metabolism, detoxification of the cell (enzymes in the smooth ER detoxify chemicals), and calcium storage. It also is a large transporter of nutrient found in each cell.
2,325,000,000 YBN	199) Golgi Body (Golgi Apparatus, dictyosome) evolves in eukaryote cell. The primary function of the Golgi apparatus is to process proteins targeted to the plasma membrane, lysosomes or endosomes, and those that will be formed from the cell, and sort them within vesicles. It functions as a central delivery system for the cell. Most of the transport vesicles that leave the endoplasmic reticulum (ER), specifically rough ER, are transported to the Golgi apparatus, where they are modified, sorted, and shipped towards their final destination. The Golgi apparatus is present in most eukaryotic cells, but tends to be more prominent where there are many substances, such as proteins, being secreted. For example, plasma B cells, the antibody-secreting cells of the immune system, have prominent Golgi complexes.
2,310,000,000 YBN	200) The golgi body in eukaryote cells makes lysosomes which fuse with endosomes. The various molecules in lysosomes digest the contents of the endosome, which then exits the cell as waste.
2,305,000,000 YBN	63) A parasitic bacterium, a bacterium that can only live in other bacteria, closely related to Rickettsia prowazekii, an aerobic alpha-proteobacteria that causes louse-borne typhus, enters an early eukaryote cell. As time continues a symbiotic relationship evolves, where the Rickettsia forms the mitochondria, organelles of every euokaryote cell. The mitochondria perform the Acid Citric Cycle (Krebs Cycle), using oxygen to breakdown glucose into CO2 and H2O, and provide up 38 ATP molecules. Mitochondria reproduce by themselves, and are not created by the DNA in the cell nucleus. As time continues some of the DNA from the mitochondria merges with the cell nucleus DNA. Mitochondria produce sterol used to make the eukaryote cell wall flexible. Because mitochondria need Oxygen, but the level of oxygen is very low on earth, oxygen may be provided by photosynthesizing cyanobacteria living near these cells. All eukaryotes alive today either have mitochondria except the amitochondriate excavates (metamonads), the most ancient of the eukaryotes alive today. That parabasalids have hydrogenosomes, anaerobic organelles that seem to have evolved from mitochondria, many people think amitochondriate species lost their mitochondria over time.1 This changes the eukaryote cell from an anaerobic to aerobic unicellular organism. This early mitochondria may have "tubular christae". Perhaps there was a period of time where a system evolved to make sure both halves received mitochondria during cell division. Protists with discoidal mitochondrial cristea will later evolve from the Bikont tubular mitochondrial christae branch. For the most part: 1) Excavates, Amoebozoa, and Chromealveolates have or had tubular christae, 2) Discicristata (Euglenozoa) have discoidal christae. 3) Cryptomonads, Glaucophytes, Red Algae, Green Algae, Plants, Fungi, Animals all have flat christae. From this point on, all eukaryotes will need Oxygen to use mitochondria and receive the ATP made by mitochondria. 2 One theory is that, as more O2 is produced at the surface of the ocean, protists (which require oxygen for mitochondria) can move to the ocean floor. 3 FOOTNOTES 1. ^ http://comenius.susqu.edu/BI/202/Protists/EUKARYA-DOMAIN.htm 2. ^ Richard Cowen, "History of Life", (Malden, MA: Blackwell, 2005). 3. ^ Richard Cowen, "History of Life", (Malden, MA: Blackwell, 2005).
2,303,000,000 YBN 1	203) Bikonts (two cilia) evolve from Unikonts (one cilium). Bikonts (also called anterokonts for having anterior {forward facing} cilia) will evolve into the vast majority of the Protist and all of the Plant Kingdoms. The Unikonts will evolve into the ameobozoa (tenatively), and the opisthokonts (ancestrally posterior cilium) which include the entire Fungi and Animal Kingdoms.1 2 3 Since members of both the unikont (animals, fungi) and bikont (metamonads, plants) can reproduce sexually, sex had to evolve before this branching, presuming sexual reproduction is strictly inherited and did not evolve twice. FOOTNOTES 1. ^ Nucleic Acids Research Pages 865-878 v26 4 865 MW Gray, BF Lang, R Cedergren, GB Golding, C Lemieux, D Sankoff, M Turmel, N Brossard, E Delage, TG Littlejohn, I Plante, P Rioux, D Saint-Louis, Y Zhu, and G Burger MORE INFO [1] THOMAS CAVALIER-SMITH, "Economy, Speed and Size Matter: Evolutionary Forces Driving Nuclear Genome Miniaturization and Expansion", * Oxford Journals * Life Sciences * Annals of Botany * Volume 95, Number 1 *, (2005). [2] Thomas Cavalier-Smith and Ema E. -Y. Chao, "Phylogeny of Choanozoa, Apusozoa, and Other Protozoa and Early Eukaryote Megaevolution", Springer New York, (2003). [3] Michael W. Gray, B. Franz Lang, Robert Cedergren, G. Brian Golding, Claude Lemieux, David San, "Genome structure and gene content in protist mitochondrial DNAs", Oxford Journals, (1997).
2,300,000,000 YBN	47) Most recent evidence of uraninite, a mineral that cannot exist for much time if exposed to oxygen, indicating that free oxygen is accumulating in the air of earth for the first time.1 FOOTNOTES 1. ^ Richard Cowen, "History of Life", (Malden, MA: Blackwell, 2005).
2,300,000,000 YBN	48) Oldest Red Beds, iron oxide formed on land, begin here and are evidence of more free oxygen in the air of earth.1 2 FOOTNOTES 1. ^ Richard Cowen, "History of Life", (Malden, MA: Blackwell, 2005). 2. ^ http://www.es.ucsc.edu/~pkoch/lectures/lecture5.html
2,300,000,000 YBN 10 11 12	219) Genetic comparison shows the oldest line of eukaryotes still in existence, the oldest living protists, in the Phylum "Metamonada" (Excavates) originating now. 1 2 3 This is where the eukaryote line is created and separates from the archaebacteria (archaea) line. Most of these species have an excavated ventral feeding groove, and all lack mitochondria. Mitochondria are thought to have been lost secondarily, although this is not certain. PHYLUM Metamonada ORDER Carpediemondida ORDER Diplomonadida ORDER Retortamonadida CLASS Parabasalia ORDER Trichomonadida ORDER Hypermastigida CLASS Anaeromonada ORDER Oxymonadida ORDER Trimastigida Includes Diplomonad "Giardia", and Parabasalid "Trichomonas vaginalis". The trophozoite form of Giardia does age and die. Most Metamonads reproduce asexually through closed (the nuclear membrane does not dissolve during mitosis) mitosis (and involves an external spindle? is pluromitosis?), but some species are "faculatively sexual" (can reproduce sexually in addition to asexually). So already by the time of these most ancient of the now living eukaryotes, sex had evolved. eat bacteria? Some people have this phylum as part of the group "Excavates" which includes the Phyla (Metamonada, Percolozoa, and Euglenozoa). The classification of the protists is far from complete and settled. There are currently more than one existing classification scheme for the protists. features of parabasalia and metamonada: gamete type: flagellated haplontic and diplontic condensed chromosomes in some species mitotic spindle: parabasalia: external metamonadea: internal polar structures: parabasalia: flagellar root me tamonadea: kinetosome flagella: parabasalia: 4 to many metamonadea: 2,44 hetero kont, isokont, anisokont: anisokont 5 (Anisokont flagella are those flagella that are unequal in length, form, or direction. 6 ) (Isokont flagella are those flagella that are equal in length, form, and direction.7 ) (The name heterokont refers to the characteristic form of these cells, which typically have two unequal flagella. The anterior or tinsel flagellum is covered with lateral bristles or mastigonemes, while the other flagellum is whiplash, smooth and usually shorter, or sometimes reduced to a basal body. The flagella are inserted subapically or laterally, and are usually supported by four microtubule roots in a distinctive pattern. 8 ) flagellate stages: trophic life forms: unicellular: flagellated multicellular: none cell covering: naked 9 FOOTNOTES 1. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004). 2. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). 3. ^ S. Blair Hedges, "The Origin and Evolution of Model Organisms", Nature Reviews Genetics 3, 838-849; doi:10.1038/nrg929, (2002). 4. ^ Michael Sleigh, "Protozoa and Other Protists", (London; New York: Edward Arnold, 1989). p98-99 5. ^ Michael Sleigh, "Protozoa and Other Protists", (London; New York: Edward Arnold, 1989). p98-99 6. ^ http://comenius.susqu.edu/bi/202/Protists/terms/anisokont.htm 7. ^ http://comenius.susqu.edu/bi/202/Protists/terms/anisokont.htm 8. ^ "Heterokonts". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Heterokonts 9. ^ Michael Sleigh, "Protozoa and Other Protists", (London; New York: Edward Arnold, 1989). p98-99 10. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004). 11. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). 12. ^ S. Blair Hedges, "The Origin and Evolution of Model Organisms", Nature Reviews Genetics 3, 838-849; doi:10.1038/nrg929, (2002).
2,156,000,000 YBN 2	150) Amino acid sequence comparison shows the eubacteria and archaebacteria line separating here at 2,156 mybn, first archaebacteria.1 FOOTNOTES 1. ^ Russell F. Doolittle, Da-Fei Feng, Simon Tsang, Glen Cho, Elizabeth Little, "Determining Divergence Times of the Major Kingdoms of Living Organisms with a Protein Clock", Science, (1996). 2. ^ Russell F. Doolittle, Da-Fei Feng, Simon Tsang, Glen Cho, Elizabeth Little, "Determining Divergence Times of the Major Kingdoms of Living Organisms with a Protein Clock", Science, (1996).
2,000,000,000 YBN 1 2 3 4	293) Genetic comparison shows the the Eukaryote Phylum "Loukozoa" (Jakobea and Malawimonadea) originating now. These species have mitochondria with tubular cristae, and are the most ancient species that still have mitochondria.1 2 3 4 This species is the most ancient known species to have a shell. This first hard shells (lorika) made of calcium carbonate (Calcite CaCO3), plates of silica (SiO2), or carbon-based molecules evolve around the single-celled species living in the ocean. 5 Perhaps this shell served to protect the cell from external damage from being eaten by other eukaryotes (zooplankton), infection by bacteria or viruses, control of buoyancy, to filter UV light, against damage by non-living sources. 6 Jakobids and Malawimonads are also grouped as Excavates because they have a ventral feeding groove. Jakobids are flagellates with two flagella located at the anterior end of a ventral feeding groove (i.e., are excavate), with mitochondria, freely swimming or loricate (with protective shell). Flagellar apparatus with two basal bodies giving rise to two major microtubular roots, which support the margins of the ventral groove. Other cytoskeletal microtubules arise directly or indirectly from the basal bodies, no extrusomes. Jakobids have tubular mitochondrial cristae (transforming to flat cristae in Jakoba libera). (1) This indicates that flat evolved from tubular cristae. PHYLUM Loukozoa ORDER Jakobida ORDER Malawimonadida Reproduction=mitosis? ORDER Jakobida FAMILY Histionidae The jakobid family "Histionidae" reproduce asexually by binary fission. In this family no sexual reproduction has been observed yet. (1) FAMILY Jakobidae FOOTNOTES 1. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004). 2. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). 3. ^ S. Blair Hedges, "The Origin and Evolution of Model Organisms", Nature Reviews Genetics 3, 838-849; doi:10.1038/nrg929, (2002). 4. ^ estimate from S. L. Baldauf, "The Deep Roots of Eukaryotes", Science 13 June 2003: Vol. 300. no. 5626, pp. 1703 - 1706 DOI: 10.1126/science.1085544, (2003).
1,990,000,000 YBN	202) Eukaryotes with discoidal cristae mitochondria split from the tubular christae line.1 This is the origin of the Discicristata: species that have discoid mitochondrial cristae and, in some cases, a deep (excavated) ventral feeding groove.2 The Discicristata are Acrasid slime molds, vahlkampfiid amoebas, euglenoids, trypanosomes, and leishmanias.
1,990,000,000 YBN	301) Haplodiplontic (Diplohaplontic, Diplobiontic) life cycle (organism with both diploid and haploid "alternate life stages" that reproduce asexually by mitosis) with "sporic meiosis" evolves. In this life cycle haploid gametes fuse to form a diploid zygote which divides by meiosis producing haploid spores that produce (differentiate?) gametes, starting the cycle again. Initially these species are single celled in both stages (like Haptophyta). All plants, most brown algae, blastocladiid chytrids, many red algae, and some filamentous green algae (e.g. Cladophora) and foraminifera have haplodiploid life cycles. Initially, these organisms are single celled, but later the mitosis stages will become multicellular when the cells that result from mitosis stick together. The only? example of this is Haptophyta, where diploid cells divide in sporic meiosis, into haploid cells (gamonts) which then divide into gametes. Of the diplohaplonic species, those where the haploid and diploid stages look the same are called "isomorphic" and those where the two stages look different are called "heteromorphic". In land plants the haploid (gametophyte) stage is reduced to only a few cells. Since double DNA chromosomes (diploid) provides more possibilities than a single chromosome, diploid organisms have a selective advantage over haploid organisms. 1 FOOTNOTES 1. ^ Raven, Evert, Eichhorn, "Biology of Plants", (New York: Worth Publishers, 1992).
1,988,000,000 YBN 3	317) Eukaryotes that have mitochondria with flat christae evolve from those with tubular christae.1 2 FOOTNOTES 1. ^ http://nar.oxfordjournals.org/cgi/content/full/26/4/865 2. ^ http://microscope.mbl.edu/scripts/protist.php?func=integrate&myID=P1901&chinese_ flag=&system=&version=&documentID=&excludeNonLinkedIn=&imagesOnly= 3. ^ guess based on one jakobid having tubular that change to flat, aside from that cryptomonads are firs
1,982,000,000 YBN 1 2 3	87) Genetic comparison shows the most primitive living members of the Phylum "Euglenozoa" (euglenids, leishmania, trypanosomes, kinetoplastids) evolved at this time.1 2 3 This is the oldest eukaryote to exhibit colonialism. Perhaps eukaryote colonialism is partially or fully inherited from prokaryotes, but colonialism may have evolved independently again in eukaryotes. This is the most ancient species known to have a cell covering, which is of the type "pellicle". No examples of sexual reproduction in the group have been found. 4 Reproduction is through closed mitosis and involves an internal spindle. 5 At least one account of a sexual cycle has been reported in Scytomonas. 6 The chloroplasts are contained in three membranes and are pigmented similarly to the plants, suggesting they were retained from some captured green alga. All Euglenozoa have mitochondria with discoid cristae, which in the kinetoplastids characteristically have a DNA-containing granule or kinetoplast associated with the flagellar bases. I think they are still haploid, mitosis duplicates in nucleus? Euglenozoa age? This group is sometimes called "Discicristates" because all members have mitochondria with "discoidal cristae". 7 Euglenids are the first eukaryotes with an eyespot. Most colored euglenids also have a stigma or eyespot, which is a small splotch of red pigment on one side of the flagellar pocket. This shades a collection of light sensitive crystals near the base of the leading flagellum, so the two together act as a sort of directional eye. Euglenozoa eyepots evolved from chloroplasts. This is the beginning of a light sensory system which evolves to eyes? A small number of euglinids have chloroplasts and can photosynthesize. In these species, the chloroplasts contain three membranes and are thought to have evolved at least 900 million years later from a captured green alga. Euglenoids, however, share reproductive habits with their kinetoplastid relations by reproducing mainly by asexual binary fission. Euglenoids reproduce very rapidly, absorbing their flagellum and dividing haploid cells through mitosis. Mitosis produces 4-8 flagellated haploid cells, called zoospores. The zoospores then break out of the parent cell and grow to full size. 8 condensed chromosomes: yes in all kinetoplasts, and some euglenophyta. 9 polar structures: none 10 number of flagella: kinetoplastids=(1 in some) 2, euglenophyta=2 (4 in some) 11 life forms: 12 unicellular: flagellated 13 multic ellular: colonial 14 cell covering: pellicle 15 2. Euglenoids are small (10-500 µm) freshwater unicellular organisms. 3. One-third of all genera have chloroplasts; those that lack chloroplasts ingest or absorb their food. 4. Their chloroplasts are surrounded by three rather than two membranes. a. Their chloroplasts resemble those of green algae. b. They are probably derived from a green algae through endosymbiosis. 5. The pyrenoid outside the chloroplast produces an unusual type of carbohydrate polymer (paramylon) not seen in green algae. 6. They possess two flagella, one of which typically is much longer and than the other and projects out of a vase-shaped invagination; it is called a tinsel flagellum because it has hairs on it. 7. Near the base of the longer flagellum is a red eyespot that shades a photoreceptor for detecting light. 8. They lack cell walls, but instead are bounded by a flexible pellicle composed of protein strips side-by-side. 9. A contractile vacuole, similar to certain protozoa, eliminates excess water. 10. Euglenoids reproduce by longitudinal cell division; sexual reproduction is not known to occur. 16 PHYLUM Euglenozoa CLASS Euglenoidea CLASS Diplonemea CLASS Kinetoplastea CLASS Postgaardea Those Euglnozoa that do not photosynthesize feed on bacteria (phagocytosis) or feed through absorption (osmosis) of nutrients. Most are small, around 15-40 µm in size, although many euglenids get up to 500 µm long. Most Euglenozoa have two flagella, usually one leading and one trailing. Some euglenozoa cause parasitic disease in other species. A kinetoplastid member of Euglenozoa, such as trypanosoma brucei which causes African sleeping sickness, is transmitted from host to host by a vector, most commonly the tsetse fly. In most forms there is an associated cytostome (mouth) supported by one of three microtubule groups that arise from the flagellar bases. Average life cycle=? days Average age of euglenozoa life=? days Trypanosomes (Kinetoplastids) typically have complex life-cycles involving more than one host, and go through various morphological stages. 1000 Species of Euglenoids (euglenophyta). FOOTNOTES 1. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004). 2. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). (1600mybn) 3. ^ Russell F. Doolittle, Da-Fei Feng, Simon Tsang, Glen Cho, Elizabeth Little, "Determining Divergence Times of the Major Kingdoms of Living Organisms with a Protein Clock", Science, (1996). (1800-1900 for eukaryote/prokaryote separation)
1,982,000,000 YBN 21 22 23	294) Genetic comparison shows the Phylum "Percolozoa" (also called "Heterolobosea"1 ) (acrasid slime molds) evolved at this time.2 3 4 Percolozoa are a group of heterotrophic colourless protozoa, including many that can transform between amoeboid, flagellate, and encysted stages. These are collectively referred to as amoeboflagellates, schizopyrenids, or vahlkampfids. They also include the acrasids, a group of social amoebae that aggregate to form sporangia.5 6 7 Very closely related to Euglenozoa. All characteristics are like Euglenozoa: Percolozoa have mitochondria with discoid christae. No examples of sexual reproduction in the group have been found. Reproduction is through closed mitosis and involves an internal spindle. 8 No chloroplasts (check) or (The chloroplasts are contained in three membranes and are pigmented similarly to the plants, suggesting they were retained from some captured green alga.9 ) I think they are still haploid, mitosis duplicates in nucleus? Percolozoa age? Percolozoa are sometimes included in the group "Discicristates" because all members have mitochondria with "discoidal cristae". No eyespots. closed mitosis with internal spindle. 10 The Percolozoa are the most ancient species to have members that move by pseudopodia, like amoeba. PHYLUM Percolozoa 11 CLASS Heterolobosea ORDER Schizopyrenida Singh, 1952 ORDER Acrasida Shröter, 1886 (acrasids, cellular slime molds) ORDER Lyromonadida Cavalier-Smith, 1993 CLASS Percolatea 12 ORDER Acrasida (acrasids, cellular slime molds): a. Cellular slime molds (Phylum Acrasiomycota) (ORDER Acrasida13 ) exist as individual amoeboid cells. (Plasmodial slime molds, mycetozoa, which evolve later, exist as a plasmodium. ) b. They live in soil and feed on bacteria and yeast. c. As food runs out, amoeboid cells release a chemical that causes them to aggregate into a pseudoplasmodium. d. The pseudoplasmodium stage is temporary; it gives rise to sporangia that produce spores. e. Spores survive until more favorable environmental conditions return; then they germinate. f. Spore germinate to release haploid amoeboid cells, which is again the beginning of asexual cycle. g. Asexual cycle occurs under very moist conditions. 14 Percolozoa feed on bacteria (phagocytosis) or feed through absorption (osmosis) of nutrients. (check) Most are small, around 15-40 µm in size, although many euglenids get up to 500 µm long. The flagellate stage is slightly smaller, with two or four anterior flagella anterior to the feeding groove. Average life cycle=? days Average age of Percolozoa life=? days Most Percolozoa are found as bacterivores in soil, freshwater, and on feces. There are a few marine and parasitic forms, including the species Naegleria fowleri, which can become pathogenic in humans and is often fatal. The group is closely related to the Euglenozoa, and share with them the unusual though not unique characteristic of having mitochondria with discoid cristae. The presence of a ventral feeding groove in the flagellate stage, as well as other features, suggests that they are part of the excavate group.15 The amoeboid stage is roughly cylindrical, typically around 20-40 μm in length. They are traditionally considered lobose amoebae, but are not related to the others and unlike them do not form true lobose pseudopods. Instead, they advance by eruptive waves, where hemispherical bulges appear from the front margin of the cell, which is clear. The flagellate stage is slightly smaller, with two or four anterior flagella anterior to the feeding groove.16 Usually the amoeboid form is taken when food is plentiful, and the flagellate form is used for rapid locomotion. However, not all members are able to assume both forms. The genera Percolomonas, Lyromonas, and Psalteriomonas are known only as flagellates, while Vahlkampfia, Pseudovahlkampfia, and the acrasids do not have flagellate stages. As mentioned above, under unfavourable conditions, the acrasids aggregate to form sporangia. These are superficially similar to the sporangia of the dictyostelids, but the amoebae only aggregate as individuals or in small groups and do not die to form the stalk.17 The Heterolobosea were first defined by Page and Blanton in 1985 as a class of amoebae, and so only included those forms with amoeboid stages. Cavalier-Smith created the phylum Percolozoa for the extended group, together with the enigmatic flagellate Stephanopogon. (currently I have stephanopogon colpoda images under ciliates...18 ) He maintained the Heterolobosea as a class for amoeboid forms, but most others have expanded them to include the flagellates as well.19 Stephanopogon closely resembles certain ciliates and was originally classified with them, but is now considered a flagellate. 20 FOOTNOTES 1. ^ Ted Huntington. 2. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004). 1961mybn 3. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). 1600 mybn 4. ^ Russell F. Doolittle, Da-Fei Feng, Simon Tsang, Glen Cho, Elizabeth Little, "Determining Divergence Times of the Major Kingdoms of Living Organisms with a Protein Clock", Science, (1996). 1800-1900 mybn 5. ^ "Percolozoa". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Percolozoa 6. ^ http://microscope.mbl.edu/scripts/protist.php?func=integrate&myID=P2989 7. ^ Raven, Evert, Eichhorn, "Biology of Plants", (New York: Worth Publishers, 1992). p178 8. ^ Michael Sleigh, "Protozoa and Other Protists", (London; New York: Edward Arnold, 1989). p98-99 9. ^ Ted Huntington. 10. ^ http://microscope.mbl.edu/scripts/protist.php?func=integrate&myID=P2989 11. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=114287 12. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=114287 13. ^ Ted Huntington. 14. ^ http://www.sirinet.net/~jgjohnso/apbio30.html 15. ^ "Percolozoa". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Percolozoa 16. ^ "Percolozoa". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Percolozoa 17. ^ "Percolozoa". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Percolozoa 18. ^ Ted Huntington. 19. ^ "Percolozoa". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Percolozoa 20. ^ "Stephanopogon". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Stephanopogon 21. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004). 1961mybn (1961) 22. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). 1600 mybn (1600mybn) 23. ^ Russell F. Doolittle, Da-Fei Feng, Simon Tsang, Glen Cho, Elizabeth Little, "Determining Divergence Times of the Major Kingdoms of Living Organisms with a Protein Clock", Science, (1996). 1800-1900 mybn (1800-1900(for eukaryote/prokaryote separation)
1,980,000,000 YBN 1	38) Multicellularity evolves in a protist. Multicellularity is a very important event in the evolution of life on earth. With multicellular organisms, larger sized organisms could evolve. There are many uncertainties surrounding the origin of multicellularity. Multicellularity may have evolved independently for Plants, Fungi and Animals, or multicellularity may have evolved only once in eukaryotes. The key feature of this cell is that a multicellular organism is made from a single cell and the multicellular organism is not a collection of independent cells (colonialism). The main difference between this organism and single-celled organisms is the way the cells stay fastened together after cell division. Which species was the first multicellular species is not clear. Multicellularity is found in all 3 life cycles (haplontic, diplontic, haplodiplontic). The 3 main life cycle types (haplontic, etc.) probably evolved in single cell species before multicellularity evolved. If multicellularity evolved once and is inherited, perhaps all multicellular organism descended from a single haplodiplontic organism. These multicellular organisms have undifferentiated cells in the multicellular stage (all cells in the haploid or diploid multicellular organism are made of one kind of cell). Dinophyta, and Fungi are multicellular Haplontic species. Most animals are multicellular Diplontic species. Most brown algae and all plants are multicellular Haplodiplontic species. The vast majority of multicellular organisms reproduce only through sex, although there are exceptions (like some plants and rotifers) which have lost the ability to sexually reproduce or can also reproduce asexually. In multicellularity, one cell goes on to produce all the cells in a multicellular species, so that each individual organism is genetically unique. This cell is usually a diploid zygote, but can be a haploid cell. This protist is most likely sexual, and multicellularity evolved only in a species that reproduces sexually. Some describe algae multicellularity as "filamentous".1 The first multicellular eukaryuotes are presumably undifferentiated. For haplontic these cells are all gametes, for diplontic these cells are all capable of meiosis to form gametes, for haplodiplontic, in the haploid stage the cells are all gamete producing, in the diploid stage the cells are all spore producing. Some people think that multicellular organisms arose at least six times: in animals, fungi and several groups of algae. 2 What did the first multicellular organism look like? Perhaps it was a haplontic protist that only did one or more haploid mitoses, but this time the cells stuck together (perhaps similar to the way bacteria form filaments). An interesting aspect of multicellular organisms is that oxygen must still reach each cell for mitochondria to work, and so this requires that the cells be only 1 cell thick, or if thicker have some kind of (circulatory) system for oxygen to reach each cell. FOOTNOTES 1. ^ Michael Sleigh, "Protozoa and Other Protists", (London; New York: Edward Arnold, 1989).
