I don't see any post about this anywhere on Sciforums and I think it's an important discovery. The more the fossil record grows, the more it supports the fact of evolution.

http://news.bbc.co.uk/1/hi/sci/tech/4879672.stm

That's awesome. It's kinda funny to think that thing might be my great^1000 grandfather :p . Now why would god create an animal that swims in water, but has an early development of wrists?

Now why would god create an animal that swims in water, but has an early development of wrists?

Allows fish to move easier through shallow waters probably.

I don't see any post about this anywhere on Sciforums and I think it's an important discovery. The more the fossil record grows, the more it supports the fact of evolution.

http://news.bbc.co.uk/1/hi/sci/tech/4879672.stm

I was going to start a thread on it as well.
Transition Fossil Found (http://http://www.nytimes.com/2006/04/06/science/06fossil.html?th&emc=th)

Before I latch on to this I will want to do more research. There have been in the past remarkable fake fossil records.

Just because they say it is does not mean it is.
I'm a skeptic about any thing until I feel that the original source is trustworthy in my mind especially now a days in our media driven technological society that can create identity theft and make plain women stunning.

Before I latch on to this I will want to do more research. There have been in the past remarkable fake fossil records.

Just because they say it is does not mean it is.
I'm a skeptic about any thing until I feel that the original source is trustworthy in my mind especially now a days in our media driven technological society that can create identity theft and make plain women stunning.


Skepticism is a good thing. However, I have seen this reported on several highly rated news outlets. I am quite sure this is the real deal.

I have been to several evolution forums, and they are all abuzz.

Here is another article on it, complete with picture of the fossil and a model.

http://articles.news.aol.com/news/article.adp?id=20060406093109990001&ncid=NWS00010000000001

For those of us who study paleontology and vertebrate evolution, this is no surprise. Just read any books on the subject over the last fifty years and you'll see what I mean: we've known this all along. The morphological facts have always been there, but the creationists (now called "intelligent design" advocates) have been constantly denying and fighting the logical derivatives of what lies before their eyes that we have been excavating. We've already given them Coelacanths and Lungfishes as evidence of ocean-dwelling animals that evolved features that adapted them to be land-dwelling. Don't be surprised to read denials about this new finding as well.

For those of us who study paleontology and vertebrate evolution, this is no surprise.
Am I to infer from this that you study paleontology and vertebrate evolution?

Tiktaalik roseae now has its own homepage at: http://tiktaalik.uchicago.edu/

The important trait in Tiktaalik roseae (375 mya) is not that it had fins with structured bones that enabled it to walk on land, but that it has a fully-developed jawed crocodile-like mobile head, and that means that it had a well-developed brain. This is what links it to be an ancestor to modern tetrapods. It is thought to have evolved from Panderichthys – a lobed-finned Sarcopterygii fish (see below). For current discussions about Tiktaalik rosea go to: http://www.earthhistory.co.uk/technical-issues/tiktaalik-roseae/
http://scienceblogs.com/pharyngula/2006/04/tiktaalik_makes_another_gap.php

http://graphics8.nytimes.com/images/2006/04/05/science/05cnd-fossil.190.jpg[IMG/]

The earliest known fish fossils are being found in the Chengjiang fauna area near Kunming China in Yunnan Province are the best example we have of fast evolution radiating out from the “Cambrian Explosion.” Thousands of fossils have been found there dating back to 535 mya. Most of these are jawless soft-bodied fish in the subphylum Cephalochordates, but two species are among the oldest fossil “vertebrate” fish ever found, however none have bony skeletons or teeth. One species is a form of Cathaymyrus, a subphylum of Cephalochordates that include the present-day lancelets (Amphioxus). Lancelets are an important marine species to study because they have neural crest-like cells: a sign of a developing brain. DNA comparisons using lancelets suggests that vertebrate lineages may go back as far as 750 mya. Some paleontologists even believe that Cathaymyrus are the lineage that eventually evolved into humans. But the most well-known fossil at Chengjiang is the Myllokunmingia (530 mya) – a primitive Agnatha vertebrate fish that is thought to be related to present-day hagfish. Hagfish (and lampreys) are thought to have branched out from lancelets.

Other earliest known vertebrate fossils were found in the Deadwood Formation of Wyoming and the Burgess Shale Site in British Columbia Canada. These Late Cambrian (~500 mya) bone fossils are in the class called Agnatha that include lampreys and hagfish. Agnatha is a class in the phylum Chordata that is thought to be a sister class to Cephalochordata (see chart below). They are vertebrates, but they do not have a fully-developed compartmentalized brain like modern-day tetrapods have. They have a very simple brain. In the embryonic stage the nerve cord does not develop a neural crest that leads to separate compartments, such as a hypothalamus, or to a organized sensory limbic system that would enable it to have complex sense organs.

Placoderms (360-420 mya) are extinct but are said to have evolved from an advanced Agnatha. They were heavily-armored “jawed” fish with a cartilaginous skeleton. Some, however, evolved with a partial bony skeleton and a mobile head (sharks are thought to have evolved from an ancestral Placoderm). The mobile head of Placoderms is also articulated with a bony joint but is certainly not as advanced as Tiktaalik roseae. Placoderms lacked teeth.

Most fish today (95%) are bony fish called Teleostomi fish in the class Osteichthyes – a sister group ancestral related to the jawless Agnatha vertebrates. Sarcopterygii are “lobe-finned” Teleostomi fish that include rhipidistian fish, lungfish, and coelacanths. Rhipidistian fish evolved into lungfish. Most all paleontologists today think that either lungfish or coelacanths evolved into tetrapods that eventually evolved into humans. Lungfish - as the name implies - have lungs that it can use to breathe in or out of the water and have been around for 400 million years. Coelacanths, however, give birth to live young (live birth), and this sets them apart from all other fish.

Chordata:
A. Tunicata: sea squirts and tunicates
B. Cephalochordata:
1. Cathaymyrus or Branchiostoma: lancelet Amphioxus*
2. Pikaia: extinct invertebrate, a very primitive chordata, (Burgess Shale, 505 mya)
C. Vertebrata (7 classes):
1. Agnatha: jawless vertebrates
a. Myllokunmingia (530 mya)
b. Myxini or Hyperotreti: present-day hagfish,
c. Cephalaspidomorphi or Osteostracans
1. Hyperoartia: present-day lampreys
d. Gnathostomata: vertebrates with jaws
1. Placoderms: extinct, evolved from Agnatha
2. Chondrichthyes or “cartilaginous” fish: present-day sharks
3. Osteichthyes or “bony fish”:
1. Actinopterygii/Teleostoi or “ray-finned” fish: ~24,000 species, comprises 95%
of present-day fish and half of all vertebrates
2. Sarcopterygii or “lobe-finned” fish: present-day lungfish and coelacanths
4. amphibia
5. reptilia
6. aves
7. mammalian

* The lancelet does not have a vertebrate column: it has a notochord that gives it skeletal support. Above the notochord is a nerve cord but it has no brain, no eyes, and no heart; although it does have a single ventral blood vessel. It is thought that vertebrates evolved from ancestors similar to lancelets. However some paleontoligists believe that chordates evolved from tunicates via way of neotomy – the retention of juvenile features into the adult stage (tunicates have notochord, dorsal nerve cord, and a heart).
See: “The Biology of Chordates” http://ebiomedia.com/prod/BOchordates.html
also “The Early Vertebrates”
http://www-geology.ucdavis.edu/~cowen/HistoryofLife/CH07.html

Evolution of Tetrapod Legs from Sacropterygian Fish:

[IMG]http://people.eku.edu/ritchisong/forelimbs3.gif

Source: http://people.eku.edu/ritchisong/342notes1.htm

For a list of subphylum and classes of fish in the phylum Chordata, and a hypothetical list of the subclasses that led to tetrapod amphibians and mammals, see: http://en.wikipedia.org/wiki/Chordata
http://www.fmnh.helsinki.fi/users/haaramo/metazoa/Deuterostoma/Chordata/Vertebrata.htm#Actinopterygii

For a list of websites related to the Myllokunmingia or Haikouella found in China see:
http://www.factbites.com/topics/Myllokunmingia

http://graphics8.nytimes.com/images/2006/04/05/science/05cnd-fossil.190.jpg

Valich:

Thanks for the links. I personally find vertebrate evolution exceptionally fascinating, even though I specialized in botany.

Got any good links for the evolutionary loss of the sperm flagella in the flowering plants (which flagella are still present in the conifers)?

I'm very interested in the evolution of eukaryotes and prokaryotes but I don't know much about botany. Do any flowering plants have flagella? Flagella need a lquid - usually water - in order to fertilize. In terms of evolution the origin of flagella and the loss of flagella seem to coincide. Flagella are found in some mosses, ferns, and in some protists (some green algae - not all, heterokonts, dinoflagellates, cryptomonads, haptophytes, and euglenids). This seems to be the transition area. In his study guide, Dr. David Dilkes asks his students, "Give two reasons for the loss of flagella in plants." He doesn't give the answer, but I'm sure that contacting him would be an excellent resource for you. One answer would have to be lack of accessible surrounding moisture (ddilkes@credit.erin.utoronto.ca).