1,978,000,000 YBN 1	15) Multicellularity with differentiation evolves. Multicellular organisms are no longer all haploid or diploid gamete producing cells (or spore producing if haplodiplontic), but are made of gamete (or spore) producing cells in addition to somatic cells which copy asexually through mitosis. Now, in addition to being large multicell organisms, multicellular organisms can have differentiated cells that form a variety of different shaped structures, and perform different functions. This process will evolve to the metazoan multicellular differentiation that arises from a single zygote cell, where cells have different functions and shapes. Differentiation evolves for a second time in eukaryotes? this is not the first monoadmulti one cell leading to a multicellular organism (attached, free, interchangible)? where a multicellular organism is made from one cell (interchangable, specific cells: genetic specificity). It is unknown how multicellular life stages happen. For example, why one specific cell line of many produced from mitosis of a zygote will go on to do meiosis producing the haploid gamete cells which will fuse to form the next zygote, but the many other cells made from, for example, one of the two cells made after the zygote divides, will not contain the line of cells that ultimately make the gamete producing cells which continue the life cycle of the organism. Since presumably each cell in an organism contains an identical genome, perhaps a gamete producing cell can be made from any cell if specific proteins are present, or perhaps there is a protein which simply points to a certain location in the DNA which is located at a different location in the DNA for every cell, or perhaps some other explanation answers the question of how cell differentiation can happen when each cell has the same genome. A (diploid) zygote cell (the cell made by two merging gamete cells) now divides to form all cells in the differentiated multicellular organism, and is said to be "totipotent". Totipotent cells differentiate into "pluripotent" cells which can make most but not all cells in the organism. Pluripotent cells differentiate into "multipotent" (can make a number of cells) or "unipotent" cells (can only make one kind of cell). FOOTNOTES 1. ^ Ted Huntington. guess. is after haploid mitosis? after fusion?
1,974,000,000 YBN	169) For those that think algae are plants, this is where the plant kingdom begins with the evolution of brown algae (phaeophyta).1 FOOTNOTES 1. ^ Michael Sleigh, "Protozoa and Other Protists", (London; New York: Edward Arnold, 1989).
1,973,000,001 YBN 1 2 3	88) Genetic comparison shows the ancestor of the "Chromalveolates" evolving now. Chromalveolates include the Chromista and Alveolata. The Chromista include the 3 Phyla Haptophyta, Cryptophyta (Cryptomonads), and Heterokontophyta (brown algae {kelp}, diatoms, water molds). Alveolata include the 3 Phyla Dinoflagellata, Apicomplexa (Malaria, Toxoplasmosis), and Ciliophora (ciliates).1 2 3 Chromealveolates have mitochondria with tubular cristae. Thomas Cavalier-Smith writes: "The chromalveolate clade (Cavalier-Smith 1999) and its constituent taxa, kingdom Chromista (Cavalier-Smith 1981) and protozoan infrakingdom Alveolata (Cavalier-Smith 1991b), were all proposed based on morphological, biochemical, and evolutionary reasoning about protein targeting before there was sequence evidence for any of them. Now all are strongly supported by such evidence. Chromalveolates comprise all algae with chlorophyll c (the chromophyte algae) and all their nonphotosynthetic descendants. They arose by a single symbiogenetic event in which an early unicellular red alga was phagocytosed by a biciliate host and enslaved to provide photosynthate (Cavalier-Smith 1999, 2002c, 2003a). The strongest evidence that this occurred once only in their cenancestor is the replacement of the red algal plastid glyceraldehyde phosphate dehydrogenase (GAPDH) by a duplicate of the gene for the cytosolic version of this enzyme in all four chromalveolate groups with plastids: the alveolate sporozoa and dinoflagellates and the chromist cryptomonads and chromobiotes (Fast et al. 2001). It would be incredible for such gene duplication, retargeting by acquiring bipartite targeting sequences, and loss of the original red algal gene to have occurred convergently in four groups, but it was already pretty incredible that these groups would all have evolved a similar protein-targeting system independently and all happened to enslave a red alga, evolve chlorophyll c, and place their plastids within the rough endoplasmic reticulum (ER) independently. Yet many assumed just this because of the false dogma that symbiogenesis is easy and the failure of all these groups to cluster in rRNA trees. For chromobiotes this retargeting of GAPDH has been demonstrated only for heterokonts-information is lacking for haptophytes. However, there are five strong synapomorphies for Chromobiota, making it highly probable that the group is holophyletic (Cavalier-Smith 1994). They share the presence of the periplastid reticulum in the periplastid space instead of a nucleomorph like cryptomonads, they uniquely make the carotenoid fucoxanthin and chlorophyll c3, they uniquely have a single autofluorescent cilium, and they have tubular mitochondrial cristae with an intracristal filament. Five plastid genes now extremely robustly support the monophyly of both chromists and chromobiotes (Yoon et al. 2002). We are confident that comparable sequence evidence from nuclear genes will also eventually catch up with the general biological evidence for the holophyly of chromobiotes to convince even the most skeptical, who ignore or discount such valuable evidence that chromobiotes are holophyletic." 4 Chromista include phyla: Heterokontophyta (heterokonts) (many classes) (includes colored: golden algae, axodines, diatoms, yellow-green algea, brown algae, colorless: water moulds, slime nets) Haptophyta Cryptophyta (cryptomonads) (many genera) Alveolates include the phyla: Dinoflagellata (Dinoflagellates) Apicomplexa (Apicomplexans) Ciliophora (ciliates) In 1981 Cavalier-Smith created a new kingdom called "Chromista" in which all chromalveolates are placed. 5 There are a number of classification schemes for the kingdom Protista and no one system has emerged as most popular yet. FOOTNOTES 1. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004). 2. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). (1600mybn) 3. ^ Sandra L. Baldauf, A. J. Roger, I. Wenk-Siefert, W. F. Doolittle, "A Kingdom-Level Phylogeny of Eukaryotes Based on Combined Protein Data", Science, Vol 290, num 5493, p 972, (2000). has heterkonts before ciliophora and apicomplexa branch MORE INFO [1] "Brown alga". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Brown_alga
1,972,000,000 YBN 1 2 3	304) Genetic comparison shows the ancestor of Chromalveolate Phlyum Haptophyta evolving now.1 2 3 Some Haptophytes are haplodiploid (alternate between haploid and diploid cycles that both have mitosis), and this group is the most primitive with a haplodiploid life cycle. Haptophytes are single cellular.4 Haptophytes are found only in all oceans (marine) and are flagellates, almost all with plastids with chlorophylls a and c, with two flagella and one additional locomotor/feeding organelle, the haptonema.5 Haptophyta are a group of algae (phytoplankton). The chloroplasts are pigmented similarly to those of the heterokonts, such as golden algae, but the structure of the rest of the cell is different, so it may be that they are a separate line whose chloroplasts are derived from similar endosymbionts.6 The cells typically have two slightly unequal flagella, both of which are smooth, and a unique organelle called a haptonema, which is superficially similar to a flagellum but differs in the arrangement of microtubules and in its use.7 Haptophytes have tubular mitochondria cristae.8 Most haptophytes are coccolithophores, which live strictly in the oceans (marine) and are ornmmented with calcified scales called coccoliths, which are sometimes found as microfossils. Other planktonic haptophytes of note include Chrysochromulina and Prymnesium, which periodically form toxic marine algal blooms. Both molecular and morphological evidence supports their division into five orders.9 10 Emiliania is a small organism that is famous for turning huge portions of the ocean bright turquoise during its blooms. They are also known for contributing to the white cliffs of Dover because of the calcite in their coccolith cell structure. They play a very important role in the carbon cycle in the ocean because they form calcium carbonate exoskeletons that sink to the bottom of the ocean floor when they die. They are also one of the worlds major calcite producers.11 Sexual reproduction: Asexual, Open mitosis with spindle nucleating (originating?12 ) in cytoplasm.13 Phaeocystis colonial cells diploid, motile cells haploid or diploid; reproduction by vegetative division of non-motile cells and fragmentation of colonies, vegetative division of motile cells, or by fusion of gametes.14 Members of the Haptophytes Genus "Phaocystis" form colonies (see photo15 ). Haptophytes are also called "Prymnesiophytes" 16 Some Haptophyta have hard shell made of calcium carbonate evolves around the single-celled species living in the ocean. KINGDOM Protista (Chromalveolata) PHYLUM Haptophyta CLASS Pavlovophyceae ORDER Pavlovales CLASS Prymnesiophyceae ORDER Prymnesiales ORDER Phaeocystales ORDER Isochrysidales ORDER Coccolithales FOOTNOTES 1. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004). 2. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). (1600mybn) 3. ^ Sandra L. Baldauf, A. J. Roger, I. Wenk-Siefert, W. F. Doolittle, "A Kingdom-Level Phylogeny of Eukaryotes Based on Combined Protein Data", Science, Vol 290, num 5493, p 972, (2000). (has heterkonts before ciliophora and apicomplexa branch)
1,971,000,000 YBN 1 2 3	305) Genetic comparison shows the ancestor of the Chromalveolate Phylum "Cryptophyta" (Cryptomonads) evolving now.1 2 3 The cryptomonads are a small group of flagellates, most of which have chloroplasts. They are common in freshwater, and also occur in marine and brackish habitats. Each cell has an anterior groove or pocket with typically two slightly unequal flagella at the edge of the pocket. 4 Cryptomonads distinguished by the presence of characteristic extrusomes called ejectisomes, which consist of two connected spiral ribbons held under tension. If the cells are irritated either by mechanical, chemical or light stress, they discharge, propelling the cell in a zig-zag course away from the disturbance. Large ejectisomes, visible under the light microscope, are associated with the pocket; smaller ones occur elsewhere on the cell. 5 Cryptomonads have one or two chloroplasts, except for Chilomonas which has leucoplasts and Goniomonas which lacks plastids entirely. These contain chlorophylls a and c, together with phycobilins and other pigments, and vary in color from brown to green. Each is surrounded by four membranes, and there is a reduced cell nucleus called a nucleomorph between the middle two. This indicates that the chloroplast was derived from a eukaryotic symbiont, shown by genetic studies to have been a red alga. 6 A few cryptomonads, such as Cryptomonas, can form palmelloid stages, but readily escape the surrounding mucus to become free-living flagellates again. Cryptomonad flagella are inserted parallel to one another, and are covered by bipartite hairs called mastigonemes, formed within the endoplasmic reticulum and transported to the cell surface. Small scales may also be present on the flagella and cell body. The mitochondria have flat cristae, and mitosis is open; sexual reproduction has also been reported.7 Originally the cryptomonads were considered close relatives of the dinoflagellates because of their similar pigmentation. Later botanists treated them as a separate division, Cryptophyta, while zoologists treated them as the flagellate order Cryptomonadida. There is considerable evidence that cryptomonad chloroplasts are closely related to those of the heterokonts and haptophytes, and the three groups are sometimes united as the Chromista. However, the case that the organisms themselves are related is not very strong, and they may have acquired chloroplasts independently.8 Crytomonads often forms blooms in greater depths of lakes, or during winter beneath the ice. The cells are usually brownish in color, and have a slit-like furrow at the anterior. They are not known to produce any toxins and are used to feed small zooplankton, which is the food source for small fish in fish farming. 9 Reproduction: Number of species: Size and shape: 10-50 μm in size and flattened in shape Mitochondria Christae: flat 10 11 12 (which is unusual, as most chromalveolates have tubular christae). Cryotphyta may be more closely related to the Plant Kingdom and nearest Glaucophyta which also have flat christae. After one species of jakobid that changes tubular to flat christae, cryptophyta are the most ancient phylum to have flat christae. 13 14 KINGDOM Protista (Chromalveolata) PHYLUM Cryptophyta CLASS Cryptomonadea ORDER Pyrenomonadales Novarino & Lucas, 1993 ORDER Cryptomonadales Pascher, 1913 FOOTNOTES 1. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004). 2. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). (1600mybn) 3. ^ Sandra L. Baldauf, A. J. Roger, I. Wenk-Siefert, W. F. Doolittle, "A Kingdom-Level Phylogeny of Eukaryotes Based on Combined Protein Data", Science, Vol 290, num 5493, p 972, (2000). has heterkonts before ciliophora and apicomplexa branch
1,970,000,000 YBN 1 2 3	306) Genetic comparison shows the ancestor of the Chromalveolate Phylum "Heterokontophyta" (Heterokonts also called Stramenopiles) evolving now. Heterokonts include brown algae, diatoms, golden algae, axodines, yellow-green algae, water moulds and slime nets.1 2 3 Heterkonts evolved very near the same time as the Euglinozoa did. Heterokonts all have mitochondria with tubular christae. The motile cells of heterokonts all have two unequal cilia (flagella), one "tinsel" (covered with hairs {mastigonemes}) cilium and one "whiplash" (free of hair) cilium.4 KINGDOM Protista (Chromalveolata) PHYLUM Heterokontophyta Colored groups CLASS Chrysophyceae (golden algae) CLASS Synurophyceae CLASS Actinochrysophyceae (axodines) CLASS Pelagophyceae CLASS Phaeothamniophyceae CLASS Bacillariophyceae (diatoms) CLASS Raphidophyceae CLASS Eustigmatophyceae CLASS Xanthophyceae (yellow-green algae) CLASS Phaeophyceae (brown algae) Colorless groups CLASS Oomycetes(water moulds) CLASS Hypochytridiomycetes CLASS Bicosoecea CLASS Labyrinthulomycetes(slime nets) CLASS Opalinea CLASS Proteromonadea FOOTNOTES 1. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004). 2. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). (1600mybn) 3. ^ Sandra L. Baldauf, A. J. Roger, I. Wenk-Siefert, W. F. Doolittle, "A Kingdom-Level Phylogeny of Eukaryotes Based on Combined Protein Data", Science, Vol 290, num 5493, p 972, (2000). has heterkonts before ciliophora and apicomplexa branch
1,969,000,000 YBN 6 7 8	307) Chromalveolate Heterokont, Brown Algae (Phaeophyta) evolves now.1 2 3 Brown Algae is the most genetically ancient multicellular organism still living on earth. In addition to being first to evolve multicellularity, cell differentiation (cells of different types) is already present in all brown algae. Genetic comparison shows the ancestor of the Chromalveolate Heterokont Brown Algae (Phaeophyta) evolving now. Brown Algae is the most genetically ancient multicellular organism still living on earth. In addition to being first to evolve multicellularity, cell differentiation (cells of different types) is already present in all brown algae. Brown algae belong to a large group called the heterokonts, most of which are colored flagellates. Most contain the pigment fucoxanthin, which is responsible for the distinctive greenish-brown color that gives brown algae their name. Brown algae are unique among heterokonts in developing into multicellular forms with differentiated tissues, but they reproduce by means of flagellate spores, which closely resemble other heterokont cells. Genetic studies show their closest relatives are the yellow-green algae. 4 Most Brown algae are haplodiplontic. KINGDOM Protista (Chromalveolata) PHYLUM Heterokontophyta Colored groups CLASS Phaeophyceae (brown algae) Some people view brown algae as being in the plant kingdom, and others as being a multicellular protist in the protist kingdom. 2. Brown algae range from small forms with simple filaments to large multicellular (50-100 m long) seaweeds. (Fig. 30.8) 3. Brown algae have chlorophylls a and c and a fucoxanthin that give them their color. 4. Their reserve food is a carbohydrate called laminarin. 5. Seaweed refers to any large, complex alga. 6. Their cell walls contain a mucilaginous water-retaining material that inhibits desiccation. 7. Laminaria is an intertidal kelp that is unique among protists; this genus shows tissue differentiation. 8. Nereocystis and Macrocystis are giant kelps found in deeper water anchored to the bottom by their holdfasts. 9. Individuals of the genus Sargassum sometimes break off from their holdfasts and form floating masses. 10. Brown algae provide food and habitat for marine organisms, and they are also important to humans. a. Brown algae are harvested for human food and for fertilizer in several parts of the world. b. They are a source of algin, a pectin-like substance added to give foods a stable, smooth consistency. 11. Most have an alternation of generations life cycle. 12. Fucus is an intertidal rockweed; meiotic cell division produces gametes and adult is always diploid. 5 FOOTNOTES 1. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004). 2. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). 3. ^ Sandra L. Baldauf, A. J. Roger, I. Wenk-Siefert, W. F. Doolittle, "A Kingdom-Level Phylogeny of Eukaryotes Based on Combined Protein Data", Science, Vol 290, num 5493, p 972, (2000). has heterkonts before ciliophora and apicomplexa branch 4. ^ "Phaeophyta". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Phaeophyta 5. ^ http://www.sirinet.net/~jgjohnso/apbio30.html 6. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004). (1973mybn) 7. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). (1600mybn) 8. ^ Sandra L. Baldauf, A. J. Roger, I. Wenk-Siefert, W. F. Doolittle, "A Kingdom-Level Phylogeny of Eukaryotes Based on Combined Protein Data", Science, Vol 290, num 5493, p 972, (2000). has heterkonts before ciliophora and apicomplexa branch