"Several hypotheses on the origin of cilia and flagella in eukaryotes have been proposed. The endosymbiont model postulates that these organelles may have derived from the symbiotic inclusion of spirochete bacteria, while the autogenous hypothesis favors the idea that cilia developed from further specialization of the cytoskeleton. In either case, the ancestral origin of the axoneme has been key for establishing main phylogenetic divergences. For instance, at the root of the eukaryote tree, the distinction between opisthokonts (animals, fungi, Chonozoa) and anterokonts (all other eukaryotes comprising plants and biciliates/bikonts) is based on whether the cilium is posterior or anterior. Cilia and flagella structure and function are very well conserved across evolution. The high degree of sequence conservation between flagellar proteins of unicellular organisms such as the biflagellate alga Chlamydomonas reinhardtii and mammalian ciliary proteins suggests that the functional role of the genes encoding cilia has been preserved throughout evolution. Chlamydomonas has been an advantageous system for studies of assembly and motility of cilia due to the ability to generate and detect mutants that cannot swim, and then to biochemically characterize their flagella. From these studies we can know that eukaryotic flagella are composed of more than 200 proteins. This large number of components is also present in mammalian cilia. Despite their overall structural similarities, the specialization of cilia for particular functions has resulted in significant variations of structure and regulation. To address these functional adaptations, a variety of model systems have been used. For instance, the gill cilia in mollusks have been studied for their capability to coordinate a precise filter feeding mechanism, the sperm flagellum in sea urchin employed for waveform motion analysis, the oviduct cilia in quail for analysis of ciliogenesis, and the cilia of the fish lateral line organ probed to understand sensory mechanistics. In the last few years, the generation of gene-targeted mice with deficient axonemal components has been critical for the investigation of numerous ciliary functions necessary for mammalian physiology, and their relation to human pathology." http://hmg.oxfordjournals.org/cgi/content/full/12/suppl_1/R27

"the ancestor of all extant eukaryotes must have been a single-celled organism with a 9+2 flagellum. Therefore, the central pair microtubule complex evolved very early as an essential element in flagellar motility, and this machinery has survived with little modification during evolution into today's phylogenetically diverse organisms. Flagella become paralyzed when either the central pair or radial spokes are missing."
http://www.jcb.org/cgi/content/full/166/5/709

In spermophyta seed plants the flagella is very reduced. See excellent evolutionary chart: http://www.erin.utoronto.ca/~w3bio151y/Dilkes10.html

Flagella in methanogens, cyanobacteria, spirochetes, spirilla, pseudomonads, vibrios:
http://www.bact.wisc.edu/Bact303/MajorGroupsOfProkaryotes

"Extreme segregation distortion [of alleles] occurs most commonly in spermatogenesis; meiotic drive alleles increase their transmission to the next generation by sabotaging gametes carrying alternative alleles. Causes defective, “curlicue” flagella, poor motility and impairs capacitation in wild-type sperm [in mice]."
http://www.universitychica.com/

Flagella need a liquid for fertilization: "The synapomorphies of the group [Charophyta] are said to include the the dissolution of the nuclear membrane during mitosis and the presence of paired flagella (when flagella are present at all) directed perpendicularly to each other.In addition, the charophytes are strongly inclined toward growth as long filaments." Evidently in some Charophyta green algae flagella are present and in some they are not, so this might be the place to look for the evolutionary transition.
http://www.palaeos.com/Plants/default.2.htm

There's a number of websites related to loss of flagella in protists:

"Flagella become paralyzed when either the central pair or radial spokes are missing," see "Bend propagation drives central pair rotation in Chlamydomonas reinhardtii flagella": http://72.14.207.104/search?q=cache:IBr-TJm4gvQJ:www.upstate.edu/cdb/mitcheld/publications/JCBv166p709.pdf+evolutionary+loss+of+the+sperm+fla gella&hl=en&gl=us&ct=clnk&cd=3

Loss of phototrophic nanoflagellates (PNAN): http://www.pubmedcentral.gov/articlerender.fcgi?artid=239220

Loss of flagella in Pennales:
http://www.elsevier.de/elsevier/journals/files/protist/issue4_99/0025.pdf.

No flagella found in pelobiont protist Pelomyxa corona:
http://72.14.207.104/search?q=cache:zf-3L2CK3kMJ:protistology.ifmo.ru/num3_4/frolov.pdf+loss+of+flagella+in+protist&hl=en&gl=us&ct=clnk&cd=4

Loss of flagella in Volvox with pics:
http://protist.i.hosei.ac.jp/PDB/Images/Chlorophyta/Volvox/

Flagella in ferns: http://www.yorku.ca/plants/163.PDF

Links to evolution of flagella: http://www.simonyi.ox.ac.uk/dawkins/WorldOfDawkins-archive/Catalano/box/published.shtml

"Because of multiciliate sperm, cycads show a nice connecting link with the more primitive spore-producing ferns, which must depend on free environmental water for the transport of their sperm, and the advanced seed plants in which the sperm are non-flagellated and non-motile." http://waynesword.palomar.edu/ww0803.htm

"The cilium in its early form would have been too short to function as a rowing device. What could it have done? The first flagellates are long gone, but we can still learn from the ones at the base of the family tree as it now exists. The soil dwelling flagellate Phalansterium is about as basal as any. It is hard to watch in action, but it probably uses its cilium to sense the environment and to collect bacteria to eat. The eukaryote family tree has two main branches, leading to plants and animals. At the base of these branches we find water dwelling flagellates that push water in opposite directions. Mastigamoeba creep along surfaces and move their cilium to create a slight current toward themselves, drawing in food particles. Choanoflagellates, on the line leading to animals, use their cilium to push water away. This draws in more water, and food along with it." http://www.talkdesign.org/faqs/icdmyst/ICDmyst.html

"Endogonales linker group from chytrids (loss of flagella) to ascomycetes and stem of other zygomycetes" http://taipan.nmsu.edu/EPWS472/zygo.html

"A monophyletic Kingdom Fungi is well defined and supported, and contemporary studies support the group as being most closely related to animals, possibly through a choanoflagellate-like ancestor....The Chytridiomycota is the only taxon within Kingdom Fungi that includes representatives which produce a flagellated stage at some point in their life cycle. Current phylogenetic analyses agree that some lineage of the Chytridiomycota occupies the most basal branch of Kingdom Fungi --a finding consistent with a choanoflagellate ancestor; however, there is conflict in the literature as to which group of the Chytridiomycota is most basal.... Is a choanoflagellate ancestor for fungi well supported? Where is the origin of DAP lysine biosynthesis in the fungal ancestry? Can character evolution (flagella, hyphae, etc.) be traced?.... Limited molecular data do not support the monophyly of either the chytrids or the zygomyctes, suggesting multiple losses of the flagellum. In addition the association of many zygomycete groups with arthropods suggests the possibility of multiple origins of a terrestrial fungus. We should be able to address the paraphyly of the Chytridiomycota/Zygomycota clades, the origin of nonplant associated terrestrial fungi (i.e., multiple orgins of terrestrial fungi), character evolution (loss of flagella, modes of sexual reproduction, etc.), and realignment of major taxa of early diverging fungi....aquatic fungi known as chytrids. Controversy exists still about whether the group is monophyletic and about the number of times flagella were lost among the group." http://lsb380.plbio.lsu.edu/network%20folder/network%20proposal

"soil-dwelling -proteobacterium Sinorhizobium meliloti engages in a symbiosis with legumes....Expression of chemotaxis and flagellar biosynthetic genes decreased sharply in minimal medium; these made up one-quarter of the 250 genes whose expression decreased. Loss of motility and partial loss of flagella were previously found in starved S. meliloti cultures (36). However, because our exponentially growing cultures were obviously not starving, this suggests that motility in S. meliloti is additionally linked to metabolic state. Alternatively, down-regulation of motility and chemotaxis may be linked to increased exo expression in minimal medium. Faster-swarming S. meliloti mutants show an increased proportion of motile and flagellated cells, more and longer flagella per cell, and decreased EPS synthesis (37). Consistent with this idea, we saw similar decreases in flagellar and chemotaxis gene expression when nodD3 is overexpressed during growth in TY, another condition that increases EPS synthesis (see below). Moreover, strains overproducing succinoglycan, either by deletion of exoR or by constitutive expression of exoS, show greatly reduced expression of flagellar and chemotaxis genes (data not shown); motility assays and microscopy show that these two mucoid strains are nonmotile and lack flagella (D. H. Wells, E. J. Chen, and S.R.L., unpublished data). This pattern of coordinate synthesis suggests that genes involved in EPS production and motility may be part of a complex multitrait adaptation, perhaps related to biofilm formation, that responds to diverse environmental stimuli." http://www.pnas.org/cgi/content/full/101/47/16636

Valich:

The sea plants have a very intersting morphology. They are also very diverse, from the extensively abundant unicellular diatoms, to the red algae, green algae, brown algae, etc., all of which seem to have arisen separately from non-plant eukaryotic ancestors by ingestion of prokaryotic photosynsthesizing cells which survived to become a 'chloroplast' with its own separate circular DNA [similar to mitochondria in the eukaruyotes] in each respective lineage.

Some sea plants have both haploid and diploid as the same full-sized adult morphology, whereas others have a diminutive haploid, and still others have the standard haploid as a single cell (egg and sperm), diploid as the adult plant.

It is far more complex than in animals (which have diploid as the adult, haploid as the sex cells, always).

In the land plants, which are believed derived from a green-algae ancestor, the mosses-liverworts have the haploid as the larger morphology, and the diploid is just a small little growth that arises where the egg cell is fertilized inside of an 'archegonium' which contains the egg, by a flagellated sperm that swims through rain water. The small diploid growth then 'fruits' and produces haploid spores (with four cell-nuclei inside each spore body), starting the process anew.

In the fern alliance, the haploid is about the same size as in the mosses/liverworts - about the size of your little pinky's fingernail, and likewise photosynthetic, but the diploid that arises by essentially the same method (flagellated sperm swimming through rainwater, fertilizing an egg inside of an 'archegonium') grows large and becomes vascular, with roots and shoots. It too produces 'fruiting bodies' (sori in ferns, on the underside of the leaves) that release spores, starting the process anew.

In the conifers and cycads, the spores are pollen and are produced in male cone structures, and when they land on a cone with a haploid archegonium (female cone), they grow a pollen-tube down into the archegonium, and release their flagellated sperm, which swim not through rain-water, but through the watery-medium of the pollen-tube, and fertilize the egg, which then grows into the baby diploid plant, but with subsequent arrested growth to allow the baby diploid to be coated and become a seed.

In flowering plants (both monocots and dicots), the same release of pollen occurs, but from a flower, not a cone, and when the pollen lands on a female flower, it grows a pollen tube down towards a very-highly-reduced archegonial structure. However, the sperm that are released are not flagellated as in the cone-plants and in the spore-bearing plants.

It would be interesting to see if they still have the DNA mechanisms for the formation of flagella, and perhaps just a few changes to prevent them from forming (much like chickens have the DNA mechanism for the formation of teeth - they just need the right hormone, but it is not longer produced because of a minor DNA change). I suspect they do.

So, what is the evolutionary advantage of not having the flagella on the sperm?

As you know from your readings, flagella and cilia are hypothesized to have originated from ingestion of prokaryotic cells, which became incorporated in the eukaryote which ingested them, conferring some advantage when they were not 'eaten alive' but instead became part of the eukaryotic cell.

Anyway, I find all of this fascinating, and every time a question is answered, it raises another one anew.

You appear to be well-read in biology - so perhaps you might pose this as an area of research to budding biologists.

Thanks for your efforts here. You might want to check out some of my other posts in nuclear physics, which is my field of expertise.

Regards,



Walter L. Wagner (Dr.)


PS On the post re biofuels, it's been suggested that various algae produce copious amounts of oils that could become bio-diesel. Do you have any ideas on how best to go about growing such algae, and can this be done in tanks on land? To me, it seems difficult to grow large quantities of algae on an economic basis competitive with growing of land plants for their oils, sugars, etc., though I know we routinely harvest some kelps, etc. for some purposes for our agars, ice-creams, and spam-musubis, etc.

Your insight might be a boon to a future bio-fuel economy!

Skepticism is a good thing. However, I have seen this reported on several highly rated news outlets. I am quite sure this is the real deal.

I have been to several evolution forums, and they are all abuzz.

No need for skepticism here, Tiktaalik is a great find! And it was reported in Nature, so: rock!
We've been talking about it in one latvian forum for weeks.

p.s. I'm extasic about the name they've given it, it sounds very cute when pronounced in latvian.

I’m not referring specifically to this case, but in general publication in Nature is by no means and assurance of accuracy. Nature and Science, the two premier generalist journals, have more retractions and corrections than any other high-impact journal. This is because they give high priority to publishing novel and exciting new discoveries which, by their nature, have only a relatively small amount of data and limited research performed on them.

Slightly out of topic: which journal would you suggest then?
I'm not a science student, but have a very keen interest in nature sciences and cosmology,
and don't like being fed bullshit or dumbed down text.

Actually the usual way is that novel findings are verfied independently in various journals. Nature and Science actually do not provide dumbed down text but rather more compressed versions as you would see in other journals. Fossil finds are a special case because they are not based on experiments that could be reproduced in similar systems. What could happen is that it turns out to be a fake, like the fake fossil bird that was presented in National Geographics (not science journal btw.). Interestingly, Nature and Science both rejected manuscripts regardings the finds of that fossil bird (before it turned out to be a fake, of course). Anyway, with time this finding might get consolidated, however it is already exciting as it is.

I didn't say I think Nature is dumbed down, of course not, I suggested criteria upon which Hercules might suggest me some other good journals on subjects that interest me.
I like Nature, but I'm not competent to judge which other less known journals are good.

The more the fossil record grows, the more it supports the fact of evolution.

http://news.bbc.co.uk/1/hi/sci/tech/4879672.stm

Unless of course a 3m fish with arms was just another reject from God's R&D labs. ;)

As you know from your readings, flagella and cilia are hypothesized to have originated from ingestion of prokaryotic cells, which became incorporated in the eukaryote which ingested them, conferring some advantage when they were not 'eaten alive' but instead became part of the eukaryotic cell.

Thanks for your efforts here. You might want to check out some of my other posts in nuclear physics, which is my field of expertise.You relay a lot of info that my brain has to digest. And it is very greatly appreciated! So unlike other critical replies on these forums that only tend to criticize, yours is very constructive.

By "ingestion" are you referring to endosymbiosis? If so, we are then in total constructive agreement. Endosymbiosis refers to the taking in to the membrane cell wall. Normally, we do not call this "ingestion."

No need for skepticism here, Tiktaalik is a great find! And it was reported in Nature, so: rock!
We've been talking about it in one latvian forum for weeks.

p.s. I'm extasic about the name they've given it, it sounds very cute when pronounced in latvian.No one is being skeptical here. This is indeed the so called "missing link" of the creationists that everyone was after. What I am emphasizing is the fact that Tiktaalik is not so important as the missing link of crawling out of water - something that paleontologists knew for decades - but the fact that it has a large completely-mobile head. This is an indication that it had a very well-developed brain. And this is what so dramatically sets it apart from Lungfish and Ceolocanths.

...flagella and cilia are hypothesized to have originated from ingestion of prokaryotic cells, which became incorporated in the eukaryote which ingested them, conferring some advantage when they were not 'eaten alive' but instead became part of the eukaryotic cell.
Endosymbiosis as the basis of eukaryotic cilia and flagella is one theory of their origin but has never been the most widely held theory. Or if it was, it certainly isn’t now. Close homologues of dynein ATPase motors (ie. the “motor” protein complexes that drive cilia/flagellum motion) have been identified in bacteria which suggests that eukaryotic cilia and flagella evolved from pre-existing bacterial components without the need for a hypothetical “spirochete endosymbiote”.

Yep. By 'ingestion" I meant being taken into the cell, but not 'digested', but instead remaining alive, aka "endosymbiosis". Over the ages, such 'organelles' become modified to a specialized function; thus mitochondria have DNA and ribosomes like that of bacteria, and likewise chloroplasts have their own separate DNA and ribosomes similar to the cyanobacteria. I haven't seen the data on the chloroplasts of the various types of algae to see to which separate lines of cyanobacteria they might be linked, if that is possible to determine.

Now, whether or not cilia and flagella arose by the same type of process as for those organelles is apparently debatable, though again, I haven't seen enough data on the subject to make an educated 'guess'. It appears that they are NOT separate 'organelles' with membranes, DNA and ribosomes, as are the mitochondria and chloroplasts, which argues against their origins in the same manner as those organelles, though I haven't yet excluded that as a possibility.

Now, in reading back through the Cycas genus of cycads, and viewing the many cilia obtained at the links provided by Valich, another question comes to mind:

Why do some sperm have flagella, and others cilia? Are they related? - I thought the microtubules were sufficiently different that they are posited to have separate origins?

And then back to my original question:

In the land plants, we see a trend from the mosses/liverworts having flagellated sperm for propulsion to the egg in an archegonium, to cycads having cilliated sperm for propulsion through a pollen tube to an egg in an archegonium, to flowering plants having sperm which 'drift', unaided by cillia or flagella, through a pollen tube to an egg in a highly reduced 'archegonial' structure (and coupled with "double fertilization").

So, what advantage is there to losing the flagella/cilia in the sperm? And, is the cilia of the cycads related to the flagella of the mosses, or did it arise separately? If so, is it a 'regurgitation' of a formerly lost trait (but with much of the original cellular mechanisms still intact, but just rendered non-functional), now rendered useful (by recovery of the de-activated piece)?

Anyway, I find plant evolution to be every bit as fascinating, if not more so, as animal evolution (which animals leave much better fossils, apparently, and like the dinosaurs, are much more lively than their contemporaneous plants, and thus make for more interesting videos for the kids).

I don't see how growing algae sufficiently enough can ever be a competitive bio-fuel.

"What is the evolutionary advantage of not having the flagella on the sperm?" What is the "advantage" in plants that pollinate in a dry environment?

Cilium and flagellum serve the same purpose so there's probably an environmentally determined evolutionary pressure: cilium mostly found in protozoans, flagellum in eukaryotes.

When you were referring to "conifers and cycads (grow a pollen-tube down into the archegonium, and release their flagellated sperm, which swim not through rain-water, but through the watery-medium of the pollen-tube)" were you just referring to clubmosses and ferns, or also pines, firs, and spruces?

As I said, I'm very weak in botany, but many biologist look at cyanobacteria as a possible universal common ancestor. If you looked through some of the web links that I provided, I noticed photos of some types of algae that had two flagellum almost 180 degrees apart? This seems dysfunctional. Perhaps in some species, when they started to evolve apart like that, they were eventually lost as vestigial organs.

"The synapomorphies of the group [Charophyta] are said to include the the dissolution of the nuclear membrane during mitosis and the presence of paired flagella (when flagella are present at all) directed perpendicularly to each other.In addition, the charophytes are strongly inclined toward growth as long filaments." In some green algae flagellum are present and in some they are not, so this might be the place to look for evolutionary loss. http://www.palaeos.com/Plants/default.2.htm

"Flagella become paralyzed when either the central pair or radial spokes are missing," see "Bend propagation drives central pair rotation in Chlamydomonas reinhardtii flagella": http://72.14.207.104/search?q=cache...us&ct=clnk&cd=3

"The first flagellates are long gone, but we can still learn from the ones at the base of the family tree as it now exists. The soil dwelling flagellate Phalansterium is about as basal as any. It is hard to watch in action, but it probably uses its cilium to sense the environment and to collect bacteria to eat. The eukaryote family tree has two main branches, leading to plants and animals. At the base of these branches we find water dwelling flagellates that push water in opposite directions. Mastigamoeba creep along surfaces and move their cilium to create a slight current toward themselves, drawing in food particles. Choanoflagellates, on the line leading to animals, use their cilium to push water away. This draws in more water, and food along with it." http://www.talkdesign.org/faqs/icdmyst/ICDmyst.html

Limited molecular data do not support the monophyly of either the chytrids or the zygomyctes, suggesting multiple losses of the flagellum. In addition the association of many zygomycete groups with arthropods suggests the possibility of multiple origins of a terrestrial fungus. We should be able to address the paraphyly of the Chytridiomycota/Zygomycota clades, the origin of nonplant associated terrestrial fungi (i.e., multiple orgins of terrestrial fungi), character evolution (loss of flagella, modes of sexual reproduction, etc.). Controversy exists still about whether the group is monophyletic and about the number of times flagella were lost among the group." http://lsb380.plbio.lsu.edu/network...work%20proposal