1,968,000,000 YBN 21 22 23	308) Chromalveolate Heterokont, Diatoms evolve.1 2 3 Genetic comparison shows the ancestor of the Chromalveolate Heterokont Diatoms evolving now. Diatoms are diplontic. 4 Diatoms are a very common types of phytoplankton. Most diatoms are unicellular, although some form chains or simple colonies. A characteristic feature of diatom cells is that they are encased within a unique cell wall made of silica. These walls show a wide diversity in form, some quite beautiful and ornate, but usually consist of two symmetrical sides with a split between them, hence the group name. 5 Life Cycle When a cell divides each new cell takes as its epitheca a valve of the parent frustule, and within ten to twenty minutes builds its own hypotheca; this process may occur between one and eight times per day. Availability of dissolved silica limits the rate of vegetative reproduction, but also because this method progressively reduces the average size of the diatom frustule in a given population there is a certain threshold at which restoration of frustule size is neccesary. Auxospores are then produced, which are cells that posses a different wall structure lacking the siliceous frustule and swell to the maximum frustule size. The auxospore then forms an initial cell which forms a new frustule of maximum size within itself. 6 KINGDOM Protista (Chromalveolata) PHYLUM Heterokontophyta Colored groups CLASS Bacillariophyceae (diatoms) There are more than 200 genera of living diatoms, and it is estimated that there are approximately 100 000 extant species (Round & Crawford, 1990). Diatoms are a widespread group and can be found in the oceans, in freshwater, in soils and on damp surfaces. 7 Their chloroplasts are typical of heterokonts, with four membranes and containing pigments such as fucoxanthin. Individuals usually lack flagella, but they are present in gametes and have the usual heterokont structure, except they lack the hairs (mastigonemes) characteristic in other groups. 8 Most diatom species are non-motile but some are capable of an oozing motion. As their relatively dense cell walls cause them to readily sink, planktonic forms in open water usually rely on turbulent mixing of the upper layers by the wind to keep them suspended in sunlit surface waters. Some species actively regulate their buoyancy to counter sinking. 9 Diatoms cells are contained within a unique silicate (silicic acid) cell wall comprised of two separate valves (or shells). The biogenic silica that the cell wall is composed of is synthesised intracellularly by the polymerisation of silicic acid monomers. This material is then extruded to the cell exterior and added to the wall. Diatom cell walls are also called frustules or tests, and their two valves typically overlap one other like the two halves of a petri dish. In most species, when a diatom divides to produce two daughter cells, each cell keeps one of the two valves and grows a smaller valve within it. As a result, after each division cycle the average size of diatom cells in the population gets smaller. Once such cells reach a certain minimum size, rather than simply divide vegetatively, they reverse this decline by forming an auxospore. This expands in size to give rise to a much larger cell, which then returns to size-diminishing divisions. Auxospore production is almost always linked to meiosis and sexual reproduction. 10 Diatoms are traditionally divided into two orders: centric diatoms (Centrales), which are radially symmetric, and pennate diatoms (Pennales), which are bilaterally symmetric. The former are paraphyletic to the latter. A more recent classification is that of Round & Crawford (1990), who divide the diatoms into three classes: centric diatoms (Coscinodiscophyceae), pennate diatoms without a raphe (Fragilariophyceae), and pennate diatoms with a raphe (Bacillariophyceae). It is probable there will be further revisions as our understanding of their relationships increases. 11 Planktonic forms in freshwater and marine environments typically exhibit a "bloom and bust" lifestyle. When conditions in the upper mixed layer (nutrients and light) are favourable (e.g. at the start of spring) their competitive edge (Furnas, 1990) allows them to quickly dominate phytoplankton communities ("bloom"). 12 When conditions turn unfavourable, usually upon depletion of nutrients, diatom cells typically increase in sinking rate and exit the upper mixed layer ("bust"). This sinking is induced by either a loss of buoyancy control, the synthesis of mucilage that sticks diatoms cells together, or the production of heavy resting spores.13 In the open ocean, the condition that typically causes diatom (spring) blooms to end is a lack of silicon. Unlike other nutrients, this is only a major requirement of diatoms so it is not regenerated in the plankton ecosystem as efficiently as, for instance, nitrogen or phosphorus nutrients. This can be seen in maps of surface nutrient concentrations - as nutrients decline along gradients, silicon is usually the first to be exhausted (followed normally by nitrogen then phosphorus).14 Heterokont chloroplasts appear to be derived from those of red algae, rather than directly from prokaryotes as occurs in plants. This suggests they had a more recent origin than many other algae. However, fossil evidence is scant, and it is really only with the evolution of the diatoms themselves that the heterokonts make a serious impression on the fossil record. 15 The earliest known fossil diatoms date from the early Jurassic (~185 Ma; Kooistra & Medlin, 1996), although recent genetic (Kooistra & Medlin, 1996) and sedimentary (Schieber, Krinsley & Riciputi, 2000) evidence suggests an earlier origin. Medlin et al. (1997) suggest that their origin may be related to the end-Permian mass extinction (~250 Ma), after which many marine niches were opened. The gap between this event and the time that fossil diatoms first appear may indicate a period when diatoms were unsilicified and their evolution was cryptic (Raven & Waite, 2004). Since the advent of silicification, diatoms have made a significant impression on the fossil record, with major deposits of fossil diatoms found as far back as the early Cretaceous, and some rocks (diatomaceous earth, diatomite, kieselguhr) being composed almost entirely of them. 16 Although the diatoms may have existed since the Triassic, the timing of their ascendancy and "take-over" of the silicon cycle is more recent. 17 3. Diatoms are the most numerous unicellular algae in the oceans. (Fig. 30.6a) 4. They are extremely numerous and an important source of food and O2 in aquatic systems. 5. Diatom cell walls consist of two silica-impregnated halves or valves. a. When diatoms reproduce asexually, each received one old valve. b. The new valve fits inside the old one; therefore, the new diatom is smaller than the original one. c. This continues until they are about 30 percent of their original size. d. Then they reproduce sexually; a zygote grows and divides mitotically to form diatoms of normal size. 6. The cell wall has an outer layer of silica (glass) with a variety of markings formed by pores. 7. Diatom remains accumulate on the ocean floor and are mined as diatomaceous earth for use as filters, abrasives, etc. 18 Life Cycle (cont.) Many neritic planktonic diatoms alternate between a vegetative reproductive phase and a thicker walled resting cyst or statospore stage. The siliceous resting spore commonly forms after a period of active vegetative reproduction when nutrient levels have been depleted. Statospores may remain entirely within the the parent cell, partially within the parent cell or be isolated from it. An increase in nutreint levels and/or length of daylight cause the statospore to germinate and return to its normal vegatative state. Seasonal upwelling is therefore a vital part of many diatoms life cycle as a provider of nutrients and as a transport mechanism which brings statospores or their vegetative products up into the photic zone.19 The resting spore morphology of some species is similar to that of the corresponding vegetative cell, whereas in other species the resting spores and the vegetative cells differ strongly. The two valves of a resting spore may be similar or distinctly different. Often the first valve formed is more similar to the valves of the vegetative cells than the second valve. 20 FOOTNOTES 1. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004). 2. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). 3. ^ Sandra L. Baldauf, A. J. Roger, I. Wenk-Siefert, W. F. Doolittle, "A Kingdom-Level Phylogeny of Eukaryotes Based on Combined Protein Data", Science, Vol 290, num 5493, p 972, (2000). has heterkonts before ciliophora and apicomplexa branch 4. ^ Michael Sleigh, "Protozoa and Other Protists", (London; New York: Edward Arnold, 1989). p98-99 5. ^ "Diatom". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Diatom 6. ^ http://www.ucl.ac.uk/GeolSci/micropal/diatom.html 7. ^ "Diatom". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Diatom 8. ^ "Diatom". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Diatom 9. ^ "Diatom". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Diatom 10. ^ "Diatom". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Diatom 11. ^ "Diatom". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Diatom 12. ^ "Diatom". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Diatom 13. ^ "Diatom". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Diatom 14. ^ "Diatom". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Diatom 15. ^ "Diatom". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Diatom 16. ^ "Diatom". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Diatom 17. ^ "Diatom". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Diatom 18. ^ http://www.sirinet.net/~jgjohnso/apbio30.html 19. ^ http://www.ucl.ac.uk/GeolSci/micropal/diatom.html 20. ^ http://www.ucl.ac.uk/GeolSci/micropal/diatom.html 21. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004). (1973mybn) 22. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). (1600mybn) 23. ^ Sandra L. Baldauf, A. J. Roger, I. Wenk-Siefert, W. F. Doolittle, "A Kingdom-Level Phylogeny of Eukaryotes Based on Combined Protein Data", Science, Vol 290, num 5493, p 972, (2000). has heterkonts before ciliophora and apicomplexa branch
1,967,000,000 YBN 23 24 25	309) Chromalveolate Heterokont, Water molds (Oomycetes OemISETEZ) evolve.1 2 3 Genetic comparison shows the ancestor of the Chromalveolate Heterokont Water molds (Oomycetes OemISETEZ) evolving now. Oomycetes (Water molds), with about 580 species, vary from unicellular, to multicellular highly brached filamentous forms. 4 The filamentous form is called "coenocytic" (grows as a large multinucleate cell that results from multiple nuclear divisions without cell divisions, also called "mycelium" in fungi) 5 6 Oomycetes grow by closed (or nearly closed) mitosis with pairs of centrioles near the poles 7 . Filamentous forms grow by mitosis, but only the nucleus is duplicated (karyokinesis), no septa (horizontal cell wall) is constructed, making these multinucleate very large single cells. Technically, filamentous oomycetes are 3 celled multicellular organisms because a septa forms between the vegetative filament and the diploid sporangium (and oogonium) cells (and the haploid antheridium multinucleate cells are not free swimming), but many people label oomycetes as single celled organism. But it appears clear that oomycetes would be constructed of many cells if a cell wall was built at mitosis. Sexual forms are diploid and reproduce by conjugation. Water Molds are microscopic organisms that reproduce both sexually and asexually and are composed of mycelia, or a tube-like vegetative body (all of an organism's mycelia are called its thallus). The name "water mould" refers to the fact that they thrive under conditions of high humidity and running surface water. 8 Water molds were originally classified as fungi, but are now known to have developed separately and show a number of differences. Their cell walls are composed of cellulose rather than chitin and lack septa (a wall that divides two spaces) except where reproductive cells are produced, in addition to having gene sequences more closely related to brown algae than fungi.9 Also, in the vegetative state they have diploid nuclei, whereas fungi have haploid nuclei. 10 11 The oomycetes include the water molds, white rusts and the downy mildews. Many oomycetes are multinucleate filaments (hyphae) that resemble fungi. These hyphae have no cross walls, but are one long hollow tube and are called "coenocytic". They were once thought to be related to the fungi, but their cell walls are made of cellulose, not chitin as they are in the true fungi. The superficial resemblance of the fungi and the oomycetes is likely a case of convergent evolution. Both groups have a filamentous (hyphal) body form with a high surface area to volume ration which facilitates uptake of nutrients from their surroundings. 12 The oomycetes are saprobic and parasitic forms, including water molds like Saprolegnia and downey mildews like Peronospora. 13 1. These organisms (and slime molds) resemble fungi but all have flagellated cells which fungi never do. 2. Water molds possess a cell wall but it is made of cellulose, not chitin as in fungi. 3. Water molds produce diploid (2n) zoospores and meiosis produces the gametes. 14 2. Aquatic water molds parasitize fishes, forming furry growths on their gills, and decompose remains. 3. Terrestrial water molds parasitize insects and plants; a water mold caused the 1840s Irish potato famine. 4. Water molds have a filamentous body but cell walls are composed largely of cellulose. 5. During asexual reproduction, they produce diploid motile spores (2n zoospores) with flagella. 6. Unlike fungi, the adult is diploid; gametes are produced by meiosis. 7. Eggs are produced in enlarged oogonia. 15 KINGDOM Protista (Chromalveolata) PHYLUM Heterokontophyta Colorless groups CLASS Oomycetes (water moulds) Oomycetes have mitochondria with tubular christae. 16 Water mould motile cells are produced as asexual spores called zoospores, which capitalize on surface water (including precipitation on plant surfaces) for movement. The Zoospores have 2 unequal anterior (apical) flagella. They also produce sexual spores, called oospores, that are translucent double-walled spherical structures used to survive adverse environmental conditions. 17 The water molds are among the most important plant pathogenic (capable of causing disease) organisms that may be facultatively or obligately parasitic. The majority can be divided into three groups, although more exist. 18 19 * The Phytophthora group is a genus that causes diseases such as dieback, potato blight (caused the potato famine in Ireland), sudden oak death and rhododendron root rot. 20 * The Pythium group is a genus that is more ubiquitous than Phytophythora and individual species have larger host ranges, usually causing less damage. Pythium damping off is a very common problem in greenhouses where the organism kills newly emerged seedlings. Mycoparasitic members of this group (e.g. P. oligandrum) parasitise other oomycetes and fungi and have been employed as biocontrol agents . One Pythium species, Pythium insidiosum is also known to infect mammals. 21 * The third group are the downy mildews, which are easily identifable by the appearance of white "mildew" on leaf surfaces (although this group can be confused with the unrelated powdery mildews). 22 A male nuclei from a multinucleate haploid cell is transfered to into the haploid egg cell; the male gamete is not free moving, only the female gametes are although contained within the oogonium. FOOTNOTES 1. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004). 2. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). 3. ^ Sandra L. Baldauf, A. J. Roger, I. Wenk-Siefert, W. F. Doolittle, "A Kingdom-Level Phylogeny of Eukaryotes Based on Combined Protein Data", Science, Vol 290, num 5493, p 972, (2000). has heterkonts before ciliophora and apicomplexa branch 4. ^ Raven, Evert, Eichhorn, "Biology of Plants", (New York: Worth Publishers, 1992). 5. ^ http://www.ilmyco.gen.chicago.il.us/Terms/coeno128.html#coeno128 6. ^ "Coenocyte". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Coenocyte 7. ^ Michael Sleigh, "Protozoa and Other Protists", (London; New York: Edward Arnold, 1989). 8. ^ "Water moulds". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Water_moulds 9. ^ http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/P/Protists.html#Water_Mol ds 10. ^ "Water moulds". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Water_moulds 11. ^ http://www.plantbio.uga.edu/zoosporicfungi/oomycete.htm 12. ^ http://kentsimmons.uwinnipeg.ca/16cm05/1116/16protists.htm 13. ^ Michael Sleigh, "Protozoa and Other Protists", (London; New York: Edward Arnold, 1989). 14. ^ http://www.sirinet.net/~jgjohnso/apbio30.html 15. ^ http://www.sirinet.net/~jgjohnso/apbio30.html 16. ^ http://microscope.mbl.edu/scripts/protist.php?func=integrate&myID=P2734&chinese_ flag=&system=&version=&documentID=&excludeNonLinkedIn=&imagesOnly= 17. ^ "Water moulds". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Water_moulds 18. ^ "Water moulds". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Water_moulds 19. ^ http://www.plantbio.uga.edu/zoosporicfungi/oomycete.htm 20. ^ "Water moulds". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Water_moulds 21. ^ "Water moulds". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Water_moulds 22. ^ "Water moulds". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Water_moulds 23. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004). (1973mybn) 24. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). (1600mybn) 25. ^ Sandra L. Baldauf, A. J. Roger, I. Wenk-Siefert, W. F. Doolittle, "A Kingdom-Level Phylogeny of Eukaryotes Based on Combined Protein Data", Science, Vol 290, num 5493, p 972, (2000). has heterkonts before ciliophora and apicomplexa branch
1,966,000,000 YBN 1 2 3	310) Chromalveolate Alveolata (Ciliates, Dinoflagellates, Apicomplexans) evolve.1 2 3 Genetic comparison shows the ancestor of the Chromalveolate Alveolata (Ciliates, Dinoflagellates, Apicomplexans) evolving now. The alveolates are a major line of protists. There are three main groups, which are very divergent in form, but are now known to be close relatives based on various ultrastructural and genetic similarities: Ciliates Very common protozoa, with many short cilia arranged in rows Apicomplexa Parasitic protozoa that lack locomotive structures except in gametes Dinoflagellates Mostly marine flagellates, many of which have chloroplasts4 The most notable shared characteristic is the presence of cortical alveoli, flattened vesicles packed into a continuous layer supporting the membrane, typically forming a flexible pellicle. In dinoflagellates they often form armor plates. Alveolates have mitochondria with tubular cristae, and their flagella or cilia have a distinct structure.5 The Apicomplexa and dinoflagellates may be more closely related to each other than to the ciliates. Both have plastids, and most share a bundle or cone of microtubules at the top of the cell. In apicomplexans this forms part of a complex used to enter host cells, while in some colorless dinoflagellates it forms a peduncle used to ingest prey. 6 DOMAIN Eukaryota - eukaryotes KINGDOM Protozoa (Goldfuss, 1818) R. Owen, 1858 - protozoa SUBKINGDOM Biciliata INFRAKINGDOM Alveolata Cavalier-Smith, 1991 PHYLUM Myzozoa Cavalier-Smith & Chao, 2004 PHYLUM Ciliophora (Doflein, 1901) Copeland, 1956 - ciliates Relationships between some of these the major groups were suggested during the 1980s, and between all three by Cavalier-Smith, who introduced the formal name Alveolata in 1991. They were confirmed by a genetic study by Gajadhar et al. Some studies suggested the haplosporids, mostly parasites of marine invertebrates, might belong here but they lack alveoli and are now placed among the Cercozoa. The development of plastids among the alveolates is uncertain. Cavalier-Smith proposed the alveolates developed from a chloroplast-containing ancestor, which also gave rise to the Chromista (the chromalveolate hypothesis). However, as plastids only appear in relatively advanced groups, others argue the alveolates originally lacked them and possibly the dinoflagellates and Apicomplexa acquired them separately. FOOTNOTES 1. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004). 2. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). (1600mybn) 3. ^ Sandra L. Baldauf, A. J. Roger, I. Wenk-Siefert, W. F. Doolittle, "A Kingdom-Level Phylogeny of Eukaryotes Based on Combined Protein Data", Science, Vol 290, num 5493, p 972, (2000). has heterkonts before ciliophora and apicomplexa branch