"soil-dwelling -proteobacterium Sinorhizobium meliloti engages in a symbiosis with legumes....Expression of chemotaxis and flagellar biosynthetic genes decreased sharply in minimal medium; these made up one-quarter of the 250 genes whose expression decreased. Loss of motility and partial loss of flagella were previously found in starved S. meliloti cultures... and additionally linked to metabolic state. Alternatively, down-regulation of motility and chemotaxis may be linked to increased exo expression in minimal medium. Faster-swarming S. meliloti mutants show an increased proportion of motile and flagellated cells, more and longer flagella per cell, and decreased EPS synthesis. Consistent with this idea, we saw similar decreases in flagellar and chemotaxis gene expression when nodD3 is overexpressed during growth in TY, another condition that increases EPS synthesis. Moreover, strains overproducing succinoglycan, either by deletion of exoR or by constitutive expression of exoS, show greatly reduced expression of flagellar and chemotaxis genes; motility assays and microscopy show that these two mucoid strains are nonmotile and lack flagella. This pattern of coordinate synthesis suggests that genes involved in EPS production and motility may be part of a complex multitrait adaptation, perhaps related to biofilm formation, that responds to diverse environmental stimuli." http://www.pnas.org/cgi/content/full/101/47/16636

http://loom.corante.com/img/Bork%20tree%20750.jpg

see: http://loom.corante.com/archives/2006/03/03/tree_of_life_c_2006.php

Tiktaalik roseae is a transitional species from aquatic fish to terrestrial land tetrapods. Or the "missing link" between the aquatic Ichthyostega fish and the amphibian Acanthostega.
http://www.nationmaster.com/wikimir/images/upload.wikimedia.org/wikipedia/en/thumb/4/4b/PleaisaidesZICA.png/200px-PleaisaidesZICA.png

Ichthyostega and Acanthostega are both in the genus "Eusthenopteron" and had internal nostrils which are found only in land animals and sarcopterygian fish. Eusthenopteron's notoriety comes from the pattern of its fin endoskeleton, which bears a distinct humerus, ulna, and radius and femur, tibia, and fibulare (in the pelvic fin). This is the characteristic pattern seen in tetrapods. It is now known to be a general character of fossil sarcopterygian fins. Coelacanths, although still alive today, are thought to have been the original ancestral species to Ichthyostega, which then evolved into Tiktaalik roseae.
http://www.nature.com/news/2006/060403/images/060403-7_large.jpg

http://www.nationmaster.com/wikimir/images/upload.wikimedia.org/wikipedia/commons/thumb/d/db/Fishapods.jpg/350px-Fishapods.jpg Late Devonian vertebrate saw lobe-finned fish like Panderichthys having descendants such as Eusthenopteron which could breathe air in muddy shallows, then Tiktaalik whose limb-like fins could take it onto land, preceding the first tetrapod amphibians such as Acanthostega whose feet had eight digits, and Ichthyostega with developed limbs, negotiating weed-filled swamps. Lobe-finned fish evolved into Coelacanth species which survive to this day.


"THE "GREAT" TRANSITION" by Neil Shubin

"The most primitive known tetrapod, is aquatic. It is not remotely specialized for life on land. It has fingers and toes but they are set within a limb that looks like a flipper. The limbs are delicate structures and seem unable to have supported the weight of the animal on land. It has a pair of hind limbs, but behind that is a tail that resembles that of a fish. Most important, this tetrapod has big gills.

The inescapable conclusion is that the most primitive tetrapod was an aquatic creature. The implications are profound: The fish-to-tetrapod transition likely happened not in creatures that were adapting to land but in creatures living in water. Moreover, everything special about tetrapods—limbs, digits, ribs, neck, the lot--might well have evolved in water, not on land....Buried within a 370-million-year-old shallow stream was a collection of whole skeletons, one on top of the other. One of these creatures is an astonishing new kind of fish.

The new fish has fins, scales, and gills. By all definitions, it is a fish. This designation seems to hold until we look at its skeleton. Inside the fin is the skeletal pattern of all tetrapod limbs, in primitive form. It has an arm bone, a forearm, even a wrist. The new fish has a neck much like that of the earliest amphibians. The skull of this fish is not cone-shaped, as fish skulls are, but flattened like a crocodile's, with a nostril on either side. This creature also has expanded ribs, something unknown in any fish.

Modern fish have adapted to live in very different environments, including on the sea floor, in the shallows of lakes or streams, even partly in air. To cope with these environments, they have a remarkable set of features that enable them to walk, breathe, and even climb. For example, the various species of walking fish have evolved "armlike" bones and joints allowing them to prop up and propel their bodies along the ground. Some fish, like the mudskipper, maneuver in mudflats and spend a considerable period of their lives outside water, able to breathe air because the back of their mouth can absorb oxygen and relay it to the bloodstream. Mudskippers can hop good distances on the mudflats; some of them even climb trees by reaching up the trunk with their front fins and holding on with their hind fins.

What is important is that these various adaptations to land have evolved many times in fish. Several different kinds of fish climb trees; in addition, there are many different species of fish that breathe air, live part of their life on land, and walk about. The boundary between water and land is quite porous and bridged by modern fish from around the world. In fact, the adaptations we see in the fossils of the fish-tetrapod transition seem almost trivial in comparison to the living animals.

We now know that the "great" transformation from water to land has so many fossil intermediates that we can no longer conveniently distinguish between fish and tetrapod, that living fish are bridging the water-to-land transition today, that some of the genes implicated in the ancient transition still reside and mutate in living animals, making everything from fish fins to human hands."

The evolutionary biologist Neil H. Shubin is chair of the Department of Organismal Biology and Anatomy at the University of Chicago. Excerpted from "Intelligent Thought," by John Brockman, 2006.

Tiktaalik roseae is 382 million years old and clarifies the evolutionary development from fish to animals with four limbs (tetrapods). Prior to this the earliest tetrapods were dated to about 376 million years ago. Coelacanths are Sarcopterygii or “lobe-finned” fish thought to be ancestral to Tiktaalik roseae, which is also classified as fossil Sarcopterygian fish.
In the Coelacanth, the skull is in two parts with an intracranial joint which allows up and down movement between them. A strong pair of muscles beneath the skull-base lowers the front half of the skull, giving the Coelacanth a powerful bite . Until the Tiktaalik roseae finding, the Coelacanth was the only living animal found with this type of structure. The eyes and olfactory organs are in the front part of the skull, and tiny brain and inner ear are in the rear. In the middle of the snout is a large cavity filled with a jelly-like sac which opens to the outside through three pores and may be used to detect weak electric currents and help the coelacanth to find prey. Most of the skeleton is made of cartilage. In place of the vertebral column, a large notochord extends from the skull to the tip of the caudal fin and serves as a backbone.
http://sacoast.uwc.ac.za/education/resources/fishyfacts/images/internal-anatomy.gif
http://sacoast.uwc.ac.za/education/resources/fishyfacts/coelacanth.htm
Fins on freshwater fish first began transforming into limbs some 380 million years ago and this was the evolutionary step that opened the way for vertebrates—animals with backbones—to emerge from the water. Tiktaalik roseae’s wide head and sharp teeth suggest it hunted much like a crocodile and that it also breathed air. The side of the snout has a big pair of external nostrils. The creature's long snout seems to be adapted for snapping at prey and hunting with its head above water like a crocodile.
Tiktaalik and the formerly discovered Elpistostege is placed between Panderichthys and tetrapods on the phylogenetic tree The following paper provides the data used to consider Tiktaalik as a new species: location found, taxonomy, nomenclature, and description of the fossil. The head was remarkably well preserved, and three specimens were found. Coelacanth has long been considered a transitional form because of its bony fins, but when discovered alive, did not use them for walking or raising itself up in any way. The second paper discusses the pectoral fin of Tiktaalik, which is “morphologically and functionally transitional between a fin and a limb.” The front fins allowed the creature to hoist itself up and drag its tail behind. Wrist bones containing five digits extend distally and are new features of this fossil:

“Here we report the discovery of a well-preserved species of fossil sarcopterygian fish from the Late Devonian of Arctic Canada that represents an intermediate between fish with fins and tetrapods with limbs, and provides unique insights into how and in what order important tetrapod characters arose. Although the body scales, fin rays, lower jaw and palate are comparable to those in more primitive sarcopterygians, the new species also has a shortened skull roof, a modified ear region, a mobile neck, a functional wrist joint, and other features that presage tetrapod conditions. The morphological features and geological setting of this new animal are suggestive of life in shallow-water, marginal and subaerial habitats… During the origin of tetrapods in the Late Devonian (385–359 million years ago), the proportions of the skull were remodelled, the series of bones connecting the head and shoulder was lost, and the region that was to become the middle ear was modified. At the same time, robust limbs with digits evolved, the shoulder girdle and pelvis were altered, the ribs expanded, and bony connections between vertebrae developed…. Panderichthys possesses relatively few tetrapod synapomorphies [convergent features], and provides only partial insight into the origin of major features of the skull, limbs and axial skeleton of early tetrapods[. In view of the morphological gap between elpistostegalian fish and tetrapods, the phylogenetic framework for the immediate sister group of tetrapods has been incomplete and our understanding of major anatomical transformations at the fish–tetrapod transition has remained limited.

A phylogenetic analysis of sarcopterygian fishes and early tetrapods supports the hypothesis that Tiktaalik is the sister group of tetrapods or shares this position with Elpistostege. Tiktaalik retains primitive tetrapodomorph features such as dorsal scale cover, paired fins with lepidotrichia, a generalized lower jaw, and separated entopterygoids in the palate, but also possesses a number of derived features of the skull, pectoral girdle and fin, and ribs that are shared with stem tetrapods such as Acanthostega and Ichthyostega. Tiktaalik is similar to these forms in the possession of a wide spiracular tract and the loss of the opercular, subopercular and extrascapulars. The pectoral girdle is derived [sic] in the degree to which the scapulocoracoid is expanded dorsally and ventrally, and the extent to which the glenoid fossa is oriented laterally. The pectoral fin is apomorphic [i.e., derived, more developed] in the elaboration of the distal endoskeleton, the mobility of segmented regions of the fin, and the reduction of lepidotrichia distally.”1

“The pectoral skeleton of Tiktaalik is transitional between fish fin and tetrapod limb. Comparison of the fin with those of related fish reveals that the manus [hand] is not a de novo novelty of tetrapods; rather, it was assembled in fishes over evolutionary time to meet the diverse challenges of life in the margins of Devonian aquatic ecosystems. The concept of “missing links” has a powerful grasp on the imagination: the rare transitional fossils that apparently capture the origins of major groups of organisms are uniquely evocative. But the concept has become freighted with unfounded notions of evolutionary ‘progress’ and with a mistaken emphasis on the single intermediate fossil as the key to understanding evolutionary transitions. Much of the importance of transitional fossils actually lies in how they resemble and differ from their nearest neighbours in the phylogenetic tree, and in the picture of change that emerges from this pattern.