1,964,000,000 YBN 12 13 14	312) Ciliates evolve.1 2 3 Genetic comparison shows the ancestor of the Chromalveolate Alveolata Ciliates evolving now. The ciliates are one of the most important groups of protists, common almost everywhere there is water - lakes, ponds, oceans, and soils, with many ecto- (lives on host) and endosymbiotic (lives in host) members, as well as some obligate (depends on host for survival) and opportunistic parasites (does not depend on host for survival). Ciliates tend to be large protists, a few reaching 2 mm in length, and are some of the most complex in structure. The name ciliate comes from the presence of hair-like organelles called cilia, which are identical in structure to flagella but typically shorter and present in much larger numbers. Cilia occur in all members of the group, although the peculiar suctoria only have them for part of the life-cycle, and are variously used in swimming, crawling, attachment, feeding, and sensation.4 Unlike other eukaryotes, ciliates have two different sorts of nuclei: a small, diploid micronucleus (reproduction), and a large, polyploid macronucleus (general cell regulation). The latter is generated from the micronucleus by amplification of the genome and heavy editing. The high degree of polyploidi allows the cell to sustain an appropriate level of transcription. Division of the macronucleus does not occur by a mitotic process but segregation of the chromosomes is by a different process, whose mechanism is unknown. This process is not perfect, and after about 200 generations the cell shows signs of aging (has so many mutations that it does not function properly). Periodically the macronuclei is (must be?) regenerated from the micronuclei. In most, this occurs during sexual reproduction, which is not usually through syngamy but through conjugation. Here two cells line up, the micronuclei undergo meiosis, some of the haploid daughters are exchanged and then fuse to form new micro- and macronuclei.5 With a few exceptions, there is a distinct cytostome or mouth where ingestion takes place. Food vacuoles are formed through phagocytosis and typically follow a particular path through the cell as their contents are digested and broken down via lysosomes so the substances the vacuole contains are then small enough to diffuse through the membrane of the food vacuole into the cell. Anything left in the food vacuole by the time it reaches the cytoproct (anus) is discharged via exocytosis. Most ciliates also have one or more prominent contractile vacuoles, which collect water and expel it from the cell to maintain osmotic pressure, or in some function to maintain ionic balance. These often have a distinctive star-shape, with each point being a collecting tube.6 Most ciliates feed on smaller organisms (heterotrophic), such as bacteria and algae, and detritus swept into the mouth by modified oral cilia. These usually include a series of membranelles to the left of the mouth and a paroral membrane to its right, both of which arise from polykinetids, groups of many cilia together with associated structures. This varies considerably, however. Some ciliates are mouthless and feed by absorption, while others are predatory and feed on other protozoa and in particular on other ciliates. This includes the suctoria, which feed through several specialized tentacles.7 Ciliates and Amoeboids have in common: Food is digested in food vacuoles. Excess water is expelled by contractile vacuoles. 8 DOMAIN Eukaryota - eukaryotes KINGDOM Protozoa (Goldfuss, 1818) R. Owen, 1858 - protozoa SUBKINGDOM Biciliata INFRAKINGDOM Alveolata Cavalier-Smith, 1991 PHYLUM Ciliophora (Doflein, 1901) Copeland, 1956 - ciliates CLASS Karyorelictea CLASS Heterotrichea CLASS Spirotrichea CLASS Litostomatea CLASS Phyllopharyngea CLASS Nassophorea CLASS Colpodea {possibly in phylum percolozoa} CLASS Prostomatea CLASS Oligohymenophorea CLASS Plagiopylea In some forms there are also body polykinetids, for instance, among the spirotrichs where they generally form bristles called cirri. More often body cilia are arranged in mono- and dikinetids, which respectively include one and two kinetosomes (basal bodies), each of which may support a cilium. These are arranged into rows called kineties, which run from the anterior to posterior of the cell. The body and oral kinetids make up the infraciliature, an organization unique to the ciliates and important in their classification, and include various fibrils and microtubules involved in coordinating the cilia.9 The infraciliature is one of the main component of the cell cortex. Another are the alveoli, small vesicles under the cell membrane that are packed against it to form a pellicle maintaining the cell's shape, which varies from flexible and contractile to rigid. Numerous mitochondria and extrusomes are also generally present. The presence of alveoli, the structure of the cilia, the form of mitosis and various other details indicate a close relationship between the ciliates, Apicomplexa, and dinoflagellates. These superficially dissimilar groups make up the alveolates.10 Ciliates move by coordinated strokes of hundreds of cilia projecting through holes in a semirigid pellicle. They discharge long, barbed trichocysts for defense and for capturing prey; toxicysts release a poison. Most are holozoic and ingest food through a gullet and eliminate wastes through an anal pore. During asexual reproduction, ciliates divide by transverse binary fission. Ciliates possess two types of nuclei-a large macronucleus and one or more small micronuclei. a. The macronucleus controls the normal metabolism of the cell. b. The micronucleus are involved in sexual reproduction. 1) The macronucleus disintegrates and the micronucleus undergoes meiosis. 2) Two ciliates then exchange a haploid micronucleus. 3) The micronuclei give rise to a new macronucleus containing only housekeeping genes. Ciliates are diverse. a. Members of the genus Paramecium are complex. (Fig. 30.13b) b. The barrel-shaped didinia expand to consume paramecia much larger than themselves. c. Suctoria rest on a stalk and paralyze victims, sucking them dry. d. Stentor resembles a giant blue vase with stripes. (Fig. 30.13a) 11 Could the 2 nuclei in ciliates be the result of an earlier fusion (or engulfing) of 2 prokaryotes? FOOTNOTES 1. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004). 2. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). 3. ^ Sandra L. Baldauf, A. J. Roger, I. Wenk-Siefert, W. F. Doolittle, "A Kingdom-Level Phylogeny of Eukaryotes Based on Combined Protein Data", Science, Vol 290, num 5493, p 972, (2000). has heterkonts before ciliophora and apicomplexa branch 4. ^ "Ciliates". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Ciliates 5. ^ "Ciliates". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Ciliates 6. ^ "Ciliates". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Ciliates 7. ^ "Ciliates". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Ciliates 8. ^ http://www.sirinet.net/~jgjohnso/apbio30.html 9. ^ "Ciliates". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Ciliates 10. ^ "Ciliates". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Ciliates 11. ^ http://www.sirinet.net/~jgjohnso/apbio30.html 12. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004). (1973mybn) 13. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). (1600mybn) 14. ^ Sandra L. Baldauf, A. J. Roger, I. Wenk-Siefert, W. F. Doolittle, "A Kingdom-Level Phylogeny of Eukaryotes Based on Combined Protein Data", Science, Vol 290, num 5493, p 972, (2000). has heterkonts before ciliophora and apicomplexa branch
1,963,000,000 YBN 50 51 52	313) Dinoflagellates evolve.1 2 3 Genetic Ribosomal RNA comparison shows Chromalveolate Alveolata, Dinoflagellates evolve. Dinoflagellates reproduce mainly by haploid mitosis, but also reproduce sexually. In dinoflagellates, the chromosomes are always visible and do not condense prior to mitosis. The chromosomes are attached to the nuclear envelope, which persists during mitosis. 4 The main method of reproduction of the dinoflagellates is by longitudinal cell division, with each daughter cell receiving one of the flagella ad a portion of the theca and then constructing the missing parts in a very intricate sequence. Some nonmotile species form zoospores, which may be colonial. A number of species reproduce sexually, mostly by isogamy, but a few species reproduce by heterogamy (anisogamy). 5 Dinoflagellate zygotes are similar to some acritarchs (early eukaryote fossils). 6 Some Dinoflagellates produce cysts. 7 The dinoflagellates are a large group of flagellate protists. Most are marine plankton, but they are common in fresh water habitats as well; their populations are distributed depending on temperate, saltiness, or depth. About half of all dinoflagellates are photosynthetic, and these make up the largest group of eukaryotic algae aside from the diatoms. Being primary producers make them an important part of the food chain. Some species, called zooxanthellae, are endosymbionts of marine animals and protozoa, and play an important part in the biology of coral reefs. Other dinoflagellates are colorless predators on other protozoa, and a few forms are parasitic. 8 Some dinoflagellates are reported to be filamentous (multicellular). 9 Mitochond ria christae are tubular. 10 Dinoflagellates are haploid (haplontic). 11 DOMA IN Eukaryota - eukaryotes KINGDOM Protozoa (Goldfuss, 1818) R. Owen, 1858 - protozoa SUBKINGDOM Biciliata INFRAKINGDOM Alveolata Cavalier-Smith, 1991 PHYLUM Dinoflagellata Bütschli, 1885 CLASS Dinophyceae (Bütschli, 1885) Pascher, 1914 CLASS Blastodiniophyceae Fensome et al., 1993 CLASS Noctiluciphyceae Fensome et al., 1993 CLASS Syndiniophyceae Loeblich III, 1976 12 Most dinoflagellates are unicellular forms with two dissimilar flagella. One of these extends towards the posterior, called the longitudinal flagellum, while the other forms a lateral circle, called the transverse flagellum. In many forms these are set into grooves, called the sulcus and cingulum. The transverse flagellum provides most of the force propelling the cell, and often imparts to it a distinctive whirling motion, which is what gives the name dinoflagellate refers to (Greek dinos, whirling). The longitudinal acts mainly as the steering wheel, but providing little propulsive force as well. 13 Dinoflagellates have a complex cell covering called an amphiesma, composed of flattened vesicles, called alveoli. In some forms, these support overlapping cellulose plates that make up a sort of armor called the theca. These come in various shapes and arrangements, depending on the species and sometimes stage of the dinoflagellate. Fibrous extrusomes are also found in many forms. Together with various other structural and genetic details, this organization indicates a close relationship between the dinoflagellates, Apicomplexa, and ciliates, collectively referred to as the alveolates. 14 The chloroplasts in most photosynthetic dinoflagellates are bound by three membranes, suggesting they were probably derived from some ingested alga, and contain chlorophylls a and c and fucoxanthin, as well as various other accessory pigments. However, a few have chloroplasts with different pigmentation and structure, some of which retain a nucleus. This suggests that chloroplasts were incorporated by several endosymbiotic events involving already colored or secondarily colorless forms. The discovery of plastids in Apicomplexa have led some to suggest they were inherited from an ancestor common to the two groups, but none of the more basal lines have them. 15 All the same, the dinoflagellate still consists of the more common organelles such as rough and smooth endoplasmic reticulum, Golgi apparatus, mitochondria, lipid and starch grains, and food vacuoles. Some have even been found with light sensitive organelle such as the eyespot or a larger nucleus containing a prominent nucleolus. 16 Life-cycle Dinoflagellates have a peculiar form of nucleus, called a dinokaryon, in which the chromosomes are attached to the nuclear membrane. These lack histones and remained condensed throughout interphase rather than just during mitosis, which is closed and involves a unique external spindle. This sort of nucleus was once considered to be an intermediate between the nucleoid region of prokaryotes and the true nuclei of eukaryotes, and so were termed mesokaryotic, but now are considered advanced rather than primitive traits.17 In most dinoflagellates, the nucleus is dinokaryotic throughout the entire life cycle. They are usually haploid, and reproduce primarily through fission, but sexual reproduction also occurs. This takes place by fusion of two individuals to form a zygote, which may remain mobile in typical dinoflagellate fashion or may form a resting cyst, which later undergoes meiosis to produce new haploid cells.18 However, when the conditions become desperate, usually starvation or no light, their normal routines change dramatically. Two dinoflagellates will fuse together forming a planozygote. Next is a stage not much different from hibernation called hypnozygote when the organism takes in excess fat and oil. At the same time its shape is getting fatter and the shell gets harder. Sometimes even spikes are formed. When the weathers allows it, these dinoflagellates break out of their shell and are in a temporary stage, planomeiocyte, when they quickly reforms their individual thecas and return to the dinoflagellates at the beginning of the process.19 Ecology and fossils Dinoflagellates sometimes bloom in concentrations of more than a million cells per millilitre. Some species produce neurotoxins, which in such quantities kill fish and accumulate in filter feeders such as shellfish, which in turn may pass them on to people who eat them. This phenomenon is called a red tide, from the color the bloom imparts to the water. Some colorless dinoflagellates may also form toxic blooms, such as Pfiesteria. It should be noted that not all dinoflagellate blooms are dangerous. Bluish flickers visible in ocean water at night often come from blooms of bioluminescent dinoflagellates, which emit short flashes of light when disturbed.20 Dinoflagellate cysts are found as microfossils from the Triassic period, and form a major part of the organic-walled marine microflora from the middle Jurassic, through the Cretaceous and Cenozoic to the present day. Arpylorus, from the Silurian of North Africa was at one time considered to be a dinoflagellate cyst, but this palynomorph is now considered to be part of the microfauna. It is possible that some of the Paleozoic acritarchs also represent dinoflagellates.21 Chloroplast features: 22 Chloroplasts: Brown 23 Mitochondria christae are tubular. 24 Nuclear features: 25 Gamete type: flagellated 26 Dinoflagellates are haploid (haplontic). 27 has condensed chromosomes. 28 Mitotic spindle: external. 29 po lar structures: none, and centrioles 30 Flagellar features: 31 Number of flagella: 2 32 Heterokont, isokont, or anisokont: anisokont 33 shaft features: paraxial rod, hairs 34 flagellate stages: gamete, trophic, zoospore 35 trophic: (trophozoites) The activated, feeding stage in the life cycle of protozoan parasites. 36 A protozoan, especially of the class Sporozoa, in the active stage of its life cycle. 37 The feeding stage of a protozoan (as distinct from reproductive or encysted stages). 38 zoospore: A zoospore is a motile asexual spore utilizing a flagellum for locomotion. Also called a swarm spore, these spores are used by some algae and fungi to propagate themselves.39 Golgi type: dictyosome 40 Food stores: 41 carbohydrate: alpha 1-4 glucan 42 fat=yes 43 extrusomes: tricocysts, nematocysts 44 eyespot type: cytoplasmic stigma, ? 45 Life Forms: 46 unicellular: flagellate, amoeboid, coccoid 47 multicellular: filementous 48 Cell covering: pellicle with plates. 49 FOOTNOTES 1. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). 2. ^ Sandra L. Baldauf, A. J. Roger, I. Wenk-Siefert, W. F. Doolittle, "A Kingdom-Level Phylogeny of Eukaryotes Based on Combined Protein Data", Science, Vol 290, num 5493, p 972, (2000). has heterkonts before ciliophora and apicomplexa branch 3. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). 4. ^ http://microscope.mbl.edu/scripts/protist.php?func=integrate&myID=P8047&chinese_ flag=&system=&version=&documentID=&excludeNonLinkedIn=&imagesOnly= 5. ^ http://microscope.mbl.edu/scripts/protist.php?func=integrate&myID=P8047&chinese_ flag=&system=&version=&documentID=&excludeNonLinkedIn=&imagesOnly= 6. ^ http://microscope.mbl.edu/scripts/protist.php?func=integrate&myID=P8047&chinese_ flag=&system=&version=&documentID=&excludeNonLinkedIn=&imagesOnly= 7. ^ Raven, Evert, Eichhorn, "Biology of Plants", (New York: Worth Publishers, 1992). p98-99 8. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=199167&tree=0.1 9. ^ "Dinoflagellate". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Dinoflagellate 10. ^ "Dinoflagellate". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Dinoflagellate 11. ^ "Dinoflagellate". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Dinoflagellate 12. ^ "Trophozoites". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Trophozoites 13. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=199167&tree=0.1 14. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=199167&tree=0.1 15. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=199167&tree=0.1 16. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=199167&tree=0.1 17. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=199167&tree=0.1 18. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=199167&tree=0.1 19. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=199167&tree=0.1 20. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=199167&tree=0.1 21. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=199167&tree=0.1 22. ^ "Dinoflagellate". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Dinoflagellate 23. ^ "Dinoflagellate". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Dinoflagellate 24. ^ "Dinoflagellate". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Dinoflagellate 25. ^ "Dinoflagellate". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Dinoflagellate 26. ^ "Dinoflagellate". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Dinoflagellate 27. ^ "Dinoflagellate". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Dinoflagellate 28. ^ "Dinoflagellate". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Dinoflagellate 29. ^ "Dinoflagellate". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Dinoflagellate 30. ^ "Dinoflagellate". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Dinoflagellate 31. ^ "Dinoflagellate". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Dinoflagellate 32. ^ "Dinoflagellate". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Dinoflagellate 33. ^ "Dinoflagellate". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Dinoflagellate 34. ^ "Dinoflagellate". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Dinoflagellate 35. ^ "Dinoflagellate". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Dinoflagellate 36. ^ http://www.yourdictionary.com/ahd/t/t0378700.html 37. ^ http://www.biology-online.org/dictionary/trophozoite 38. ^ "Zoospore". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Zoospore 39. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004). 40. ^ "Dinoflagellate". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Dinoflagellate 41. ^ "Dinoflagellate". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Dinoflagellate 42. ^ "Dinoflagellate". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Dinoflagellate 43. ^ "Dinoflagellate". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Dinoflagellate 44. ^ "Dinoflagellate". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Dinoflagellate 45. ^ "Dinoflagellate". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Dinoflagellate 46. ^ "Dinoflagellate". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Dinoflagellate 47. ^ "Dinoflagellate". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Dinoflagellate 48. ^ "Dinoflagellate". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Dinoflagellate 49. ^ "Dinoflagellate". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Dinoflagellate 50. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). (1973mybn) 51. ^ Sandra L. Baldauf, A. J. Roger, I. Wenk-Siefert, W. F. Doolittle, "A Kingdom-Level Phylogeny of Eukaryotes Based on Combined Protein Data", Science, Vol 290, num 5493, p 972, (2000). has heterkonts before ciliophora and apicomplexa branch (1600mybn) 52. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004).