“The fins are adapted to flex gently upwards - as if the fin were being used to support the body. One of the interesting differences between fins and Tiktaalik limbs is that the later contain bones that comprise mobile wrist and ankles….Although the small distal bones bear some resemblance to tetrapod digits in terms of their function and range of movement, they are still very much components of a fin. There remains a large morphological gap between them and digits as seen in, for example, Acanthostega: if the digits evolved from these distal bones, the process must have involved considerable developmental repatterning. The implication is that function changed in advance of morphology.”2

“Of course, there are still major gaps in the fossil record. In particular we have almost no information about the step between Tiktaalik and the earliest tetrapods, when the anatomy underwent the most drastic changes, or about what happened in the following Early Carboniferous period, after the end of the Devonian, when tetrapods became fully terrestrial. But there are still large areas of unexplored Late Devonian and Early Carboniferous deposits in the world – the discovery of Tiktaalik gives hope of equally ground-breaking find to come.”3

1Daeschler et al., “A Devonian tetrapod-like fish and the evolution of the tetrapod body plan,” Nature 440, 757-763 (6 April 2006) | doi:10.1038/nature04639; Received 11 October 2005; ; Accepted 8 February 2006.

2Shubin et al., “The pectoral fin of Tiktaalik roseae and the origin of the tetrapod limb,” Nature 440, 764-771 (6 April 2006) | doi:10.1038/nature04637; Received 11 October 2005; ; Accepted 8 February 2006.

3Per Erik Ahlberg and Jennifer A. Clack, “Palaeontology: A firm step from water to land,” Nature 440, 747-749 (6 April 2006) | doi:10.1038/440747a.

http://afarensis.blogsome.com/images/Fin1.JPG

“If the five radials of Tiktaalik are homologous to digits, then the axis of the tetrapod limb would extend from the humerus through digit three. Unfortunately, the absence of a well-defined axis in other tetrapodomorphs leaves uncertain whether a central axis is primitive for tetrapods or if it evolved separately in Tiktaalik. Testing these competing hypotheses awaits the discovery of other tetrapodomorph fins with axes that project into the distalfin. The pectoral skeleton of Tiktaalik is transitional between fish
fin and tetrapod limb.” http://afarensis.blogsome.com/2006/04/19/tiktaalik-roseae-and-the-origins-of-tetrapods/

Taxonomy of lungfishes presents some difficulty because of their resemblances to both fish and land-dwelling vertebrates, and have been classified in a variety of ways, ranging from class Dipnoi, to infraclass Dipnomorpha, to order Dipteriformes. However, there is general agreement that there are two main subcategories, here given as orders: Vertebrata is a subphylum of chordates, specifically, those with backbones or spinal columns. ...

A Partial Taxonomy of the Tetrapods:
Phylum Chordata
Class Dipnoi (lungfish)
Class Sarcopterygii
Subclass Coelacanthimorpha (Coelacanths)
Subclass Tetrapodomorpha
Genus Eusthenopteron
Genus Panderichthys (also had large tetrapod-like head)
Genus Tiktaalik roseae
Superclass Tetrapoda
Family Elginerpetontidae
Family Acanthostegidae
Family Ichthyostegidae
Family Whatcheeriidae
Family Crassigyrinidae
Family Loxommatidae
Family Colosteidae
Class Amphibia - Amphibians
Class Sauropsida - Reptiles
Class Aves - Birds
Class Synapsida - Mammal-like reptiles
Class Mammalia - Mammals

Tiktaalik (pronounced "tic-TAH-lick") rosea is an icon of evolution in action - like Archaeopteryx, the famous fossil that bridged the gap between reptiles and birds. As such, it is a blow to proponents of intelligent design.

It was a predator with sharp teeth, a crocodile-like head, and a body that grew up to 2.75 metres (9ft) long. It had eyes on top of the skull rather than on the side like fish, and the beginnings of a neck. It lived in shallow waters, pulling itself along the bottom with its arm-like fins. It used its neck to raise its head above the surface, to breathe and possibly to capture prey. It could also move its head independently of its shoulders like land animals can do today. But the creature’s jaws and snout were very fishlike and it had scales and fins. Three specimens of the creature were found, providing a clear picture of a pivotal moment in the evolution of life.

Dr Clack said that, judging from the fossil, the first evolutionary transition from sea to land probably involved learning how to breathe air. "Tiktaalik has lost a series of bones that, in fishes, covers the gill region and helps to operate the gill-breathing mechanism," she said. "The air-breathing mechanism it had would have been elaborated and having lost the series of bones that lies between the head and the shoulder girdle means it's got a neck, it can raise its head more easily in order to gulp the air. "The flexible robust limbs appear to be connected with pushing the head out of the water to breathe the air….it probably had lung as well as gills [to breathe].” http://www.guardian.co.uk/science/story/0,,1747926,00.html

Palaeontologists knew that lobe-finned fishes evolved into land-living creatures during the Devonian Period. But fossil records showed a gap between Panderichthys, a fish that lived about 385 million years ago which shows early signs of evolving land-friendly features, and Acanthostega, the earliest known tetrapod (four-limbed animals) dating from about 365 million years ago.
http://newsimg.bbc.co.uk/media/images/41525000/gif/_41525972_fish_transition_416.gif

The team found the three fossils in an area of the Arctic called the Nunavut Territory. "When we look inside the fin, we see a shoulder, we see an elbow, and we see an early version of a wrist, which is very similar to that of all animals that also walk on land," said Professor Shubin. Professor Jennifer Clack, from the University of Cambridge, said that the find could prove to be as much of an "evolutionary icon" as Archaeopteryx - an animal believed to mark the transition from reptiles to birds. http://news.bbc.co.uk/2/hi/science/nature/4879672.stm

http://afarensis.blogsome.com/images/T1b.JPG

Notice the mammal-like ribs: “The back of its head also had features like those of land-dwellers. It probably had lungs as well as gills [like lungfish], and it had overlapping ribs that could be used to support the body against gravity,” Shubin said.

From: http://afarensis.blogsome.com/2006/04/19/tiktaalik-roseae-and-the-origins-of-tetrapods

Valich:

Thanks for your dedication to this area.

Just a thought. For the animals, arthropods colonized the land first (they already had legs!), and during the time that Tiktaalik was crawling around in the water, the air must have been teeming with lots of flying insects; a food resource most fish would not have access too.

By bringing the head out of the water, some fish could grab those insects. Over time, it would make sense for the eyes to adjust to a forward vision (both eyes on top of the head) to enhance the capability of correctly aiming for and grabbing a flying insect.

Likewise, allowing the head independent motion would facilitate grabbing of flying insects.

I suspect that those traits arose first, in that order, and it would be interesting to find additional fish transitional to Tiktaalik to see if my suspicion is correct.

Finally, by moving the head forward by propulsion of fins firmly on the underwater ground, the head could be positioned to accurately catch such flying insect. Thus, it would be advantageous to have firm control over those fins for fine motor movement, which would give rise to bones and muscle attachments in the frontal limbs (and possibly posterior limbs too).

Once those adaptations are in place, such fish might grow larger to capture other food sources besides flying insects (which I understand grew huge, up to a foot in size, in those days), likely other fish in shallow waters trying to get away from a monster fish with its head out of the water.

Anyway, just a thought.

Now, back to the genus Cycas. Its sperm have thousands of cilia, not two flagella. We usually see cilia in single-celled organisms, though even large land animals have cilia I believe (such as lung tissue, which we use to clean the cells of foreign particulate matter). So, what happened to the cilia in the lower land plants (mosses/liverworts) in their sperm, which have flagella instead? Are cilia something that lie dormant through extensive changes in species over time, being able to erupt anew (as a genetic fluke again triggering a long-dormant cilia pathway) when environmental conditions favor their presence?

Reading through some of your links, I now suspect that cone-structures likely arose twice in the plants. Cycas does not have cones (the seeds are on the tips of specialized leaves, and is a primitive cycad, whereas the more advanced cycads have the seed-bearing leaves reduced to a cone structure, which morphologically look very much like pine cones, etc. They are hard to tell apart, just by superficial examination, for a lay person.

However, as you likely know, the conifers (pines, etc.) have a high-quality wood, and are nothing like the trunks of the cycads, which do not branch, and are rather like palms in morphology.

Instead, the conifers have wood similar to Ginkgo (which also bears seeds, but not in a cone), etc.

I suspect therefore that the morphology of a cone arose independently in both the cycads and in the conifers (due to similar environmental pressures and advantages); with the cycads initially having seeds on leaf tips (like in Cycas) which became modified into cones in more advanced cycads; and with the woody plants developing various types of reproductive structures (cones, flowers, etc.) from early modified leaves. The monocots are believed to be an early flower that reduced and lost its ability to form wood trunks, and then subsequently enhanced to form the typical monocot trunk. I won't go into the differences between the two in this little post.

Anyway, that is my surmise regarding the cone-bearing plants; do you have any insight along those lines?

DNA analysis has now pushed the time-line back for vertebrata to about 560 mya: Arthropoda evolved ~500 mya. Do you have any evidence to the contrary? I don't know.

From what I have been reading, cilium is a mutation of flagellum: multiple short hair appendages compared to the longer flagellum.

Cycads evolved during the Permian over 200 million years ago and are almost extinct: few and far between in the rain-soaked tropics. In this water-soaked environment the multiciliate sperm can swim. The cilium - sometimes called a spiral band of flagella - are effective. Why a spiral band? Still, although they are closely related to ferns, fern habitat area are not so moist, and some have lost their flagella. Therefore, I think it is better to look for this loss in the evolution of fungi when cytrids diverged from the group: they lost flagella. I'm looking into it - time permitting - but I'm mostly researching genetics and bilateria eukaryote paleontology.