1,962,000,000 YBN 8 9 10	314) Apicomplexans evolve.1 2 3 Genetic comparison shows Apicomplexans evolve. The Apicomplexa are a large group of protozoa, characterized by the presence of an apical complex at some point in their life-cycle. They are exclusively parasitic, and completely lack flagella or pseudopods except for certain gamete stages. Diseases caused by Apicomplexa include:4 * Babesiosis (Babesia) * Cryptosporidiosis (Cryptosporidium) * Malaria (Plasmodium) * Toxoplasmosis (Toxoplasma gondii)5 Most members have a complex life-cycle, involving both asexual and sexual reproduction. Typically, a host is infected by ingesting cysts, which divide to produce sporozoites that enter its cells. Eventually, the cells burst, releasing merozoites which infect new cells. This may occur several times, until gamonts are produced, forming gametes that fuse to create new cysts. There are many variations on this basic pattern, however, and many Apicomplexa have more than one host.6 DOMAIN Eukaryota - eukaryotes KINGDOM Protozoa (Goldfuss, 1818) R. Owen, 1858 - protozoa SUBKINGDOM Biciliata INFRAKINGDOM Alveolata Cavalier-Smith, 1991 PHYLUM Apicomplexa CLASS Conoidasida Levine, 1988 CLASS Aconoidasida Mehlhorn, Peters & Haberkorn, 1980 CLASS Metchnikovellea Weiser, 1977 CLASS Blastocystea Cavalier-Smith, 1998 7 FOOTNOTES 1. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004). 2. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). 3. ^ Sandra L. Baldauf, A. J. Roger, I. Wenk-Siefert, W. F. Doolittle, "A Kingdom-Level Phylogeny of Eukaryotes Based on Combined Protein Data", Science, Vol 290, num 5493, p 972, (2000). has heterkonts before ciliophora and apicomplexa branch 4. ^ "Apicomplexa". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Apicomplexa 5. ^ "Apicomplexa". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Apicomplexa 6. ^ "Apicomplexa". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Apicomplexa 7. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=199436&tree=0.1 8. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004). (1973mybn) 9. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). (1600mybn) 10. ^ Sandra L. Baldauf, A. J. Roger, I. Wenk-Siefert, W. F. Doolittle, "A Kingdom-Level Phylogeny of Eukaryotes Based on Combined Protein Data", Science, Vol 290, num 5493, p 972, (2000). has heterkonts before ciliophora and apicomplexa branch MORE INFO [1] http://www.sirinet.net/~jgjohnso/apbio30.html
1,961,000,000 YBN 8 9	89) Genetic comparison shows Rhizaria (the Phyla "Radiolaria", "Cercozoa", and "Foraminifera") evolve now.1 2 This marks the beginning of the protists described as "amoeboid", because they have pseudopods. 5. Amoeboids phagocytize their food; pseudopods surround and engulf prey. 6. Food is digested inside food vacuoles. 7. Freshwater amoeboids have contractile vacuoles to eliminate excess water. 3 Some foraminifera are haplodiploid (alternate between haploid and diploid cycles that both have mitosis). The Rhizaria are a major line of protists. They vary considerably in form, but for the most part they are amoeboids with filose, reticulose, or microtubule-supported pseudopods. Many produce shells or skeletons, which may be quite complex in structure, and these make up the vast majority of protozoan fossils. Nearly all have mitochondria with tubular cristae. 4 There are three main groups of Rhizaria: Cercozoa Various amoebae and flagellates, usually with filose pseudopods and common in soil Foraminifera Amoeboids with reticulose pseudopods, common as marine benthos Radiolaria Amoeboids with axopods, common as marine plankton 5 The name Rhizaria was created recently by Cavalier-Smith in 2002. Most are biciliate amoeboflagellates at some point in the life cycle. Pseudopodia are root-like reticulopodia, filopodia and/or axopodia - not broad lobopodia as in Amoeba. All of these features can, however, be found in members of other clades. Nevertheless, the Rhizaria are supported by both rRNA and actin trees (Cavalier-Smith & Chao, 2003; Nikolaev et al. 2004). 6 A few other groups may be included in the Cercozoa, but on some trees appear closer to the Foraminifera. These are the Phytomyxea and Ascetosporea, parasites of plants and animals respectively, and the peculiar amoeba Gromia. The different groups of Rhizaria are considered close relatives based mainly on genetic similarities, and have been regarded as an extension of the Cercozoa. The name Rhizaria for the expanded group was introduced by Cavalier-Smith in 2002, who also included the centrohelids and Apusozoa. 7 FOOTNOTES 1. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). 2. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004). 3. ^ http://www.sirinet.net/~jgjohnso/apbio30.html 4. ^ "Rhizaria". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Rhizaria 5. ^ "Rhizaria". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Rhizaria 6. ^ http://www.palaeos.com/Eukarya/Units/Rhizaria/Rhizaria.html 7. ^ "Rhizaria". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Rhizaria 8. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). has 1600my for excavates, discricristales, rhizaria, chromalveolates, (1600my) 9. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004). I use this estimate
1,961,000,000 YBN 29 30	320) Rhizaria Phylum "Cercozoa" evolve now.1 2 The Cercozoa are a group of protists, including most amoeboids and flagellates that feed by means of filose pseudopods. These may be restricted to part of the cell surface, but there is never a true cytostome or mouth as found in many other protozoa. They show a variety of forms and have proven difficult to define in terms of structural characteristics, although their unity is strongly supported by genetic studies.3 The best-known Cercozoa are the euglyphids, filose amoebae with shells of siliceous scales or plates, which are commonly found in soils, nutrient-rich waters, and on aquatic plants. Some other filose amoebae produce organic shells, including the tectofilosids and Gromia. They were formerly classified with the euglyphids as the Testaceafilosia. This group is not monophyletic, but nearly all studied members fall in or near the Cercozoa, related to similarly shelled flagellates.4 Another important group placed here are the chlorarachniophytes, strange amoebae that form a reticulating net. They are set apart by the presence of chloroplasts, which apparently developed from an ingested green alga. They are bound by four membranes and still possess a vestigial nucleus, called a nucleomorph. As such, they have been of great interest to researchers studying the endosymbiotic origins of organelles.5 Other notable cercozoans include the cercomonads, which are common soil flagellates. Two groups traditionally considered heliozoa, the dimorphids and desmothoracids, belong here. Recently the marine Phaeodarea have also been included. The Cercozoa are closely related to the Foraminifera and Radiolaria, amoeboids that usually have complex shells, and together with them form a supergroup called the Rhizaria. Their exact composition and relationships are still being worked out. 6 PHYLUM Cercozoa (Cavalier-Smith 1998) 7 CLASS Spongomonadea CLASS Proteomyxidea - desmothoracids, dimorphids, gymnophryids, etc. CLASS Sarcomonadea - cercomonads CLASS Imbricatea - euglyphids and thaumatomonads CLASS Thecofilosea - tectofilosids and cryomonads CLASS Phaeodarea CLASS Chlorarachnea (Hibberd & Norris, 1984) Class Spongomonadea Chlorarachniophytes are a small group of algae occasionally found in tropical oceans. They are typically mixotrophic, ingesting bacteria and smaller protists as well as conducting photosynthesis. Normally they have the form of small amoebae, with branching cytoplasmic extensions that capture prey and connect the cells together, forming a net. They may also form flagellate zoospores, which characteristically have a single subapical flagellum that spirals backwards around the cell body, and walled coccoid cells.8 The chloroplasts were presumably acquired by ingesting some green alga. They are surrounded by four membranes, the outermost of which is continuous with the endoplasmic reticulum, and contain a small nucleomorph between the middle two, which is a remnant of the alga's nucleus. This contains a small amount of DNA and divides without forming a mitotic spindle. The origin of the chloroplasts from green algae is supported by their pigmentation, which includes chlorophylls a and b, and by genetic similarities. The only other group of algae that contain nucleomorphs are the cryptomonads, but their chloroplasts seem to be derived from a red alga.9 The chlorarachniophytes only include five genera, which show some variation in their life-cycles and may lack one or two of the stages described above. Genetic studies place them among the Cercozoa, a diverse group of amoeboid and amoeboid-like protozoa.10 Class Proteomyxidea Order Desmothoracida (Hertwig & Lesser 1874) The desmothoracids are a group of heliozoan protists, usually sessile and found in freshwater environments. Each adult is a spherical cell around 10-20 μm in diameter surrounded by a perforated organic lorica or shell, with many radial pseudopods projecting through the holes to capture food. These are supported by small bundles of microtubules that arise near a point on the nuclear membrane. Unlike other heliozoans, the microtubules are not in any regular geometric array, there does not appear to be a microtubule organizing center, and there is no distinction between the outer and inner cytoplasm. 11 Reproduction takes place by the budding off of small motile cells, usually with two flagella. Later these are lost, and pseudopods and a lorica are formed. Typically a single lengthened pseudopod will secrete a hollow stalk that attached the adult to the substrate. The form of the flagella, the tubular cristae within the mitochondria, and other characters led to the suggestion that the desmothoracids belong among what is now the Cercozoa, which has now been confirmed by genetic studies. 12 Order Heliomonadida Genus Dimorpha The dimorphids or heliomonads are a small group of heliozoa that are unusual in possessing flagella throughout their life-cycle. There are two genera: Dimorpha, a tiny organism found in freshwater, and the larger Tetradimorpha, which is distinguished by having four rather than two flagella. Bundles of microtubules, typically in square array, arise from a body near the flagellar bases and support the numerous axopods that project from the cell surface. 13 Dimorphids have a single nucleus, and mitochondria with tubular cristae. Genetic studies place them among the Cercozoa, a group including various other flagellates that form pseudopods. 14 Order Reticulosida Family Gymnophryidae (Mikrjukov & Mylnikov, 1996) The gymnophryids are a small group of amoeboids that lack shells and produce thin, reticulose pseudopods. These contain microtubules and have a granular appearance, owing to the presence of extrusomes, but are distinct from the pseudopods of Foraminifera. They are included among the Cercozoa, but differ from other cercozoans in having mitochondria with flat cristae, rather than tubular cristae. 15 Gymnophrys cometa, found in freshwater and soil, is representative of the group. The cell body is under 10 μm in size, and has a pair of reduced flagella, which are smooth and insert parallel to one another. It may also produce motile zoospores and cysts. Gymnophrys and Borkovia are the only confirmed genera, but other naked reticulose amoebae such as Biomyxa may be close relatives. 16 Class Sarcomonadea Order Cercomonadida (Poche, 1913) Cercomonads are small flagellates, widespread in aqueous habitats and especially common in soils. The cells are generally around 10 μm in length, without any shell or covering. They produce filose pseudopods to capture bacteria, but do not use them for locomotion, which usually takes place by gliding along surfaces. Most members have two smooth flagella, one directed forward and one trailing under the cell, inserted at right angles near its anterior. The nucleus is connected to the flagellar bases and accompanied by a characteristic paranuclear body. 17 Genetic studies place the cercomonads among the core Cercozoa, a diverse group of amoeboid and flagellate protozoans. They are divided into two families. The Heteromitidae tend to be relatively rigid, and produce only temporary pseudopods. The Cercomonadidae are more plastic, and when food supplies are plentiful may become amoeboid and even multinucleate. The classification of genera and species continues to undergo revision. Some genera have been merged, like Cercomonas and Cercobodo, and some have been moved to other groups. 18 Class Imbricatea Order Euglyphida (Copeland, 1956) The euglyphids are a prominent group of filose amoebae that produce shells or tests from siliceous scales, plates, and sometimes spines. These elements are created within the cell and then assembled on its surface in a more or less regular arrangement, giving the test a textured appearance. There is a single opening for the long slender pseudopods, which capture food and pull the cell across the substrate. 19 Euglyphids are common in soils, marshes, and other organic-rich environments, feeding on tiny organisms such as bacteria. The test is generally 30-100 μm in length, although the cell only occupies part of this space. During reproduction a second shell is formed opposite the opening, so both daughter cells remain protected. Different genera and species are distinguished primarily by the form of the test. Euglypha and Trinema are the most common. 20 The euglyphids are traditionally grouped with other amoebae. However, genetic studies instead place them with various amoeboid and flagellate groups, forming an assemblage called the Cercozoa. Their closest relatives are the thaumatomonads, flagellates that form similar siliceous tests. 21 Class Thecofilosea Order Tectofilosida (Cavalier-Smith & Chao, 2003) The tectofilosids or amphitremids are a group of filose amoebae with shells. These are composed of organic materials and sometimes collected debris, in contrast to the euglyphids, which produce shells from siliceous scales. The shell usually has a single opening, but in Amphitrema and a few other genera it has two on opposite ends. The cell itself occupies most of the shell. They are most often found on marsh plants such as Sphagnum. 22 This group was previously classified as the Gromiida or Gromiina. However, molecular studies separate Gromia from the others, which must therefore be renamed. They are placed among the Cercozoa, and presumably developed from flagellates like Cryothecomonas, which has a similar test. However, only a few have been studied in detail, so their relationships and monophyly are not yet certain. 23 Class: Phaeodarea (Haeckel, 1879) The Phaeodarea are a group of amoeboid protists. They are traditionally considered radiolarians, but in molecular trees do not appear to be close relatives of the other groups, and are instead placed among the Cercozoa. They are distinguished by the structure of their central capsule and by the presence of a phaeodium, an aggregate of waste particles within the cell. 24 Phaeodarea produce hollow skeletons composed of amorphous silica and organic material, which rarely fossilize. The endoplasm is divided by a cape with three openings, of which one gives rise to feeding pseudopods, and the others let through bundles of microtubules that support the axopods. Unlike other radiolarians, there are no cross-bridges between them. They also lack symbiotic algae, generally living below the photic zone, and do not produce any strontium sulphate. 25 CLASS Chlorarachnea Chlorarachniophytes are a small group of algae occasionally found in tropical oceans. They are typically mixotrophic, ingesting bacteria and smaller protists as well as conducting photosynthesis. Normally they have the form of small amoebae, with branching cytoplasmic extensions that capture prey and connect the cells together, forming a net. They may also form flagellate zoospores, which characteristically have a single subapical flagellum that spirals backwards around the cell body, and walled coccoid cells. 26 The chloroplasts were presumably acquired by ingesting some green alga. They are surrounded by four membranes, the outermost of which is continuous with the endoplasmic reticulum, and contain a small nucleomorph between the middle two, which is a remnant of the alga's nucleus. This contains a small amount of DNA and divides without forming a mitotic spindle. The origin of the chloroplasts from green algae is supported by their pigmentation, which includes chlorophylls a and b, and by genetic similarities. The only other group of algae that contain nucleomorphs are the cryptomonads, but their chloroplasts seem to be derived from a red alga. 27 The chlorarachniophytes only include five genera, which show some variation in their life-cycles and may lack one or two of the stages described above. Genetic studies place them among the Cercozoa, a diverse group of amoeboid and amoeboid-like protozoa. 28 FOOTNOTES 1. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). has 1600mybn for excavates, discricristales, rhizaria, chromalveolates 2. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004). 3. ^ "Cercozoa". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Cercozoa 4. ^ "Cercozoa". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Cercozoa 5. ^ "Cercozoa". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Cercozoa 6. ^ "Cercozoa". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Cercozoa 7. ^ "Cercozoa". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Cercozoa 8. ^ "Chlorarachniophyte". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Chlorarachniophyte 9. ^ "Chlorarachniophyte". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Chlorarachniophyte 10. ^ "Chlorarachniophyte". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Chlorarachniophyte 11. ^ "Desmothoracid". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Desmothoracid 12. ^ "Desmothoracid". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Desmothoracid 13. ^ "Dimorphid". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Dimorphid 14. ^ "Dimorphid". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Dimorphid 15. ^ "Gymnophryid". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Gymnophryid 16. ^ "Gymnophryid". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Gymnophryid 17. ^ "Cercomonad". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Cercomonad 18. ^ "Cercomonad". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Cercomonad 19. ^ "Euglyphid". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Euglyphid 20. ^ "Euglyphid". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Euglyphid 21. ^ "Euglyphid". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Euglyphid 22. ^ "Tectofilosid". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Tectofilosid 23. ^ "Tectofilosid". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Tectofilosid 24. ^ "Phaeodarea". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Phaeodarea 25. ^ "Phaeodarea". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Phaeodarea 26. ^ "Chlorarachniophyte". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Chlorarachniophyte 27. ^ "Chlorarachniophyte". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Chlorarachniophyte 28. ^ "Chlorarachniophyte". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Chlorarachniophyte 29. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). has 1600mybn for excavates, discricristales, rhizaria, chromalveolates (1600mybn) 30. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004).
1,960,000,000 YBN 30 31	319) Rhizaria Phylum "Radiolaria" evolve now.1 2 Ribosomal RNA indicates that Rhizaria Phylum "Radiolaria" evolve now. Radiolarians (also radiolaria) are amoeboid protozoa that produce intricate mineral skeletons, typically with a central capsule dividing the cell into inner and outer portions, called endoplasm and ectoplasm. They are found as plankton throughout the ocean, and their shells are important fossils found from the Cambrian onwards.3 Move by pseudopodia. 4 external tests made of silica (glass). 5 Radiolaria have a test composed of silica or strontium sulfate. Most have a radial arrangement of spines. Pseudopods (actinopods) project from an external layer of cytoplasm and are supported by rows of microtubules. Tests of dead foraminiferans and radiolarians form deep layers of ocean floor sediment. Back to the Precambrian, each layer has distinctive foraminiferans which helps date rocks. Over hundreds of millions of years, the CaCO3 shells have contributed to the formation of chalk deposits (i.e. White Cliffs of Dover, limestone of pyramids). 6 Lifecycle Simple asexual fission of radiolarian cells has been observed. Sexual reproduction has not been confirmed but is assumed to occur; possible gametogenesis has been observed in the form of "swarmers" being expelled from swellings in the cell. Swarmers are formed from the central capsule after the ectoplasm has been discarded. The central capsule sinks through the water column to depths hundreds of meters greater than the normal habitat and swells, eventually rupturing and releasing the flagellated cells. Recombination of these cells, which are assumed to be haploid, to produce diploid "adults" has not been observed however and is only inferred to occur. Comparisons of standing crops within the water column and sediment trap samples have ascertained that the average life span of radiolarians is about two weeks, ranging from a few days to a few weeks. 7 All radiolarians secrete strontium sulphate at some point in the life cycle - as the adult shell in Acantharea, and as crystals in ‘swarmer cells" produced during asexual reproduction in Polycystinea. 8 Large, planktonic forms that produce a glassy, intricate shell. 9 Radiolarians have many needle-like pseudopods supported by microtubules, called axopods, which aid in flotation. The nuclei and most other organelles are in the endoplasm, while the ectoplasm is filled with frothy vacuoles and lipid droplets, keeping them buoyant. Often it also contains symbiotic algae, especially zooxanthellae, that provide most of the cell's energy. Some of this organization is found among the heliozoa, but those lack central capsules and only produce simple scales and spines. 10 The main class of radiolarians are the Polycystinea, which produce siliceous skeletons. These include the majority of fossils. They also include the Acantharea, which produce skeletons of strontium sulfate. Despite some initial suggestions to the contrary, genetic studies place these two groups close together. They also include the peculiar genus Sticholonche, which lacks an internal skeleton and so is usually considered a heliozoan. 11 Traditionally the radiolarians also include the Phaeodarea, which produce siliceous skeletons but differ from the polycystines in several other respects. However, on molecular trees they branch with the Cercozoa, a group including various flagellate and amoeboid protists. The other radiolarians appear near, but outside, the Cercozoa, so the similarity is due to convergent evolution. The radiolarians and Cercozoa are included within a supergroup called the Rhizaria. 12 German biologist Ernst Haeckel produced exquisite (and perhaps somewhat exaggerated) drawings of radiolaria, helping to popularize these protists among Victorian parlor microscopists alongside foraminifera and diatoms. 13 PHYLUM Radiolaria (Müller 1858 emend.) 14 CLASS Polycystinea 15 16 CLASS Acantharea (Haeckel, 1881) 17 CLASS Sticholonchea 18 (CLASS Phaeodarea Haeckel, 1879 19 )? CLASS Polycystinea: The polycystines are a group of radiolarian protists. They include the vast majority of the fossil radiolaria, as their skeletons are abundant in marine sediments, making them one of the most common groups of microfossils. These skeletons are composed of opaline silica. In some it takes the form of relatively simple spicules, but in others it forms more elaborate lattices, such as concentric spheres with radial spines or sequences of conical chambers. 20 Class Acantharea The Acantharea are a small group of radiolarian protozoa, distinguished mainly by their skeletons. These are composed of strontium sulfate crystals, which do not fossilize, and take the form of either ten diametric or twenty radial spines. The central capsule is made up of microfibrils arranged into twenty plates, each with a hole through which one spine projects, and there is also a microfibrillar cortex linked to the spines by myonemes. These assist in flotation, together with the vacuoles in the ectoplasm, which often contain zooxanthellae. 21 The axopods are fixed in number. Reproduction takes place by formation of spores, which may be flagellate. These develop into mononucleate amoebae; adults are usually multinucleate. 22 Class Sticholonchea Sticholonche is a peculiar genus of protozoan with a single species, S. zanclea, found in open oceans at depths of 100-500 metres. It is generally considered a heliozoan, placed in its own order, called the Taxopodida. However it has also been classified as an unusual radiolarian, and this has gained support from genetic studies, which place it near the Acantharea.23 Sticholonche are usually around 200 μm, though this varies considerably, and have a bilaterally symmetric shape, somewhat flattened and widened at the front. The axopods are arranged into distinct rows, six of which lie in a dorsal groove and are rigid, and the rest of which are mobile. These are used primarily for buoyancy, rather than feeding. They also have fourteen groups of prominent spines, and many smaller spicules, although there is no central capsule as in true radiolarians.24 Cercozoa, originally named by Cavalier-Smith in 1998, is a diverse group of taxa united solely on molecular grounds, but supported by a number of genes (Longet et al., 2003). 25 Amongst notable members of the Cercozoa are amoeboid forms such as Difflugia, which produce agglutinated tests that may be fossilised (the record extends back to the Neoproterozoic - Finlay et al., 2004), and the Chlorarachnea (e.g. Chlorarachnion), marine amoeboid organisms which possess chloroplasts derived from a secondary endosymbiosis with a green alga. Cavalier-Smith, (2003). The nucleus of the endosymbiont in Chlorarachnion, in fact, has not fully degraded as in most secondarily plastid-bearing eukaryotes, and the chloroplast retains a small nucleomorph contained within the surrounding membranes. 26 The Polycystinea (sometimes spelled Polycistinea or Polycystina) are one group of the Radiolaria. These are not just "small shelly fauna," they are tiny shelly fauna made up of single, if rather complex, cells. The shell turns out to be made of amorphous silica -- essentially sand -- without the admixture of organics that characterize similar forms. Polycystinea are exclusively marine but found in great numbers in the oceans. Their fossil record goes back almost a billion years, well into Precambrian time.27 Like other radiolarians, the cytoplasm of Polycystinea is divided into ectoplasm and endoplasm by a perforated protein capsule -- not the nuclear membrane, but a novel structure unique to this group. The endoplasm forms a central medulla enclosed by this porous, membranous capsule. The nucleus is inside this central region. The ectoplasm is outside the capsule and forms the region known as the cortex (or calymma). The visible remains shown in the image are made up of perforated tests (the "shells"). In life, these are located in the ectoplasm. Polycystinates extend pseudopods supported by a complex microtubular array (axopods) which originate in the endoplasm. The pseudopods pass through pores in the test and extend, covered with a thin layer of cytoplasm, from the surface of the cell. Spines of the test, if any, also pass through the capsule and extend, covered with cytoplasm, from the surface of the cell. The ectoplasm is often vacuolated and frequently contains photosynthetic zooxanthellae.28 The endoplasm actually contains all of the organelles normally associated with a "normal" heterotrophic eukaryotic cell, including mitochondria, a nucleus, and a cytoskeleton. The ectoplasm is largely filled with digestive vacuoles, symbiotic algae, and the test. From an evolutionary standpoint, the Polycystina appear to be one step towards a whole different type of biological organization based on a 3-compartment cell, rather than the 2-compartment cell of metazoans. In fact, a number of polycystinean species are colonial. It is interesting to speculate on what might have evolved on this model, had circumstances been different.29 FOOTNOTES 1. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). 1600mybn for excavates, discricristales, rhizaria, chromalveolates 2. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004). 3. ^ "Radiolaria". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Radiolaria 4. ^ http://www.bio.georgiasouthern.edu/Bio-home/Pratt/boo305.htm 5. ^ http://www.bio.georgiasouthern.edu/Bio-home/Pratt/boo305.htm 6. ^ http://www.sirinet.net/~jgjohnso/apbio30.html 7. ^ http://www.ucl.ac.uk/GeolSci/micropal/radiolaria.html 8. ^ http://www.palaeos.com/Eukarya/Units/Rhizaria/Rhizaria.html 9. ^ http://www.palaeos.com/Eukarya/Units/Rhizaria/Rhizaria.html 10. ^ "Radiolaria". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Radiolaria 11. ^ "Radiolaria". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Radiolaria 12. ^ "Radiolaria". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Radiolaria 13. ^ "Radiolaria". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Radiolaria 14. ^ "Radiolaria". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Radiolaria 15. ^ "Radiolaria". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Radiolaria 16. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=198790&tree=0.1 17. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=198790&tree=0.1 18. ^ "Radiolaria". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Radiolaria 19. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=198790&tree=0.1 20. ^ "Polycystine". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Polycystine 21. ^ "Acantharea". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Acantharea 22. ^ "Acantharea". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Acantharea 23. ^ "Sticholonche". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Sticholonche 24. ^ "Sticholonche". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Sticholonche 25. ^ http://www.palaeos.com/Eukarya/Units/Rhizaria/Rhizaria.html 26. ^ http://www.palaeos.com/Eukarya/Units/Rhizaria/Rhizaria.html 27. ^ http://www.palaeos.com/Eukarya/Units/Rhizaria/Rhizaria.html 28. ^ http://www.palaeos.com/Eukarya/Units/Rhizaria/Rhizaria.html 29. ^ http://www.palaeos.com/Eukarya/Units/Rhizaria/Rhizaria.html 30. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). 1600mybn for excavates, discricristales, rhizaria, chromalveolates (1600my) 31. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004).