"Cilia differ from flagella only in their number per cell. They are usually quite short and cover often the whole surface of a cell. Cilia are rare in plants, an often cited example are the zoospores of Vaucheria sessilis. With algae (except red algae) are flagellated stages common. They are often found with the spermatozoids (male germ cells) of mosses and ferns. Early during the evolution of seed plants were flagellated stages more and more driven out. Among the few still existing exceptions are the spermatozoids of Gingko biloba and the cycads.

Movements are often controlled by extern signals. Many protists are attracted by certain sources of stimulation called taxis: light (phototactic behaviour) or certain chemicals (chemotactic behaviour). Usually follows the motion a concentration or intensity gradient. If a threshold of sensation is passed, begins a reverse reaction. During the last decades was signal recognition a much-studied topic. We know, for example, that the carotenoids within the stigma of some algae (Euglena, for example) are sensitive to blue light. The chloroplast movements of the alga Mougeotia are controlled by the phytochrome system and germ cells (of algae) react to species specific sexual attractants. But how the perceived signal is converted and how signals of the same or the opposite kind are co-ordinated in a directed movement is not even basically understood (black box). The basis of many flagella is equipped with a complexly structured basal body." http://www.biologie.uni-hamburg.de/b-online/e25/25b.htm#cilia

Tiktaalik is reported to have arisen circa 382 million years ago, long after the Arthropoda arose in the seas. I believe the Arthropoda colonized the land not long after.

However, I don't have the exact time-lines handy I believe the Arthropoda evolved from an Onychopohrean ancestor (which could metabolize Chitin, and had leg-like appendages for walking), which in turn arose from segmentned worms. I suspect this occured initially on the land, with the Chitin on the Onychophore to prevent dessication. However, since even the worms and Onychophores colonized the land, I'm not even certain if the arthropods arose on land first, and then colonized the oceans, or in the sea first, and then colonized the lands. Got any insights along those lines? In any event, it appears the flying arthropods were around when the first amphibians arose.

Yes, but by sequencing DNA from hundreds of vertebrate fossil fish, mostly coming out of the Chengjiang fauna area near Kunming China, they have projected the origin of vetebrata back to at least 560 mya. Personally, I think it's now pushed back to about 600 mya. The discovery of Myllokunmingia fengjiaoa, similar to present-day hagfish, dates to the Early Cambrian 530 mya. "Myllokunmingia is among the oldest vertebrate animal ever found...and has aroused great interest in the palaeontological community, as these fossils extend the known time-span of the vertebrates back another 50 million years." see:http://www.gs-rc.org/repo/repoe.htm

I think you should focus the origin of the evolutionary loss of flagella on more basal groups like algae and bacteria than in flowering plants, ferns or cycads. Euglena are oldest group of eukaryotic algae, abundant in freshwater, and have either one or two flagella. In chlamydomonadaceae algae (solitary doubly-flagellated plant-like algae common in fresh water and damp soil) some have two flagellum of equal length, some with one longer than the other, and others with none at all:

“Euglenophyte Flagellar Apparatus:
1. Ampulla evolved from separate flagella and the cytostome (cell mouth).
2. Contractile vacuole: adjacent to ampulla; discharges excess water into ampulla.
3. Paraflagellar rod: protein structure at the roots of flagella, makes flagella appear thicker, involved in flagella motion control.
4. Flagellar roots: bands of microtubules from flagella bases to cytoplasm, act like muscles (control cell shape); striated connective between flagella bases coordinates flagellar motion.” http://www.jochemnet.de/fiu/bot4404/BOT4404_14.html

“Fixation and Measurements of Chlamydomonas Flagella: All cells, even those without flagella, show a discontinuity in the cell membrane where the base of the flagella should be located. If you can see the "bumps" where the flagella should be, but do not see any evidence of flagella, then chances are you do indeed have a cell without flagella.” http://www.ruf.rice.edu/~bioslabs/studies/invertebrates/chlamfix.html

Flagella loss from mutations in aeromonads:

“Aeromonas salmonicida is an important pathogen of salmonid fish, producing the systemic disease furunculosis. As in Vibrio parahaemolyticus, two types of flagella are responsible for motility in aeromonads. A polar unsheathed flagellum is expressed constitutively that allows the bacteria to swim in liquid environments. In media where the polar flagellum is unable to propel the cell, aeromonads express peritrichous lateral flagella, a phenomenon associated with the colonization of surfaces, as such hyperflagellated cells demonstrate increased adherence. We have demonstrated the importance of the polar flagellum of A. hydrophila in the invasion of fish cell lines. More recently, we have described a polar flagellar gene region in A. caviae that appears to be essential for adherence to human epithelial cells in vitro. Traditionally, the genus Aeromonas has been divided on the basis of motility, with A. salmonicida being the typical nonmotile species. However, five A. salmonicida isolates were able to produce a pole-located sheathed flagellum when grown at supraoptimal incubation temperatures (30 to 37°C) and in the presence of 18% (wt/vol) Ficoll. Incubation under these conditions never renders more than 1% of the population motile (twisting/tumbling movement) or flagellated….Mutation of Aeromonas lafB or lafS or both A. caviae lateral flagellin genes caused the loss of lateral flagella and a reduction in adherence and biofilm formation…. The AH-1982 (lafB) and AH-1983 (lafS) mutant strains of A. hydrophila and mutant strain AAR9 (lafB) or tandem flagellin mutant strain AAR6 (lafA1 lafA2) of A. caviae produced polar flagella but not lateral flagella. Mutant AH-1984 (lafT) of A. hydrophila produced polar and lateral flagella but was nonmotile. Mutant AAR6 was unable to be complemented by plasmid pINA1 (lafA of A. salmonicida with the putative transposase inserted), as lateral flagella were not detected by EM.” From: “A Colonization Factor (Production of Lateral Flagella) of Mesophilic Aeromonas spp. Is Inactive in Aeromonas salmonicida Strains,” by Susana Merino, Rosalina Gavín, Silvia Vilches, Jonathan G. Shaw, and Juan M. Tomás,Departamento Microbiología, Facultad Biología, Universidad Barcelona, 08071 Barcelona, Spain, Division of Molecular and Genetic Medicine, University of Sheffield Medical School, Sheffield S10 2RX, United Kingdom, 21 October 2002. http://aem.asm.org/cgi/content/full/69/1/663

“IFT88 from Chlamydomonas (green algae) is composed of 782 amino acids. It shows 42% sequence identity with its homolog in mice. However, a BLAST search using Chlamydomonas hits many non-flagellar proteins….Mutation in IFT20 also prevents formation of flagella [9]. IFT20 is one of the smallest components, being composed of only 135 amino acids. It’s a unique protein, with none of the recognized domains, and algal sequence shows 32% identity to sequence found in mouse….mutations in IFT46 also result in the inability to assemble flagella.” From: “Assembling the Eukaryotic Flagellum: Another Example of IC?” http://www.idthink.net/biot/eflag2/index.html

See also: “Intraflagellar transport balances continuous turnover of outer doublet microtubules : implications for flagellar length control [in biflagellate alga Chlamydomonas],” Wallace F. Marshall and Joel L. Rosenbaum, Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520. The Journal of Cell Biology, Volume 155, Number 3, October 29, 2001 405-414. http://www.jcb.org/cgi/content/full/155/3/405

“Cloning and characterization of the region III flagellar operons of the four Shigella subgroups: genetic defects that cause loss of flagella of Shigella boydii and Shigella sonnei.” by A A Al Mamun, A Tominaga, and M Enomoto, Department of Biology, Faculty of Science, Okayama University, Japan. J Bacteriol. 1997 July; 179(14): 4493–4500. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=179284

Loss of flagella in pseudomonas - rod shaped, motile, gram-negative bacteria found in soil and water possessing one or more polar flagella. Transcription factor mutations causes loss of flagella:

“The pseudomonads comprise a diverse group of bacteria found ubiquitously in heterogeneous environments. Pseudomonas fluorescens, a common soil microorganism, is a proposed agent for biocontrol, plant growth promotion, and bioremediation and is closely related to Pseudomonas aeruginosa, a human pathogen in immunocompromised individuals and cystic fibrosis patients. The discovery of a large number of genes for regulatory proteins in the P. aeruginosa genome suggests that this genus is finely tuned to respond to its environment. Hence, the study of P. fluorescens in soil provides a model system to dissect genetic traits important for adaptation to various environments. Our research studies of P. fluorescens and its activity in soil have led to the discovery of adnA, a gene affecting flagellar production, motility, and attachment to sand and seeds….AdnA is a transcription factor in Pseudomonas fluorescens that affects flagellar synthesis….we identified seven different putative open reading frames (ORFs) activated by AdnA (named aba for activated by AdnA). aba120 and aba177 showed homology to flgC and flgI, components of the basal body of the flagella in Pseudomonas aeruginosa.…. Synthesis of flagella seems to progress in a cascade manner, in which expression and assembly of early genes are required before activation of late genes. FleQ and its antiactivator, FleN, are placed high in the cascade and control transcription of a number of structural genes of flagella and of fleSR, another two-component regulatory system in P. aeruginosa . FleQ regulates transcription of several flagellar genes including fliD, the flagellar cap protein that mediates attachment to respiratory mucin and is thus important in virulence of P. aeruginosa.

Under certain environmental conditions, flagella are necessary for biofilm formation in P. fluorescens, but this effect is abolished when culture conditions include iron and/or citrate in the medium. Our observations that AdnA affects phenotypes important for soil activity and biofilm formation prompted the search to identify genes regulated by this factor and provide a genetic handle by which to study the effects of a specific regulon on biofilm formation. We generated random transcriptional fusions in the genome of a host in which the adnA gene had been deleted and screened for adnA-mediated change in expression. In addition to genes coding for early components of flagella and chemotaxis, as expected by the homology of AdnA to FleQ, we found open reading frames (ORFs) affected by AdnA with no clear connection to flagellar synthesis and other ORFs with no known function. The results of sequence and promoter analyses that also examined the flanking regions of the ORFs suggest a total of 23 genes affected by AdnA including at least two multiple gene operons. Phenotype studies of the strains with insertion mutations in the absence and presence of AdnA indicate that AdnA is required for flagellar production and biofilm formation but that the biofilm formation defect can be suppressed by mutations in other genes in the AdnA regulon….The formation of flagella appeared to be affected in four of seven insertion mutants. All the insertion mutants showed lack of flagella in the absence of adnA, whereas aba120, aba160, aba175, and aba177 mutants lacked flagella in the presence of adnA. These results suggest that these insertions affected genes coding for components of the flagellum or its assembly.

Complementation with adnA did not restore the formation of flagella in four mutants (aba120, aba177, aba160, and aba175 mutants), indicating that the insertions were in genes involved in flagellar synthesis. The insertion in the aba160 mutant was in a putative rfbE gene, suggesting a role in LPS synthesis. Alterations in the expression of LPS can interfere with the assembly of flagella. Thus, it may not be surprising that AdnA affects flagellum formation at different levels, including the assembly step in which LPS seems to be involved. If this were true, the AdnA homologues would assume an essential role in pathogenesis, especially in bacterial pathogens such as P. aeruginosa and V. cholerae in which LPS is one of the most important virulence factors. The complementation with adnA in aba18, aba51, and aba203 mutants restored flagella and motility indicating that these genes are not involved in flagellar synthesis and may participate in novel aspects of cell physiology. The sequence interrupted in aba203 has no similarity to any predicted genes. The flanking regions in the insertions of aba18 and aba51 gave matches to different MCPs in P. aeruginosa. These transmembrane receptor proteins detect environmental signals and activate the components of a cytoplasmic phosphorylation cascade that controls the direction of flagellar rotation. Our results suggest that adnA is also involved in the regulation of transmembrane components of the chemotaxis system.”

From: “Genetic Analysis of the AdnA Regulon in Pseudomonas fluorescens: Nonessential Role of Flagella in Adhesion to Sand and Biofilm Formation,” by Eduardo A. Robleto, Inmaculada López-Hernández, Mark W. Silby, and Stuart B. Levy, Center for Adaptation Genetics and Drug Resistance, Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, 9 October 2002. http://jb.asm.org/cgi/content/full/185/2/453

Yes, extinct arthropoda date back to the Early Paleozoic ~500 mya. Vertebrata evolved in the ocean, but as has been shown with Tiktaalik, they did not evolve appendages to allow them to crawl on land until perhaps ~400 mya. Probably earlier?

How is it that DNA can be sequenced from fossil vertebrates (fish?) from 560 mya, when I believe that there is no actual DNA in the rocks? Aren't they instead sequencing DNA from extant fish, and comparing it with other extant notochordates and using that as an estimate for the time of divergence, by comparing similar strands of DNA for similar genes used by both, and counting up random mutations as a form of biological clock? If so, those estimates can be off.

In any event, I suspect that an accurate analysis of the arthropods would show that there were flying critters (likely insects) when Tiktaalik-like species began emerging from the waters, using the flying critters as a new and abundant food source. Intense competition for such an un-exploited abundance of food would have readily driven vertebrate fish to develop the Tiktaalik-like morphologies, as discussed previousy, including eyes designed for out-of-water use, a head that was free to move relative to the body, and fins with rudimentary bones/muscles to exert superior motor control of the bodies lunging motion. Indeed, it seems quite probable that the emergence of flying arthropoda stimulated the emergence of vertebrates that began capitalizing upon that new food source, and without those flying critters, the Tiktaalik-types would not have emerged. Quite an interesting concept, that vertebrate arms and legs are because of flies!

Only later did further competition result in actual more fully developed arms and legs, and an ability to exit the water, which also opened up many additional food sources for emerging amphibians who could crawl to a better swimmin hole.

Anyway, as I wrote previously, it's interesting to dwell on these concepts, as they stimulate new areas of potential research, and might well result in additional discoveries, which keep on enhancing our knowledge of how we got here.

Maybe I should say something that eukaryotic flagella are a totally different structure from prokaryotic ones. They are absolutely not homologous.
But that would infuse some kind of meta-knowledge to a very thorough copy/paste thread...
I think I should go back to sniggering a lot.

There's no question that amphibians, then reptiles, then mammals evolved from fish, but you're absolutely right that arthropoda date back way before fish came out of the water: anthropoda ~500 mya, vertebrata ~400 mya. Paleontologists make the projections based on the geological substratems, the environmental conditions, and the mutation rates that occur depending on a multitude of facters. I'll try to find the original article(s) that explain this deeper.

I think eukaryote and prokaryotic cells must have had a falagella and cillium common to a phenotype environmential-determined origin. Prokaryotic cells have either a whip-like flagella for locomotion or a hair like pili (cilium) for adhesion. Archaeal flagellum are thought to be analogous, but not homologous, to eubacteria in that no known bacteria has the same type of pili.

I admit that I'm not secure in this position, but in evolution I tend to examine the more environmentally-influenced factors than genotype mutations.

Valich:

I found a good web site that addresses Eukaryote evolution, giving some 60 separate lineages of Eukaryotes extant today. http://tolweb.org/Eukaryotes/3 I'm sure that more exist.

However, it still left open the question as to how the Eukaryotes developed their complexity from a far simpler eubacteria or archaea. Spindle apparatus, mitosis and meiosis are all hallmarks of the Eukaryotes, and of course such single-celled organisms left no fossil records over the billions of years of their evolution. Once such Eukaryotes dominated in the eat-or-be-eaten world in which they lived, they thereafter developed additional organelles such as mitochondria and chloroplasts, giving rise to some of the 60+ lineages currently recognized.

For an intersting development in physics, see Grav's post on the Grand Puzzle. His first post, and it's great.

Endosymbiosis. Almost every article I read about the origin of cilia and flagella in eukaryotes traces it to a prokaryote or archae symbiotic host relationship. I'll put together a brief compilation later tonight.

On the question about paleontology dating, biostratigraphy and superposition determine the age of fossils but this method of dating does not explain transitions. As you know, radiometric dating (potassium/argon, argon/argon, uranium, carbon-14) accurately establishes dates up to 50,000 mya and the decay rates tell us that the earliest known fossils were cyanobacteria (~3.5 bya) and the earth is ~4.6 bya. Paleologists correlate anatomical structures, metabolic structures, geography, climatology, genetic sequencing, polymerase chain reaction, and mutation rates. There are about a dozen computer programs that can be used to input all this data to get a phylogenetic tree, some require an unfeasible large amount of time and computational ability to run. Stephen J. Gould’s punctuated equilibrium theory was a starting point in history that led to explanations of patterns of stasis and transitions.

Mutations in DNA synthesis occur at measurable rates that vary according to exogenous factors. Taking these factors into consideration, mutation rates can be predicted and used for fossil dating. Polymerase chain reaction has successfully analyzed mammoth DNA to date them at 40,000 yrs.. Morphology in similar species can be used to establish mutation rates according to various phenotypes. Further, DNA sequences can be used in conjunction with molecular biology (genomics), molecular phylogeny (phylogenetics) and numerical morphological taxonomy (phenetics) in comparing fossils with other ancient organisms to establish a timeline.

Haplotypes are determined from different taxons and used as an out group for comparisons with other haplotypes. The base sequences are then compared:

"In the simplest case, the difference between two haplotypes is assessed by counting the number of locations where they have different bases: this is referred to as the number of substitutions (other kinds of differences between haplotypes can also occur, for example the insertion of a section of nucleic acid in one haplotype that is not present in another). Usually the number of substitutions is re-expressed as a percentage divergence, by dividing the number of substitutions by the number of base-pairs analysed: the hope is that this measure will be independent of the location and length of the section of DNA that is sequenced. An alternative approach is to determine the divergences between the genotypes of individuals by DNA-DNA hybridisation instead of by determining and comparing gene sequences. The advantage of using hybridisation rather than gene sequencing is that is based on the entire genotype, rather than a particular section of DNA. Its disadvantage is that precise haplotypes are not determined. Once the divergences between all pairs of samples have been determined, the resulting triangular matrix of differences is submitted to some form of statistical cluster analysis, and the resulting dendrogram is examined in order to see whether the samples cluster in the way that would be expected from current ideas about the taxonomy of the group, or not. Any group of haplotypes that are all more similar to one another than any of them is to any other haplotype may be said to constitute a clade. Statistical significance tests are available to examine whether it is possible to reject the hypothesis that a particular of haplotypes lie in a single clade….

Determining Haplotypes from a sequence of 261 base pairs in the mitochondrial DNA of 140 domestic dogs, 162 wolves, 5 coyotes, and 10 jackals: Evidence shows that wolves and coyotes separated about 1 mya. And have a 20-base divergence, so we can estimate that the divergence grows at a rate of about 1 substitution per 50,000 years. If all the dogs whose haplotypes are found in the large clade derive from a single parental line, we can expect that the 2.6-base divergence within that clade would have taken 130,000 years to emerge. The initial domestication of dogs did, in fact, occur 130,000 years ago, with a greater morphological change 15,000 years ago leading to the current domestic dog population.” http://gouvieux.fr.infovx.com/en/molecular+genetics

“The most commonly used methods to infer phylogenies include cladistics, phenetics, maximum likelihood, and Bayesian inference. These last two depend upon a mathematical model describing the evolution of characters observed in the species included, and are usually used for molecular phylogeny where the characters are aligned nucleotide amino acid sequences....There are three main methods of constructing phylogenetic trees: distance-based methods such as neighbour-joining, parsimony-based methods such as maximum parsimony, and character-based methods such as maximum likelihood or Bayesian inference….but phylogenetic trees hide hybridization and lateral gene transfer that may have taken place. The proposed PhyloCode technique does not assume a tree structure.