1,960,000,000 YBN 40 41	321) Rhizaria Phylum "Foraminifera" evolve now.1 2 Ribosomal RNA shows Rhizaria Phylum "Foraminifera" (also known as "Granuloreticulosea") evolve now. Forminifera are catagorized as amoeboid because they have pseudopods. 3 The Foraminifera, or forams for short, are a large group of amoeboid protists with reticulating pseudopods, fine strands that branch and merge to form a dynamic net. They typically produce a shell, or test, which can have either one or multiple chambers, some becoming quite elaborate in structure. About 250 000 species are recognized, both living and fossil. They are usually less than 1 mm in size, but some are much larger, and the largest recorded specimen reached 19 cm. As fossils, foraminifera are extremely useful. 4 Foraminifera are haplodiploid. 5 Most have a kind of shell called a "test", which is composed of calcium carbonate. 6 move by pseudopodia 7 most are marine 8 tests are major components of limestone 9 used to date marine sediments. 10 Foraminifera, especially the calcareous forms, have a fossil record stretching back to the Cambrian (Lee, 1990), and are especially important biostratigraphically. 11 b. Foraminiferans have a multi-chambered CaCO3 (calcium carbonate) shell; thin pseudopods extend through holes. 12 Of the approximately 4000 living species of foraminifera the life cycles of only 20 or so are known. There are a great variety of reproductive, growth and feeding strategies, however the alternation of sexual and asexual generations is common throughout the group and this feature differentiates the foraminifera from other members of the Granuloreticulosea. An asexually produced haploid generation commonly form a large proloculus (initial chamber) and are therefore termed megalospheric. Sexually produced diploid generations tend to produce a smaller proloculus and are therefore termed microspheric. Importantly in terms of the fossil record, many foraminiferal tests are either partially dissolved or partially disintegrate during the reproductive process.The planktonic foraminifera Hastigerina pelagica reproduces by gametogenesis at depth, the spines, septa and apertural region are resorbed leaving a tell-tale test. Globigerinoides sacculiferproduces a sac-like final chamber and additional calcification of later chambers before dissolution of spines occurs, this again produces a distinctive test, which once gametogenesis is complete sinks to the sea bed. 13 Since the meiosis products have to differentiate or mature into gametes, meiosis does not result directly in gametes, these species are haplodipoid (haplodiplontic). Modern forams are primarily marine, although they can survive in brackish conditions. A few species survive in fresh water (e.g. Lake Geneva) and one species even lives in damp rainforrest soil. They are very common in the meiobenthos, and about 40 species are planktonic. The cell is divided into granular endoplasm and transparent ectoplasm. The pseudopodial net may emerge through a single opening or many perforations in the test, and characteristically has small granules streaming in both directions. 14 The pseudopods are used for locomotion, anchoring, and in capturing food, which consists of small organisms such as diatoms or bacteria. A number of forms have unicellular algae as endosymbionts, from diverse lineages such as the green algae, red algae, golden algae, diatoms, and dinoflagellates. Some forams are kleptoplastic, retaining chloroplasts from ingested algae to conduct photosynthesis. 15 The foraminiferan life-cycle involves an alternation between haploid and diploid generations, although they are mostly similar in form. The haploid or gamont initially has a single nucleus, and divides to produce numerous gametes, which typically have two flagella. The diploid or schizont is multinucleate, and after meiosis fragments to produce new gamonts. Multiple rounds of asexual reproduction between sexual generations is not uncommon. 16 The form and composition of the test is the primary means by which forams are identified and classified. Most have calcareous tests, composed of calcium carbonate, which generally takes the form of interlocking microscopic crystals, giving it a glassy or hyaline appearance. In other forams the test may be composed of organic material, made from small pieces of sediment cemented together (agglutinated), and in one genus of silica. Openings in the test, including those that allow cytoplasm to flow between chambers, are called apertures. 17 Tests are known as fossils as far back as the Cambrian period, and many marine sediments are composed primarily of them. For instance, the nummulitic limestone that makes up the pyramids of Egypt is composed almost entirely of them. Forams may also make a significant contribution to the overall deposition of calcium carbonate in coral reefs. 18 Because of their diversity, abundance, and complex morphology, fossil foraminiferal assembleages can give accurate relative dates for rocks and thus are extremely useful in biostratigraphy. Before more modern techniques became available, the oil industry relied heavily on microfossils such as foraminifera to find potential oil deposits. 19 For the same reasons they make good biostratigraphic markers, living foraminiferal assembleages have been used as bioindicators in coastal environments, including as indicators of coral reef health. 20 Fossil foraminifera are also useful in paleoclimatology and paleoceanography. They can be used to reconstruct past climate by examining their oxygen stable isotope ratios. Geographic patterns seen in the fossil record of planktonic forams are also used to reconstruct paleo ocean current patterns. 21 Genetic studies have identified the naked amoeba Reticulomyxa and the peculiar xenophyophores as foraminiferans without tests. A few other ameoboids produce reticulose pseudopods, and were formerly classified with the forams as the Granuloreticulosa, but this is no longer considered a natural group, and most are now placed among the Cercozoa. Both the Cercozoa and Radiolaria are close relatives of the Foraminifera, together making up the Rhizaria, but the exact position of the forams is still unclear. 22 PHYLUM Foraminifera CLASS Athalamea (Haeckel, 1862) 23 CLASS Xenophyophorea (F.E. Schulze, 1904) 24 CLASS Foraminifera (Lee, 1990) 25 CLASS Foraminifera ORDER Allogromiida The Allogromiida are a small group of foraminiferans, including those that produce organic tests (Lagynacea). Genetic studies have shown that some foraminiferans with agglutinated tests, previously included in the Textulariida or as their own order Astrorhizida, also belong here. Allogromiids produce relatively simple tests, usually with a single chamber, similar to those of other protists such as Gromia. They are found in stressed environments, including both marine and freshwater forms, and are the oldest forams known from the fossil record. 26 ORDER Fusulinida The fusulinids are an extinct group of foraminiferan protozoa. They produce calcareous shells, which are of fine calcite granules packed closely together; this distinguishes them from other calcareous forams, where the test is usually hyaline. Fusulinids are important indicator fossils. 27 ORDER Globigerinida The Globigerinida are a common group of foraminiferans that are found as marine plankton (other groups are primarily benthic). They produce hyaline calcareous tests, and are known as fossils from the Jurassic period onwards. The group has included more than 100 genera and over 400 species, of which about 30 species are extant. One of the most important genera is Globigerina; vast areas of the ocean floor are covered with Globigerina ooze (named by Murray and Renard in 1873), dominated by the shells of planktonic forams. 28 ORDER Miliolida The miliolids are a group of foraminiferans, abundant in shallow waters such as estuaries and coastlines, though they also include oceanic forms. They are distinguished by producing porcelaneous tests, composed of calcite needles and organic material; the needles have a high proportion of magnesium and are oriented randomly. The test lacks pores and generally has multiple chambers, which are often arranged in a distinctive fashion called milioline. 29 ORDER Rotaliida The Rotaliida are a large and abundant group of foraminiferans. They are primarily oceanic benthos, although some are common in shallower waters such as estuaries. They also include many important fossils, such as nummulites. Rotaliids produce hyaline tests, in which the microscopic crystals may be oriented either radially (as in other forams) or obliquely. 30 ORDER Textulariida The Textulariida are a group of common foraminiferans that produce agglutinated shells, composed of foreign particles in an organic or calcareous cement. Previously they were taken to include all such species, but genetic studies have shown that they are not all closely related, and several superfamilies have been moved to the order Allogromiida. The remaining forms are sometimes divided into three orders: the Trochamminida and Lituolida (organic cement) and the Textulariida sensu stricto (calcareous cement). All three are known as fossils from the Cambrian onwards. 31 CLASS Xenophyophorea Xenophyophores are marine protozoans, giant single-celled organisms found throughout the world's oceans, but in their greatest numbers on the abyssal plains of the deep ocean. They were first described as sponges in 1889, then as testate amoeboids, and later as their own phylum of Protista. A recent genetic study suggested that the xenophyophores are a specialized group of Foraminifera. There are approximately 42 recognized species in 13 genera and 2 orders; one of which, Syringammina fragillissima, is among the largest known protozoans at a maximum 20 centimetres in diameter. 32 Abundant but poorly understood, xenophyophores are delicate organisms with a variable appearance; some may resemble flattened discs, angular four-sided shapes (tetrahedra), or like frilly or spherical sponges. Local environmental conditions-such as current direction and speed-may play a part in influencing these forms. Xenophyophores are essentially lumps of viscous fluid called cytoplasm containing numerous nuclei distributed evenly throughout. Everything is contained in a ramose system of tubes called a granellare, itself composed of an organic cement-like substance. 33 As benthic deposit feeders, xenophyophores tirelessly root through the muddy sediments on the sea floor. They excrete a slimy substance whilst feeding; in locations with a dense population of xenophyophores, such as at the bottoms of oceanic trenches, this slime may cover large areas. Local population densities may be as high as 2,000 individuals per 100 square metres, making them dominant organisms in some areas. These giant protozoans seem to feed in a manner similar to amoebas, enveloping food items with a foot-like structure called a pseudopodium. Most are epifaunal (living atop the seabed), but one species (Occultammina profunda), is known to be infaunal; it buries itself up to 6 cm deep into the sediment. 34 Their glue-like secretions cause silt and strings of their own fecal matter, called stercomes, to build up into masses (called stercomares) on their exteriors. In this way, the organisms form structures which project from the sea floor; this characteristic also explains their name, which may be translated from the Greek to mean "bearer of foreign bodies". A protective, shell-like test is thereby agglutinated around the granellare, which is composed of scavenged minerals and the microscopic skeletal remains of other organisms, such as sponges, radiolarians, and other foraminiferans. 35 Xenophyophores may be an important part of the benthic ecosystem by virtue of their constant bioturbation of the sediments, providing a habitat for other organisms such as isopods. Research has shown that areas dominated by xenophyophores have 3-4 times the number of benthic crustaceans, echinoderms, and molluscs than equivalent areas which lack xenophyophores. The xenophyophores themselves also play commensal host to a number of organisms-such as isopods (e.g., genus Hebefustis), sipunculan and polychaete worms, nematodes, and harpacticoid copepods-some of which may take up semi-permanent residence within a xenophyophore's test. Brittle stars (Ophiuroidea) also appear to have some sort of relationship with xenophyophores, as they are consistently found directly underneath or on top of the protozoans. 36 Xenophyophores are difficult to study due to their extreme fragility. Specimens are invariably damaged during sampling, rendering them useless for captive study or cell culture. For this reason, very little is known of their life history. As they occur in all the world's oceans and in great numbers, xenophyophores could be indispensable agents in the process of sediment deposition and in maintaining biological diversity in benthic ecosystems. 37 Xenophyophores are large marine Amoebae containing barite (BaSO4) crystals. 38 CLASS Athalamea Granuloreticulosea, lacking a test or shell, though some forms might be covered by a thin lorica. Pseudopods could arise anywhere over the surface of the body, and could be branched to a greater or lesser extent in different representa-tives of the group, with or without anastomosing connections in the pseudopodial network. Organisms that have not been examined by modern techniques, nor have been seen in recent years, to check the fact that they do have granular reticulopodial bidirectional streaming, have been removed from this class and placed with the amoebae of uncertain affinities. One genus remains: Reticulomyxa. 39 FOOTNOTES 1. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). has 1600mybn for excavates, discricristales, rhizaria, chromalveolates 2. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004). 3. ^ http://microscope.mbl.edu/scripts/microscope.php?func=imgDetail&imageID=83 4. ^ "Foraminifera". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Foraminifera 5. ^ "Foraminifera". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Foraminifera 6. ^ "Foraminifera". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Foraminifera 7. ^ http://www.bio.georgiasouthern.edu/Bio-home/Pratt/boo305.htm 8. ^ http://www.bio.georgiasouthern.edu/Bio-home/Pratt/boo305.htm 9. ^ http://www.bio.georgiasouthern.edu/Bio-home/Pratt/boo305.htm 10. ^ http://www.bio.georgiasouthern.edu/Bio-home/Pratt/boo305.htm 11. ^ http://www.palaeos.com/Eukarya/Units/Rhizaria/Rhizaria.html 12. ^ http://www.sirinet.net/~jgjohnso/apbio30.html 13. ^ http://www.ucl.ac.uk/GeolSci/micropal/foram.html 14. ^ "Foraminifera". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Foraminifera 15. ^ "Foraminifera". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Foraminifera 16. ^ "Foraminifera". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Foraminifera 17. ^ "Foraminifera". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Foraminifera 18. ^ "Foraminifera". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Foraminifera 19. ^ "Foraminifera". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Foraminifera 20. ^ "Foraminifera". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Foraminifera 21. ^ "Foraminifera". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Foraminifera 22. ^ "Foraminifera". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Foraminifera 23. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=101966&tree=0.1 24. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=101966&tree=0.1 25. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=101966&tree=0.1 26. ^ "Allogromiida". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Allogromiida 27. ^ "Fusulinid". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Fusulinid 28. ^ "Globigerinida". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Globigerinida 29. ^ "Miliolid". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Miliolid 30. ^ "Rotaliida". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Rotaliida 31. ^ "Textulariida". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Textulariida 32. ^ "Xenophyophore". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Xenophyophore 33. ^ "Xenophyophore". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Xenophyophore 34. ^ "Xenophyophore". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Xenophyophore 35. ^ "Xenophyophore". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Xenophyophore 36. ^ "Xenophyophore". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Xenophyophore 37. ^ "Xenophyophore". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Xenophyophore 38. ^ http://microscope.mbl.edu/scripts/protist.php?func=integrate&myID=P4356&chinese_ flag=&system=&version=&documentID=&excludeNonLinkedIn=&imagesOnly= 39. ^ http://microscope.mbl.edu/scripts/protist.php?func=integrate&myID=P2007&chinese_ flag=&system=&version=&documentID=&excludeNonLinkedIn=&imagesOnly= 40. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). has 1600mybn for excavates, discricristales, rhizaria, chromalveolates (1600mybn) 41. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004).
1,900,000,000 YBN 6 7	66) Oldest Acritarch (eucaryote) fossils.1 2 These fossils are reported to be both in Chuanlinggou Formation, China and in Russia. Acritarchs, the name coined by Evitt in 1963 which means "of uncertain origin", are an artificial group. The group includes any small (most are between 20-150 microns across), organic-walled microfossil which cannot be assigned to a natural group. They are characterised by varied sculpture, some being spiny and others smooth. They are believed to have algal affinities, probably the cysts of planktonic eukaryotic algae. They are valuable Proterozoic and Palaeozoic biostratigraphic and palaeoenvironmental tools. 3 Chitinozoa are large (50-2000 microns) flask-shaped palynomorphs which appear dark, almost opaque when viewed using a light microscope. They are important Palaeozoic microfossils as stratigraphic markers. 4 The oldest known Acritarchs are recorded from shales of Palaeoproterozoic (1900-1600 Ma) age in the former Soviet Union. They are stratigraphically useful in the Upper Proterozoic through to the Permian. From Devonian times onwards the abundance of acritarchs appears to have declined, whether this is a reflection of their true abundance or the volume of scientific research is difficult to tell. 5 FOOTNOTES 1. ^ http://www.ucl.ac.uk/GeolSci/micropal/acritarch.html 2. ^ Knoll AH (1992) The early evolution of eukaryotes: a geological perspective. Science 256: 622-627 3. ^ http://www.ucl.ac.uk/GeolSci/micropal/acritarch.html 4. ^ http://www.ucl.ac.uk/GeolSci/micropal/acritarch.html 5. ^ Lezhava A, Kameoka D, Sugino H, Goshi K, Shinkawa H, et al. 1997. Chromosomal deletions in Streptomyces griseus that remove the afsA locus. Mol. Gen. Genet. 253:478-83 6. ^ http://www.ucl.ac.uk/GeolSci/micropal/acritarch.html 7. ^ Knoll AH (1992) The early evolution of eukaryotes: a geological perspective. Science 256: 622-627
1,874,000,000 YBN	61) Oldest non-acritarch Eukaryote fossil Grypania spiralis (an alga 10 cm long) from BIF in Michigan. Oldest algae fossil. 1 2 The date of this fossil was originally 2100mybn, but Schneider measured the Marquette Range Supergroup (MRS), A rhyolite in the Hemlock Formation, a mostly bimodal submarine volcanic deposit that is laterally correlative with the Negaunee Iron-formation, yields a sensitive high-resolution ion microprobe (SHRIMP) U-Pb zircon age of 1874 ± 9 Ma. 3 In 1992, Han and Runnegar, finders of this fossil, compared the fossil to Acetabularia, a single-celled green algae. If true, this would make Grypania the oldest green algae fossil. FOOTNOTES 1. ^ Han and Runnegar 1992. T.-M. Han and B. Runnegar, Megascopic eukaryotic algae from the 2.1-billion-year-old Negaunee Iron-Formation, Michigan. Science 257 (1992), pp. 232-235 science_2100_han_runnegar_algal_cysts.pdf 2. ^ Schneider et al 2002. D.A. Schneider, M.E. Bickford, W.F. Cannon, K.J. Schulz and M.A. Hamilton, Age of volcanic rocks and syndepositional iron formations, Marquette Range Supergroup; implications for the tectonic setting of Paleoproterozoic iron formations of the Lake Superior region. Can. J. Earth Sci. 39 6 (2002), pp. 999-1012. 3. ^ Schneider et al 2002. D.A. Schneider, M.E. Bickford, W.F. Cannon, K.J. Schulz and M.A. Hamilton, Age of volcanic rocks and syndepositional iron formations, Marquette Range Supergroup; implications for the tectonic setting of Paleoproterozoic iron formations of the Lake Superior region. Can. J. Earth Sci. 39 6 (2002), pp. 999-1012.
1,870,000,000 YBN 2	151) Amino acid sequence comparison shows the archaebacteria and eukaryote line separating here at 1,870 mybn (first eukaryote, and first protist).1 FOOTNOTES 1. ^ Russell F. Doolittle, Da-Fei Feng, Simon Tsang, Glen Cho, Elizabeth Little, "Determining Divergence Times of the Major Kingdoms of Living Organisms with a Protein Clock", Science, (1996). 2. ^ Russell F. Doolittle, Da-Fei Feng, Simon Tsang, Glen Cho, Elizabeth Little, "Determining Divergence Times of the Major Kingdoms of Living Organisms with a Protein Clock", Science, (1996).
1,800,000,000 YBN	46) End of the Banded Iron Formation Rocks.1 FOOTNOTES 1. ^ Richard Cowen, "History of Life", (Malden, MA: Blackwell, 2005).
1,584,000,000 YBN 2	152) Amino acid sequence comparison shows Gram-negative and Gram-positive eubacteria here at 1,584 mybn (first Gram-positive bacteria).1 FOOTNOTES 1. ^ Russell F. Doolittle, Da-Fei Feng, Simon Tsang, Glen Cho, Elizabeth Little, "Determining Divergence Times of the Major Kingdoms of Living Organisms with a Protein Clock", Science, (1996). 2. ^ Russell F. Doolittle, Da-Fei Feng, Simon Tsang, Glen Cho, Elizabeth Little, "Determining Divergence Times of the Major Kingdoms of Living Organisms with a Protein Clock", Science, (1996).
1,576,000,000 YBN 3	67) A eukaroyte cell forms a symbiotic relationship with cyanobacteria, which form plastids (chloroplasts). Like mitochondria, these organelles copy themselves and are not made by the cell DNA.1 Depending on their morphology and function, plastids are commonly classified as chloroplasts, leucoplasts, amyloplasts or chromoplasts. 2 FOOTNOTES 1. ^ S. Blair Hedges, "The Origin and Evolution of Model Organisms", Nature Reviews Genetics 3, 838-849; doi:10.1038/nrg929, (2002). 2. ^ "Plastid". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Plastid 3. ^ S. Blair Hedges, "The Origin and Evolution of Model Organisms", Nature Reviews Genetics 3, 838-849; doi:10.1038/nrg929, (2002)., see comments
1,513,000,000 YBN 1 2	221) First fungi evolve.1 2 Genetic comparison shows fungi evolving now. This begins the fungi kingdom. Perhaps fungi evolved from the amoebozoa slime mold line, because the sporangiophore (stalk) and sporangium (ball on top) of slime molds look very similar to many fungi. FOOTNOTES 1. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004). 2. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). (c1200)
1,500,000,000 YBN 1 2	323) First plant (single cell, similar to glaucophytes) evolves.1 2 Ribosomal RNA place first plant (single cell, similar to glaucophytes) evolving here. This begins the plant kingdom. Cavelier-Smith and Ema E. -Y. Chao write: "Kingdom Plantae (sensuCavalier-Smith 1981) was originally defined as comprising all eukaryotes with chloroplasts possessing an envelope of two membranes and mitochondria with (irregularly) flat cristae. It originally included Viridaeplantae (green algae and embryophyte or "higher" plants), Rhodophyta (red algae), and Glaucophyta (e.g., Cyanophora, Glaucocystis). It was argued that all three groups diverged from a single primary symbiogenetic origin of plastids (Cavalier-Smith 1982). Both the monophyly of plastids and that of Glaucophyta and Plantae long met unreasonably strong opposition because of widespread false dogma that symbiogenesis is easy and because the three taxa usually do not group together in 18S rRNA trees. Now, however, derived features of all plastids compared with cyanobacteria and numerous molecular trees have led to the acceptance of plastid monophyly (Delwiche and Palmer 1998) and to the monophyly of glaucophyte algae. Furthermore, a sister relation between red algae and Viridaeplantae is strongly supported by concatenated protein trees for nuclei (Moreira et al. 2000; Baldauf et al. 2000) and chloroplasts (Martin et al. 1998; Turmel et al. 1999). The sister relationship between them and glaucophytes is convincingly, but significantly more weakly, supported by the same trees. Thus the case of Plantae shows that arguments from morphology and evolutionary considerations of protein targeting during symbiogenesis (Cavalier-Smith 2000b) gave the correct answer much more rapidly than single-gene trees, which still do not clearly group all three taxa together. In all our trees in the present study (and the recent tree of Edgcomb et al. 2002), Rhodophyta and Viridaeplantae are sisters, but with weak support. Glaucophyta wander aimlessly from one place to another in different trees." 3 Ribosomal RNA place first plant evolving here, although glaucophytes, the earliest living plants (for many people) do not evolve until later. FOOTNOTES 1. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004). 2. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). (c1500)
1,492,000,000 YBN 2	173) Roper Group eukaryote algea microfossils.1 FOOTNOTES 1. ^ Andrew Knoll, "Life on a Young Planet: The first 3 Billion Years", (Princeton, NJ: , 2003). 2. ^ Andrew Knoll, "Life on a Young Planet: The first 3 Billion Years", (Princeton, NJ: , 2003).
1,400,000,000 YBN 11 12 13	86) Glaucophyta evolve.1 2 3 Genetic comparison shows Phylum Glaucophyta evolving at this time. Some people catagorize Glaucophyta in the kingdom Plantae instead of Protista, and label glaucophyta the most ancient living plants. The glaucophytes, also referred to as glaucocystophytes or glaucocystids, are a tiny group of freshwater algae. They are distinguished mainly by the presence of cyanelles, primitive chloroplasts which closely resemble cyanobacteria and retain a thin peptidoglycan wall between their two membranes. 4 It is thought that the green algae (from which the higher plants evolved), red algae and glaucophytes acquired their chloroplasts from endosymbiotic cyanobacteria. The other types of algae received their chloroplasts through secondary endosymbiosis, by engulfing one of those types of algae along with their chloroplasts. 5 The glaucophytes are of obvious interest to biologists studying the development of chloroplasts: if the hypothesis that primary chloroplasts had a single origin is correct, glaucophytes are closely related to both green plants and red algae, and may be similar to the original alga type from which all of these developed. 6 Glaucophytes have mitochondria with flat cristae, and undergo open mitosis without centrioles. 7 Motile forms have two unequal flagella, which may have fine hairs and are anchored by a multilayered system of microtubules, both of which are similar to forms found in some green algae. 8 The chloroplasts of glaucophytes, like the cyanobacteria and the chloroplasts of red algae, use the pigment phycobilin to capture some wavelengths of light; the green algae and higher plants have lost that pigment. 9 There are three main genera included here. Glaucocystis is non-motile, though it retains very short vestigial flagella, and has a cellulose wall. Cyanophora is motile and lacks a cell wall. Gloeochaete has both motile and non-motile stages, and has a cell wall that does not appear to be composed of cellulose. 10 DOMAIN Eukaryota - eukaryotes KINGDOM Plantae Haeckel, 1866 - plants SUBKINGDOM Biliphyta Cavalier-Smith, 1981 PHYLUM Glaucophyta Skuja, 1954 CLASS Glaucocystophyceae Schaffner, 1922 FOOTNOTES 1. ^ S. Blair Hedges, "The Origin and Evolution of Model Organisms", Nature Reviews Genetics 3, 838-849; doi:10.1038/nrg929, (2002). 2. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). 3. ^ Hwan Su Yoon, Jeremiah D. Hackett, Claudia Ciniglia, Gabriele Pinto and Debashish, "A Molecular Timeline for the Origin of Photosynthetic Eukaryotes", Molecular Biology and Evolution, (2004). 4. ^ "Glaucophytes". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Glaucophytes 5. ^ "Glaucophytes". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Glaucophytes 6. ^ "Glaucophytes". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Glaucophytes 7. ^ http://microscope.mbl.edu/scripts/protist.php?func=integrate&myID=P6064 8. ^ "Glaucophytes". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Glaucophytes 9. ^ "Glaucophytes". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Glaucophytes 10. ^ "Glaucophytes". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Glaucophytes 11. ^ S. Blair Hedges, "The Origin and Evolution of Model Organisms", Nature Reviews Genetics 3, 838-849 (2002); doi:10.1038/nrg929, (2002). (c1500my) 12. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). (c1400) 13. ^ Hwan Su Yoon, Jeremiah D. Hackett, Claudia Ciniglia, Gabriele Pinto and Debashish, "A Molecular Timeline for the Origin of Photosynthetic Eukaryotes", Molecular Biology and Evolution, (2004). (1558my)
1,400,000,000 YBN 4	197) Opisthokonts (posterior cilium) evolve from Unikonts (ancestrally only one cilium). Opisthokonts have flat mitochondrial cristae and go on to form the Animal and Fungi kingdoms.1 2 Thomas Cavalier-Smith and Ema E.-Y. Chao write: "The term opisthokont, signifying "posterior cilium," was applied to animals, Choanozoa, and Fungi because all three groups ancestrally had a single posterior cilium (Cavalier-Smith 1987b). They were argued to be a clade because they also were characterized (uniquely at the time) by flat, nondiscoid mitochondrial cristae that were not irregularly inflated like the flat cristae of Plantae (Cavalier-Smith 1987b). Four other characters also suggested that animals and fungi were more closely related to each other than plants (chitinous exoskeletons; storage of glycogen, not starch; absence of chloroplasts; and UGA coding for tryptophane, not chain termination). However, the first three were probably ancestral states for eukaryotes and the last convergent, so the ciliary and cristal morphology were stronger indications. Although early rRNA trees did not group animals and fungi together, the opisthokonts are now consistently supported by all well-sampled rRNA trees and trees using several or many proteins, as discussed above. Moreover a derived 12-amino acid insertion in translation elongation factor 1agr and three small gaps in enolase clearly indicate that animals and fungi have a common ancestor not shared with plants (or other bikonts) or Amoebozoa (Baldauf and Palmer 1993; Baldauf 1999). Thus opisthokonts are now well accepted as a robust clade of eukaryotes (Patterson 1999)."3 FOOTNOTES 1. ^ J Mol Evol (2003) 56:540 563 Phylogeny of Choanozoa, Apusozoa, and Other Protozoa and Early Eukaryote Megaevolution Thomas Cavalier-Smith, Ema E.-Y. Chao /home/ted/ulsf/docs/cav-smith_apusozoa_fulltext.html 2. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). 3. ^ J Mol Evol (2003) 56:540 563 Phylogeny of Choanozoa, Apusozoa, and Other Protozoa and Early Eukaryote Megaevolution Thomas Cavalier-Smith, Ema E.-Y. Chao /home/ted/ulsf/docs/cav-smith_apusozoa_fulltext.html 4. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004).
1,400,000,000 YBN 62 63	220) Amoebozoa (amoeba, slime molds) evolve now.1 2 Ribosomal RNA shows the Protist Phylum Amoebozoa (also called Ramicristates) which includes amoeba and slime molds evolving now. The Amoebozoa are a major group of amoeboid protozoa, including the majority that move by means of internal cytoplasmic flow. Their pseudopodia are characteristically blunt and finger-like, called lobopodia. Most are unicellular, and are common in soils and aquatic habitats, with some found as symbiotes of other organisms, including several pathogens. The Amoebozoa also include the slime moulds, multinucleate or multicellular forms that produce spores and are usually visible to the unaided eye. 3 Mycetozoa are the slime molds. 4. Plasmodial Slime Molds 4 a. Plasmodial slime molds exist as a plasmodium. (the earlier evolved acrasid cellular slime molds exist as individual amoeboid cells.) b. This diploid multinucleated cytoplasmic mass creeps along, phagocytizing decaying plant material. c. Fan-shaped plasmodium contains tubules of concentrated cytoplasm in which liquefied cytoplasm streams. d. Under unfavorable environmental conditions (e.g., drought), the plasmodium develops many sporangia that produce spores by meiosis. e. When mature, spores are released and survive until more favorable environmental conditions return; then each releases a haploid flagellated cell or an amoeboid cell. f. Two flagellated or amoeboid cells fuse to form diploid zygote that produces a multi-nucleated plasmodium. 5 Nuclear division in giant amoebas (Peolobiont/Amoebozoa) is neither mitosis nor binary fission, but incorporates aspects of both (Fig. 3-7). Chromosomes are attached permanently to the nuclear membrane by their centromeres (MTOCs, microtubule organizing centers), and the nuclear membrane remains intact throughout division. After DNA duplication produces two chromatids, the point of attachment, the MTOC duplicates or divides, and microtubules are assembled between the two resulting MTOCs. Elongating microtubules form something akin to a spindle within the nuclear membrane that pushes the daughter chromosomes apart and elongate the membrane-bounded nucleus until it blebs in half in something akin to binary fission. Simple assembly of microtubules accomplishes the separation of daughter genomes in this simple nuclear division. In typical eukaryotic mitosis, the separation of daughter chromosomes is accomplished by a dual action, the disassembly of spindle fibers connecting the daughter chromosome to the polar MTOC, and assembly of spindle fibers running pole to pole. 6 amoeba haplodiploid? Thomas Cavalier-Smith and Ema E. -Y. Chao write: "Amoebozoa are a key protozoan phylum because of the possibility that they are ancestrally uniciliate and unicentriolar (Cavalier-Smith 2000a,b); present data on the DHFR-TS gene fusion leaves open the possibility that they might be the earliest-diverging eukaryotes (Stechmann and Cavalier-Smith 2002), but they may be evolutionarily closer to bikonts or even opisthokonts. Amoebozoa comprise two subphyla (Cavalier-Smith 1998a): Lobosa, classical aerobic amoebae with broad ("lobose") pseudopods (including the testate Arcellinida), and Conosa (slime molds {Mycetozoa, e.g., Dictyostelium} and amitochondrial-often uniciliate-archamaebae {entamoebae, mastigamoebae}). Contrary to early analyses (Sogin 1991; Cavalier-Smith 1993a), there is no reason to regard Amoebozoa as polyphyletic; the defects of those classical uncorrected rRNA trees are shown by trees using 123 proteins that robustly establish the monophyly of both Archamoebae and Conosa (Bapteste et al. 2002). Unless the tree's root is within Conosa, Dictyostelium and Entamoeba must have evolved independently from aerobic flagellates by ciliary losses. A recent mitochondrial gene tree based on concatenating six different proteins grouped Dictyostelium with Physarum (99% support) and both Mycetozoa as sisters to Acanthamoeba (99% support), thus providing strong evidence for the monophyly of Mycetozoa and the grouping of Lobosa and Conosa as Amoebozoa (Forget et al. 2002)-the same tree also strongly supports the idea based on morphology that Allomyces should be excluded from Chytridiomycetes (in the separate class Allomycetes) and is phylogenetically closer to zygomycetes and higher fungi (Cavalier-Smith 1998a, 2000c). Furthermore, the derived gene fusion between two cytochrome oxidase genes, coxI and coxII (Lang et al. 1999), strongly supports the holophyly of Mycetozoa. Since Archamoebae secondarily lost mitochondria, the root cannot lie among them either-although anaerobiosis in Archamoebae is derived, it is unjustified to conclude from this that their simple ciliary root organization, which was a key reason for considering them early eukaryotes (Cavalier-Smith 1991c), is also secondarily derived (Edgcomb et al. 2002). Thus the root of the eukaryote tree cannot lie within the Conosa. As Mycetozoa and Archamoebae have very long-branch rRNA sequences, Conosa were excluded from the analysis in Fig. 1, which includes only Lobosa. Although the monophyly of Acanthamoebida (99%) and of Euamoebida (85%) is well supported, the basal branching of the Lobosa is so poorly resolved that the monophyly of Lobosa might appear open to question. The four lobosan lineages apparently diverged early. However, in the 279- and 227-species trees, which included Conosa, anaeromonads did not intrude into the Amoebozoa as they do in Fig. 1, and Amoebozoa were monophyletic (low support) except for the exclusion of M. invertens. M. invertens is another wandering branch, which in some taxon sample/methods groups very weakly with other Amoebozoa, but more often ends up in a different place in each tree! We concur with the judgment of Milyutina et al. (2001)Edgcomb et al. (2002) that it should not be regarded as a pelobiont or Archamoeba, but as a lobosan that independently became an anaerobe with degenerate mitochondria. Its tendency to drift around the tree, coupled with its short branch, suggests that it may be a particularly early-diverging amoebozoan lineage. If so, its unicentriolar condition would give added support to the idea that Amoebozoa are ancestrally uniciliate, if it could be shown that Amoebozoa are either holophyletic or not at the base of the tree. Most, if not all, amoebae evolved from amoeboid zooflagellates by multiple ciliary losses (Cavalier-Smith 2000a). As the uniciliate condition is widespread within Amoebozoa (Cavalier-Smith 2000a, 2002b), it may be their ancestral condition; if so, ordinary nonciliate amoebozoan amoebae arose several times independently. Evolution of amoebae from zooflagellates by ciliary loss also occurred separately in Choanozoa to produce Nuclearia and in several bikont groups, notably Percolozoa (heterolobosean amoebae, e.g., Vahlkampfia) and Cercozoa. However, we cannot currently exclude the possibility that the eukaryote tree is rooted within the lobosan Amoebozoa, in which case one of its nonciliate lineages (Euamoebida or Vanellidae) might be primitively nonciliate and the earliest-diverging eukaryotic lineage. However, as the idea that the nucleus and a single centriole and cilium coevolved in the ancestral eukaryote (Cavalier-Smith 1987a) retains its theoretical merits, we think it more likely that all Amoebozoa are derived from a uniciliate ancestor and that crown Amoebozoa are a clade." 7 Amoebozoa vary greatly in size. Many are only 10-20 μm in size, but they also include many of the larger protozoa. The famous species Amoeba proteus may reach 800 μm in length, and partly on account of its size is often studied as a representative cell. Multinucleate amoebae like Chaos and Pelomyxa may be several millimetres in length, and some slime moulds cover several square feet. 8 The cell is typically divided into a granular central mass, called endoplasm, and a clear outer layer, called ectoplasm. During locomotion the endoplasm flows forwards and the ectoplasm runs backwards along the outside of the cell. Many amoebae move with a definite anterior and posterior; in essence the cell functions as a single pseudopod. They usually produce numerous clear projections called subpseudopodia (or determinate pseudopodia), which have a defined length and are not directly involved in locomotion. 9 Other amoebozoans may form multiple indeterminate pseudopodia, which are more or less tubular and are mostly filled with granular endoplasm. The cell mass flows into a leading pseudopod, and the others ultimately retract unless it changes direction. Subpseudopodia are usually absent. In addition to a few naked forms like Amoeba and Chaos, this includes most amoebae that produce shells. These may be composed of organic materials, as in Arcella, or of collected particles cemented together, as in Difflugia, with a single opening through which the pseudopodia emerge. 10 The primary mode of nutrition is by phagocytosis: the cell surrounds potential food particles, sealing them into vacuoles where the may be digested and absorbed. Some amoebae have a posterior bulb called a uroid, which may serve to accumulate waste, periodically detaching from the rest of the cell. When food is scarce, most species can form cysts, which may be carried aerially and introduce them to new environments. In slime moulds, these structures are called spores, and form on stalked structures called fruiting bodies or sporangia. 11 Most Amoebozoa lack flagella and more generally do not form microtubule-supported structures except during mitosis. However, flagella occur among the pelobionts, and many slime moulds produce biflagellate gametes. The flagella is generally anchored by a cone of microtubules, suggesting a close relationship to the opisthokonts. The mitochondria characteristically have branching tubular cristae, but have been lost among pelobionts and the parasitic entamoebids, collectively referred to as archamoebae based on the earlier assumption that the absence was primitive. 12 Traditionally all amoebae with lobose pseudopods were treated together as the Lobosea, placed with other amoeboids in the phylum Sarcodina or Rhizopoda, but these were considered to be unnatural groups. Structural and genetic studies identified several independent groups: the percolozoans, pelobionts, and entamoebids. In phylogenies based on rRNA their representatives were separate from other amoebae, and appeared to diverge near the base of eukaryotic evolution, as did most slime molds. 13 However, revised trees by Cavalier-Smith and Chao in 1996 suggested that the remaining lobosans do form a monophyletic group, and that the archamoebae and Mycetozoa are closely related to it, although the percolozoans are not. Subsequently they emended (to improve by editing14 ) the older phylum Amoebozoa to refer to this supergroup. Studies based on other genes have provided strong support for the unity of this group. Patterson treated most with the testate filose amoebae as the ramicristates, based on mitochondrial similarities, but the latter are now removed to the Cercozoa. 15 Amoebae are difficult to classify, and relationships within the phylum remain confused. Originally it was divided into the subphyla Conosa, comprising the archamoebae and Mycetozoa, and Lobosa, including the more typical lobose amoebae. Molecular phylogenies provide some support for this division if the Lobosa are understood to be paraphyletic. They also suggest the morphological families of naked lobosans may correspond at least partly to natural groups: 16 * Leptomyxida * Amoebidae * Hartmannellidae * Paramoebidae * Vannellidae * Vexilliferidae * Acanthamoebidae * Stereomyxidae 17 However, many amoebae have not yet been studied via molecular techniques, including all those that produce shells (Arcellinida). 18 PHYLUM Amoebozoa (Lühe, 1913 emend.) 19 20 Cavalier-Smith, 1998 21 CLASS Breviatea 22 CLASS Variosea 23 CLASS Phalansterea (T. Cavalier-Smith, 2000) 24 SUBPHYLUM Lobosa (Carpenter, 1861) Cavalier-Smith, 1997 25 (lobose amoebas) CLASS Amoebaea 26 CLASS Testacealobosea 27 (includes shelled lobosid amebas {testate amoebas}) CLASS Holomastigea T. Cavalier-Smith, 1997 ("1996-1997") 28 SUBPHYLUM Conosa (Cavalier-Smith, 1998) 29 INTRAPHYLUM Mycetozoa (De Bary, 1859) Cavalier-Smith, 1998 30 (Slime Molds) SUPERCLASS Eumyxa (Cavalier-Smith, 1993) Cavalier-Smith, 1998 CLASS Protostelea (C.J. Alexopoulos & C.W. Mims, 1979 orthog. emend.) 31 CLASS Myxogastrea (E.M. Fries, 1829 stat. nov. J. Feltgen, 1889 orthog. emend.) 32 (plasmodial slime molds) SUPERCLASS Dictyostelia (Lister, 1909) Cavalier-Smith, 1998 CLASS Dictyostelea™ (D.L. Hawksworth et al., 1983, orthog. emend.) 33 INTRAPHYLUM Archamoebae (Cavalier-Smith, 1983) Cavalier-Smith, 1998 CLASS Pelobiontea (F.C. Page, 1976 stat. nov. T. Cavalier-Smith, 1981) 34 CLASS Entamoebea (T. Cavalier-Smith, 1991) 35 SUBPHYLUM Lobosa SUBPHYLUM Conosa The Conosea unifies amoebae which usually possess flagellate stages or are amoeboflagellates. This clade consists of two relatively solid groups � the Mycetozoa and Archamoebae, grouped by Cavalier-Smith (1998) in the taxon Conosa, as well as a number of independent lineages, including two flagellates � Phalansterium (Cavalier-Smith et al. 2004) and Multicilia (Nikolaev et al. 2004), and two gymnamoebae � Gephyramoeba and Filamoeba (Amaral Zettler et al. 2000). Because of large variations of the substitution rates in SSU rRNA genes within this clade, its internal relationships are not resolved yet. 36 The Mycetozoa comprises two distinct groups of �slime molds� � the Myxogastria and Protostelia (Dykstra and Keller 2000). This is a well-defined group of protists, characterized by the ability to form so-called �fruiting bodies�. In some lineages of Mycetozoa the fruiting body is raised over the substratum on a distinct stalk. Both groups possess complex life cycles including an aggregation of cells, however the essential difference between them is that in Protostelia, only a pseudoplasmodium is formed (without fusion of the cells constituting the aggregate), while in Myxogastria a true plasmodium is formed (the cells completely fuse, forming a single organism) (Olive 1975; Dykstra and Keller 2000). The monophyly of Mycetozoa was proposed based on elongation factor 1-alpha gene sequences (Baldauf and Doolittle 1997) but it is not always recovered in SSU rRNA trees (Cavalier-Smith et al. 2004; Nikolaev et al. 2004). 37 The Archamoebae comprise amoeboid and amoeboflagellate protists characterized by a secondary absence of mitochondria (mostly due to parasitism or life in anoxic environments). This group includes the free-living genera Mastigamoeba, Mastigella, and Pelomyxa (the pelobionts) and the parasitic genera Entamoeba and Endolimax (the entamoebids). The consistent grouping of all these amitochondriate amoeboid organisms in both SSU rRNA and actin gene phylogenies (Fahrni et al. 2003) suggests a single loss of the mitochondria during the evolution of Amoebozoa. 38 CLASS Amoebaea ORDER Euamoebida Lepsi, 1960 39 FAMILY Amoebidae (Ehrenberg 1838) 40 The Amoebidae are a family of amoebozoa, including naked amoebae that produce multiple pseudopodia of indeterminate length. These are roughly cylindrical in form, with a central stream of granular endoplasm, and do not have subpseudopodia. During locomotion one pseudopod typically becomes dominant, and the others are retracted as the body flows into it. In some cases the cell moves by "walking", with the relatively permanent pseudopodia serving as limbs. 41 The most important genera are Amoeba and Chaos, which are set apart from the others by longitudinal ridges. They group together on molecular trees, suggesting the Amoebidae are a natural group. Shelled amoebozoans have not been studied molecularly but produce very similar pseudopodia, so although they are traditionally classified separately they may be closely related to this group. 42 GENUS Amoeba (Bery de St. Vincent 1822) 43 Amoeba (also spelled ameba) is a genus of protozoa that moves by means of temporary projections called pseudopods, and is well-known as a representative unicellular organism. The word amoeba is variously used to refer to it and its close relatives, now grouped as the Amoebozoa, or to all protozoa that move using pseudopods, otherwise termed amoeboids. 44 Amoeba itself is found in freshwater, typically on decaying vegetation from streams, but is not especially common in nature. However, because of the ease with which they may be obtained and kept in the lab, they are common objects of study, both as representative protozoa and to demonstrate cell structure and function. The cells have several lobose pseudopods, with one large tubular pseudopod at the anterior and several secondary ones branching to the sides. The most famous species, Amoeba proteus, is 700-800 μm in length, but many others are much smaller. Each has a single nucleus, and a simple contractile vacuole which maintains its osmotic pressure, as its most recognizable features. 45 Early naturalists referred to Amoeba as the Proteus animalcule, after a Greek god who could change his shape. The name "amibe" was given to it by Bery St. Vincent, from the Greek amoibe, meaning change. 46 A good method of collecting amoeba is to lower a jar upside down until it is just above the sediment surface. Then one should slowly let the air escape so the top layer will be sucked into the jar. Deeper sediment should not be allowed to get sucked in. It is possible to slowly move the jar when tilting it to collect from a larger area. If no amoeba are found, one can try introducing some rice grains into the jar and waiting for them to start to rot. The bacteria eating the rice will be eaten by the amoeba, thus increasing the population and making them easier to find. 47 Family Hartmannellidae (Volkonsky 1931) The Hartmannellidae are a common family of amoebozoa, usually found in soils. When active they tend to be roughly cylindrical in shape, with a single leading pseudopod and no subpseudopodia. This form somewhat resembles a slug, and as such they are also called limax amoebae. Trees based on rRNA show the Hartmannellidae are paraphyletic to the Amoebidae and Leptomyxida, which may adopt similar forms. 48 FAMILY Vannellidae (Bovee 1970) The Vannellidae are a distinctive family of amoebozoa. During locomotion they tend to be flattened and fan-shaped, although some are long and narrow, and have a prominent clear margin at the anterior. In most amoebae, the endoplasm glides forwards through the center of the cell, but in vannellids the cell undergoes a sort of rolling motion, with the outer membrane sliding around like a tank tread. 49 These amoebae are usually 10-40 μm in size, but some are smaller or larger. The most common genus is Vannella, found mainly in soils, but also in freshwater and marine habitats. Trees based on rRNA support the monophyly of the family. 50 SUBPHYLUM Conosa Cavalier-Smith, 1998 INTRAPHYLUM Archamoebae (Cavalier-Smith, 1983) Cavalier-Smith, 1998 CLASS Pelobiontea F.C. Page, 1976 stat. nov. T. Cavalier-Smith, 1981 ORDER Pelobiontida (Page 1976) The pelobionts are a small group of amoebozoa. The most notable member is Pelomyxa, a giant amoeba with multiple nuclei and inconspicuous non-motile flagella. The other genera, called mastigamoebae, are often uninucleate, have a single anterior flagellum used in swimming, and produce numerous determinate pseudopodia. 51 Pelobionts are closely related to the entamoebids and like them have no mitochondria; in addition, pelobionts also do not have dictyosomes. At one point these absences were considered primitive. However, molecular trees place the two groups with other lobose amoebae in the phylum Amoebozoa, so these are secondary losses. 52 SUBPHYLUM Conosa Cavalier-Smith, 1998 INTRAPHYLUM Archamoebae (Cavalier-Smith, 1983) Cavalier-Smith, 1998 CLASS Entamoebea T. Cavalier-Smith, 1991 The entamoebids or entamoebae are a group of amoebozoa found as internal parasites or commensals of animals. The cells are uninucleate small, typically 10-100 μm across, and usually have a single lobose pseudopod taking the form of a clear anterior bulge. There are two major genera, Entamoeba and Endolimax. They include several species that are pathogenic in humans, most notably Entamoeba histolytica, which causes amoebic dysentery. 53 Entamoebids lack mitochondria. This is a secondary loss, possibly associated with their parasitic life-cycle. Studies show they are close relatives of the pelobionts, another group of amitochondriate amoebae, but unlike them entamoebids retain dictyosomes. Both groups are now placed alongside other lobose amoebae in the phylum Amoebozoa. 54 Studying Entamoeba invadens, David Biron of the Weizmann Institute of Science and coworkers found that about one third of the cells are unable to separate unaided and recruit a neighboring amoeba (dubbed the "midwife") to complete the fission. He writes: 55 "When an amoeba divides, the two daughter cells stay attached by a tubular tether which remains intact unless mechanically severed. If called upon, the neighbouring amoeba midwife travels up to 200 μm towards the dividing amoeba, usually advancing in a straight trajectory with an average velocity of about 0.5 μm/s. The midwife then proceeds to rupture the connection, after which all three amoebae move on." 56 They also reported a similar behavior in Dictyostelium. 57 Entamoeba coli is a non-pathogenic species of entamoebid that is important clinically in humans only because it can be confused with Entamoeba histolytica, which is pathogenic, on microscopic examination of stained stool specimens. A simple finding of Entamoeba coli trophozoites or cysts in a stool specimen requires no treatment. 58 Entamoeba histolytica is an anaerobic parasitic protozoan, classified as an entamoebid. It infects predominantly humans and other primates. Diverse mammals such as dogs and cats can become infected but usually do not shed cysts (the environmental survival form of the organism) with their feces, thus do not contribute significantly to transmission. The active (trophozoite) stage exists only in the host and in fresh feces; cysts survive outside the host in water and soils and on foods, especially under moist conditions on the latter. When swallowed they cause infections by excysting (to the trophozoite stage) in the digestive tract. 59 Endolimax nana, a small entamoebid that is a commensal of the human intestine, causes no known disease. It is most significant in medicine because it can provide false positives for other tests, such as for the related species Entamoeba histolytica which causes amoebic dysentery, and because its presence indicates that the host once consumed feces. It forms cysts with four nuclei which excyst in the body and become trophozoites. Endolimax nana nuclei have a large endosome somewhat off-center and small amounts of visible chromatin or none at all. 60 Actinopod reproduction may involve binary fission or the formation of swarmer cells, and sexual processes occur in some groups. Their mitochondrial cristae are usually tubular, but in some groups there are vesicular or flattened, plate-like cristae. 61 FOOTNOTES 1. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004). 2. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). 3. ^ "Amoebozoa". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Amoebozoa 4. ^ http://www.sirinet.net/~jgjohnso/apbio30.html 5. ^ http://www.sirinet.net/~jgjohnso/apbio30.html 6. ^ http://www.bio.ilstu.edu/Armstrong/syllabi/222book/Chapt%203.htm 7. ^ Thomas Cavalier-Smith and Ema E. -Y. Chao, "Phylogeny of Choanozoa, Apusozoa, and Other Protozoa and Early Eukaryote Megaevolution", Springer New York, (2003) . 8. ^ "Amoebozoa". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Amoebozoa 9. ^ "Amoebozoa". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Amoebozoa 10. ^ "Amoebozoa". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Amoebozoa 11. ^ "Amoebozoa". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Amoebozoa 12. ^ "Amoebozoa". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Amoebozoa 13. ^ "Amoebozoa". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Amoebozoa 14. ^ Ted Huntington. 15. ^ "Amoebozoa". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Amoebozoa 16. ^ "Amoebozoa". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Amoebozoa 17. ^ "Amoebozoa". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Amoebozoa 18. ^ "Amoebozoa". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Amoebozoa 19. ^ "Amoebozoa". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Amoebozoa 20. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=75925 21. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=75925 22. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=75925 23. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=75925 24. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=75925 25. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=75925 26. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=75925 27. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=75925 28. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=75925 29. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=75925 30. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=75925 31. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=75925 32. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=75925 33. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=75925 34. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=75925 35. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=75925 36. ^ http://www.unige.ch/sciences/biologie/biani/msg/Amoeboids/Amoebozoa/Conosea.html 37. ^ http://www.unige.ch/sciences/biologie/biani/msg/Amoeboids/Amoebozoa/Conosea.html 38. ^ http://www.unige.ch/sciences/biologie/biani/msg/Amoeboids/Amoebozoa/Conosea.html 39. ^ http://sn2000.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=75925 40. ^ "Amoebidae". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Amoebidae 41. ^ "Amoebidae". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Amoebidae 42. ^ "Amoebidae". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Amoebidae 43. ^ "Amoeba". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Amoeba 44. ^ "Amoeba". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Amoeba 45. ^ "Amoeba". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Amoeba 46. ^ "Amoeba". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Amoeba 47. ^ "Amoeba". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Amoeba 48. ^ "Hartmannellidae". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Hartmannellidae 49. ^ "Vannellidae". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Vannellidae 50. ^ "Vannellidae". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Vannellidae 51. ^ "Pelobiont". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Pelobiont 52. ^ "Pelobiont". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Pelobiont 53. ^ "Entamoebid". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Entamoebid 54. ^ "Entamoebid". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Entamoebid 55. ^ "Entamoebid". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Entamoebid 56. ^ "Entamoebid". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Entamoebid 57. ^ "Entamoebid". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Entamoebid 58. ^ "Entamoeba coli". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Entamoeba_coli 59. ^ "Entamoeba histolytica". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Entamoeba_histolytica 60. ^ "Endolimax nana". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Endolimax_nana 61. ^ Michael Sleigh, "Protozoa and Other Protists", (London; New York: Edward Arnold, 1989). p174 62. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004). (1587mybn) 63. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). (c1400)
1,300,000,000 YBN 17 18 19 20 21	188) Green Algae, composed of the 2 Phlya Chlorophyta (volvox, sea lettuce) and Charophyta (Spirogyra) evolve. 1 2 3 4 5 6 Genetic comparison shows Green Algae, composed of the 2 Phlya Chlorophyta (volvox, sea lettuce) and Charophyta (Spirogyra) evolving now. The Green Algae are the large group of algae from which the embryophytes (higher plants) emerged. As such they form a paraphyletic group, some people placing them in the Plantae Kingdom, while others placing them in the Protist Kingdom. 7 Almost all forms have chloroplasts. They are bound by a double membrane, so presumably were acquired by direct endosymbiosis of cyanobacteria. 8 All green algae have mitochondria with flat cristae. When present flagella are typically anchored by a cross-shaped system of microtubules, but these are absent among the higher plants and charophytes. They usually have cell walls containing cellulose, and undergo open mitosis without centrioles. Sexual reproduction varies from fusion of identical cells (isogamy) to fertilization of a large non-motile cell by a smaller motile one (oogamy). However, these traits show some variation, most notably among the basal green algae, called prasinophytes. 9 The first land plants most likely evolved from green algae. 10 Here is where the green algae separate from the ancestor of the first land plants. Spirogyra reproduce through conjugation, which either was inherited from prokaryotes or evolved a second time in eukaryotes. Some filamentous green algae (e.g. cladophora) are haplodiploid (alternate between haploid and diploid cycles that both have mitosis). 1. Phylum Chlorophyta (green algae) contains about 7,000 species. 2. Most live in the ocean but are more likely found in fresh water; they can even be found on moist land. 3. Green algae are believed to be closely related to the first plants because both of these groups a. have a cell wall that contains cellulose, b. possess chlorophylls a and b, and c. store reserve food as starch inside of the chloroplast. 4. Green algae are not always green; some have pigments that give them an orange, red, or rust color. 5. Body organizations include single cells, colonies, filaments and multicellular forms. 11 C. Flagellated Green Algae 1. Chlamydomonas is a unicellular green alga less than 25 cm long. (Fig. 30.3) 2. It has a cell wall and a single, large, cup-shaped chloroplast with a pyrenoid for starch synthesis. 3. The chloroplast contains a light-sensitive eyespot (stigma) that directs the cell to light for photosynthesis. 4. Two long whip-like flagella project from the anterior end to propel the cell toward light. 5. When growth conditions are favorable, Chlamydomonas reproduces asexually with zoospores. 6. When growth conditions are unfavorable, Chlamydomonas reproduces sexually. a. Gametes from two different mating types join to form a zygote. b. A heavy wall forms around the zygote; a resistant zygospores survives until conditions are favorable. c. Some are heterogametes similar to sperm and egg that stores food, a condition called oogamy. d. In most, gametes are identical, a condition called isogamy. 12 D. Filamentous Green Algae 1. Cell division in one plane produces end-to-end chains of cells or filaments. 2. Spirogyra is a filamentous algae found on surfaces of ponds and streams. a. It has ribbon-like spiral chloroplasts. (Fig. 30.4) b. Two strands may unite in conjugation and exchange genetic material, forming a diploid zygote. c. The zygotes withstand winter; in spring they undergo meiosis to produce haploid filaments. 3. Oedogonium is another filamentous algae. a. It has cylindrical cells with netlike chloroplasts. b. During sexual reproduction, there is a definite egg and sperm. 13 E. Multicellular Green Algae 1. Multicellular Ulva is called sea lettuce because of its leafy appearance. (Fig. 30.5) 2. The thallus (body) is two cells thick but can be a meter long. 3. Ulva has an alternation of generations life cycle, as do plants, but the generations look alike. 4. The gametes look alike (isogametes) and the spores are flagellated. 5. In true plants, one generation is dominant, sperm and eggs are produced, and spores lack flagella. 14 F. Colonial Green Algae 1. Volvox is a hollow sphere with thousands of cells arranged in a single layer. (Fig. 30.6) 2. Volvox cells resembles Chlamydomonas cells; a colony arises as if daughter cells fail to separate. 3. Volvox cells cooperate when flagella beat in a coordinated fashion. 4. Some cells are specialized forming a new daughter colony within the parental colony. 5. Daughter colonies are inside a parent colony until an enzyme dissolves part of a wall so it can escape. 6. Sexual reproduction involves oogamy 15 Order Chlorococcales, probably includes the first coccoidal green algae, probably even the earliest eukaryotes, but unequivocal indentification in the Precambrien is unlikely to be achived. 16 Spirogyra reproduce through conjugation, which either was inherited from prokaryotes or evolved a second time in eukaryotes. If inherited from prokaryotes, then spirogrya would be very old although the fossil record and Ribosomal RNA put them late compared to other algae. FOOTNOTES 1. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). 2. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004). 3. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). 4. ^ Daniel S. Heckman,1 David M. Geiser,2 Brooke R. Eidell,1 Rebecca L. Stauffer,1 Natalie L. Kardos, "Molecular Evidence for the Early Colonization of Land by Fungi and Plants", Science 10 August 2001: Vol. 293. no. 5532, pp. 1129 - 1133 DOI: 10.1126/science.1061457, (2001). 5. ^ M. J. Benton, "The Fossil Record 2", (London; New York: Chapman & Hall, 1993). fr2b 6. ^ http://www.ucmp.berkeley.edu/greenalgae/greenalgae.html 7. ^ "Green algae". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Green_algae 8. ^ "Green algae". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Green_algae 9. ^ "Green algae". Wikipedia. Wikipedia, 2008. http://en.wikipedia.org/wiki/Green_algae 10. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). 11. ^ http://www.sirinet.net/~jgjohnso/apbio30.html 12. ^ http://www.sirinet.net/~jgjohnso/apbio30.html 13. ^ http://www.sirinet.net/~jgjohnso/apbio30.html 14. ^ http://www.sirinet.net/~jgjohnso/apbio30.html 15. ^ http://www.sirinet.net/~jgjohnso/apbio30.html 16. ^ M. J. Benton, "The Fossil Record 2", (London; New York: Chapman & Hall, 1993). fr2b 17. ^ S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe, "A molecular timescale of eukaryote evolution and the rise of complex multicellular life", BMC Evolutionary Biology 2004, 4:2 doi:10.1186/1471-2148-4-2, (2004). (968mybn) 18. ^ Richard Dawkins, "The Ancestor's Tale", (Boston, MA: Houghton Mifflin Company, 2004). (1300mybn) 19. ^ Daniel S. Heckman,1 David M. Geiser,2 Brooke R. Eidell,1 Rebecca L. Stauffer,1 Natalie L. Kardos, "Molecular Evidence for the Early Colonization of Land by Fungi and Plants", Science 10 August 2001: Vol. 293. no. 5532, pp. 1129 - 1133 DOI: 10.1126/science.1061457, (2001). (1061?) 20. ^ M. J. Benton, "The Fossil Record 2", (London; New York: Chapman & Hall, 1993). fr2b (1650-800mybn) 21. ^ http://www.ucmp.berkeley.edu/greenalgae/greenalgae.html (1000my)
1,300,000,000 YBN 10 11	209) Red Algae (Rhodophyta) evolve now.1 2 Genetic comparison show Phylum Rhodophyta (red algae) evolves now. There are between 2500 and 6000 species in about 670 largely marine genera. Many red algae are haplodiploid (alternate between haploid and diploid cycles that both have mitosis). The red algae (Rhodophyta) are a large group of mostly multicellular, marine algae, including many notable seaweeds. Most of the coralline algae, which secrete calcium carbonate and play a major role in building coral reefs, belong here. Red algae such as dulse and nori are a traditional part of European and Asian cuisine and are used to make certain other products like agar and food additives. 3 Many red algae have multicellular stages but these lack differentiated tissues and organs. Unlike most other algae, no cells with a flagellum are found in any member of the group. Unicellular forms typically live attached to surfaces rather than floating among the plankton, and both the larger female and smaller male gametes are non-motile, so that most have a low chance of fertilization. They have cell walls are made out of cellulose and thick gelatinous polysaccharides, which are the basis for most of the industrial products made from red algae.4 The chloroplasts of red algae are bound by a double membrane, like those of green plants; both groups (Archaeplastida) probably share a common origin. Their plastids formed by direct endosymbiosis of a cyanobacteria, and in red algae are pigmented with chlorophyll a and various proteins called phycobilins, which are responsible for their reddish color. Other algae that lack chlorophyll b appear to have acquired their chloroplasts from red algae, although their pigmentations are somewhat different.5 unicellular to multicellular (up to 1 m) mostly free-living but some parasitic or symbiotic, with chloroplasts containing phycobilins. Cell walls made of cellulose with mucopolysaccharides penetrated in many red algae by pores partially blocked by proteins (complex referred to as pit connections). Usually with separated phases of vegetative growth and sexual reproduction. Common and widespread, ecologically important, economically important (source of agar). No flagella. Ultrastructural identity: Mitochondria with flat cristae, sometimes associated with forming faces of dictyosomes. Thylakoids single, with phycobilisomes, plastids with peripheral thylakoid. During mitosis, nuclear envelope mostly remains intact but some microtubules of spindle extend from noncentriolar polar bodies through polar gaps in the nuclear envelope. Synapomorphy: No clear-cut feature available; possibly pit connections Composition: About 4,000 species. 6 CLASS Florideophyceae CLASS Bangiophyceae CLASS Rhodellophyceae DOMAIN Eukaryota - eukaryotes KINGDOM Plantae Haeckel, 1866 - plants SUBKINGDOM Biliphyta Cavalier-Smith, 1981 PHYLUM Rhodophyta Wettstein, 1922 - red algae 7 SUBPHYLUM Rhodellophytina Cavalier-Smith, 1998 CLASS Rhodellophyceae™ Cavalier-Smith, 1998 SUBPHYLUM Macrorhodophytina Cavalier-Smith, 1998 CLASS Bangiophyceae CLASS Florideophyceae There is a debate as to if Rhodophyta are plants or protists. 1. Red algae (phylum Rhodophyta) are chiefly marine multicellular algae that live in warmer seawater. 2. They are generally much smaller and more delicate that brown algae. 3. Some are filamentous, but most are branched, having a feathery, flat, or ribbon-like appearance. (Fig. 30.7) 4. Coralline algae are red algae with c