Evolutionary timelines are based on rRNA gene data, showing the separation of the three domains bacteria, archaea, and eukaryotes as described initially by Carl Woese. Trees constructed with other genes are generally similar, although they may place some early-branching groups very differently, presumably owing to rapid rRNA evolution….Molecular phylogeny is the use of a gene's molecular characteristics to classify an organism and to place it on a map of evolutionary relationships known as the phylogenetic tree. Every living organism is composed of certain substances such as DNA, RNA, and proteins. Closely related organisms generally have a high degree of agreement in the molecular structure of these substances, while the molecules of organisms distantly related usually show a pattern of dissimilarity. Molecular phylogeny uses such data to build a "relationship tree" that shows the probable evolution of various organisms. Not until recent decades, however, has it been possible to isolate and identify these molecular structures. As a result many branches of the phylogenetic tree have been disassembled and reassembled into patterns based on molecular identification rather than on the previous system of taxonomy based on morphology. It is now possible to infer a gene's relationships by the existence of molecular similarities between it and other genes, and it is also possible to use that information to determine the relationships of organisms based on the presence or absence, and the DNA sequence, of various genes. The molecular clock technique, which researchers use to date when two species diverged by comparing their DNA, deduces elapsed time from the number of differences. ” http://gouvieux.fr.infovx.com/en/phylogeny

“The molecular clock technique deduces elapsed time from the number of minor differences between their DNA sequences. It is sometimes called a gene clock. The notion of a "molecular clock" was first attributed to Emile Zuckerkandl and Linus Pauling who, in 1962, noticed that the quantity of amino acid differences in hemoglobin between lineages roughly matched the known evolutionary rate of divergence based upon fossil evidence. They generalized this observation to assert that the rate of evolutionary change of any specified protein was approximately constant over time and over different lineages. It has been applied to DNA sequence evolution also, particularly neutral evolution. Later Allan Wilson and Vincent Sarich built upon this work and the work of Motoo Kimura (1968) observed and formalized that rare spontaneous errors in DNA replication cause the mutations that drive molecular evolution, and that the accumulation of evolutionarily "neutral" differences between two sequences could be used to measure time, if the error rate of DNA replication could be calibrated. One method of calibrating the error rate was to use as references pairs of groups of living species whose date of speciation was already known from the fossil record….As DNA sequencing has become easier, phylogenies are increasingly constructed with the aid of molecular data. Computational systematics allows the use of these large data sets to construct objective phylogenies. These can filter out true synapomorphy from parallel evolution more accurately.”
http://gouvieux.fr.infovx.com/en/evolutionary+tree

“Maximum parsimony is a simple but popular technique used in cladistics to predict an accurate phylogenetic tree for a set of taxa (commonly a set of species or reproductively-isolated populations of a single species). The input data used in a maximum parsimony analysis is in the form of "characters" for a range of taxa. A character could be a binary value for the presence or absence of a feature (such as the presence of a tail), or it could be the protein or nucleic acid residue at a particular site in the organism's genome. There are a number of probabilistic and deterministic algorithms available for constructing phylogenetic trees.” http://gouvieux.fr.infovx.com/en/maximum+parsimony

That Eukaryote "Tree of Life" page makes a lot of references to endosymbiosis with protists. Prokaryotes aren't even considered as a seperate branch anymore. Instead, Archae are now seen as a seperate branch with Eubacteria being the third. They really show an excellent photo of symbiotic bacteria attached to a flagellate. And then they come right out and state: "the formation of the eukaryotic cell was a consequence of genome fusions between a host cell and endosymbionts representing distinct evolutionary lineages...The origins of mitochondria from cyanobacteria.... Chloroplasts are also rooted in endosymbiosis when a cyanobacterium took up residence in an ancient eukaryote. These primary endosymbionts were destined to become the chloroplasts which are found in eukaryotic algae." You might want to browse through some of the links on the righthand side of the page and also the reference links at the bottom.

Dinoflagellates, genus Symbiodinium, commonlly called zooxanthellae, are endosymbionts that form coral reefs by providing their hosts with energy for the carbonate deposition.

I'm focussing in on endosymbiosis in flagella development with flagellates, dinoflagellates, bacteria and algae.

Valich:

When I asserted that the single-celled organisms left no fossil records, I meant they left no fossil records of their cellular mechanisms. I am aware of the ancient cyanobactria, which apparently clumped in shallow seas, leaving fossilized formations of their entire mass. Whether each individual cell is identifiable as such I'm uncertain about, but certainly the development of the spindle apparatus, and the mechanistics of mitosis-meiosis left no fossil imprints -- instead we are left with extant descendants from which me must deduce origins.

So you agree I was correct that we cannot deduce the ages of ancient fossils from their DNA, but instead use the "biological clock" of the extant descendants. Mitochondrial DNA is sometimes used for this (such as estimating that "Eve" lived circa 120,000 years ago, as per a report I read, since the mitochondria are not present in the sperm, but only in the egg, leaving a trace of DNA for the females only), and I'm sure the much larger genome of the chromosomes allows for certain select genes, preserved in both lines, to serve as such a "clock". However, it has no where near the accuracy of radiometric and stratigraphic dating, and makes many assumptions regarding life habits.

Incidentally, the C-14 was previously accurate to only about 30,000 to 40,000 years ago, but mass-spectroscopy allows for detection of smaller amounts of C-14, pushing its accuracy back to about 60,000 to 80,000 years ago. (Due to the 'short' half-life of C-14 being 5,730 years.). Ancient fossils cannot use that technique, as the C-14 decays to nothing measureable after about 100,000 years (20- half-lifes)

However, the above being said, I have read some reports that some fossils from 60 mya did have some residual DNA still intact, and of course amber fossils likely have intact DNA, from which some direct biological clock detective work might be ascertainable.

On another note, today's MSNBC is reporting that Nature is publishing an article about interbreeding between a human ancestor (Toumai) and a chimpanzee ancestor some 5 mya, apparently about 4 million years after the initial split, and that the descendants of the hybrid product of that union is now the modern chimp.

It makes sense that such things occurred with a certain degree of frequency back then; after all, it is now postulated that the HIV virus was acquired in people when someone had sex with a chimpanzee, where apparently the HIV virus ancestor also exists. But then again, maybe someone gave it to the chimps?

This website provides extreme detail about the composition, length, structure, and function of flagellum, and has numerous links to the evolution and the various diverse containing species in the three groups: Bacteria, Archaea, and Eukaryotes. You could spend days following all their weblinks so there's no use in me posting what they state: http://gouvieux.fr.infovx.com/en/flagellum

Yes, as far as I know, any solid "absolute dating" beyond about 1 mya is from the rock that the fossils are found in. Evidence is left of cellular mechanisms, but not in the sense that you refer to such as of active metabolic changes: mitosis-meiosis.

As cited above, there are about five distinct computational methods in use to arrive at the organisms age without relying on the geological stratum. You can refer to these loosely as "biological clocks," but strictly speaking, the one method called the "molecular clock" is now considered innacurate. For example, we know that the "Cambrian Explosion" occurred in large part due to the rapid increase in atmospheric oxygen. So a number of factors alter a strict age determination based on a "biological clock."

Acritarchs are known from 1400 mya with considerable diversity by 1300 mya, but then crashed 800 mya. Apparently we don't really know what they are but they serve as a great out source marker for dating.

"The acritarchs show their greatest diversity during the Cambrian, Ordovician, Silurian and Devonian. The nature of some Acritarchs can be identified by their structure. A few can be tentatively identified by the presence of specific chemicals associated with the fossils....Acritarchs are small organic structures. In general, any small, non-acid soluble (i.e. non carbonate, non-silicate) organic structure that can not otherwise be accounted for is an acritarch. Most acritarchs are surely remains of single celled lifeforms. They are found in sedimentary rocks from the present back into the Precambrian. They are easily isolated from limestones with hydrochloric acid, and can also be isolated from silica rich rocks using hydrofluoric acid. They are excellent candidates for index fossils to be used for formation dating in the Palaeozoic and when other fossils are not available. They are also useful for palaeoenvironmental interpretation. Acritarchs include the remains of several quite different kinds of organisms including bacteria and dinoflagellates. The nature of the creatures associated with older acritarchs is generally not clear, though many are probably related to unicellular marine algae." http://gouvieux.fr.infovx.com/en/acritarch

Yeh, the MSNBC article is very interesting but I'll have to wait till it's printed in the journal Nature to read its entirety. Spurious started a new thread on that a few weeks ago on Sciforum: "New genus of monkey discovered." The original article that he posted shows a picture of its skull: http://news.bbc.co.uk/2/hi/science/nature/4759535.stm

I thought the new genus of monkey thread was about a different discovery, namely an actual new extant genus of monkey; whereas the Nature article will be about mating between pre-humans and pre-chimpanzees, giving rise to a hybrid which is the ancestor of our extant chimpanzee, using an entirely DNA analysis.

Glad we're on the same page about fossil dating techniques.

The eukaryote web page is interesting, and does detail that the mitochondria arose as endosymbiosis of bacteria, which idea has been around at least since the early 1970s when I first heard about it, and likely quite a few years before that. It has also suggested that some of the eukaryotes that were previously thought to be ancestral due to their lack of mitochondria, are now believed to have lost their mitochondria (reduction), with some of the mitochondrial DNA now found in the chromosomes.

Likewise, it details several routes for the alga and land plants (as I previously noted) by various cyanobacterial endosymbiots.

Unfortunately, it does not detail how a simple eubacteria, with a simple circular DNA, could develop into an advanced eukaryote, even without the mitochondria and cholorploasts.

I suspect that the ingestion and endosybiosis of one type into a larger cell, allowed the now internally-situated bacteria to evolve into a cellular nucleus, but how that occurred, and how it developed larger ribosomes, etc. for DNA transcription compared to the bacterial/mitochondrial ribosomes, etc. is certainly not yet clear to me.

I'm hoping that more work will be done in this area to elucidate those remaining mysteries.

Apparently these are two different monkey species. The one described in the MSNBC article is called "Toumai" or "Sahelanthropus tchadensis" and the one in the other Sciforum thread is called "Rungwecebus kipunji." The suggestion that we may have been interbreeding with monkeys for 4 million years till full speciation 5.4 mya is going to reek havoc with the creationists. http://www.livescience.com/humanbiology/ap_050406_chad_bones.html

"Evolution of Flagella" http://wiki.cotch.net/index.php/Evolution_of_flagella

"Evolution of Bacterial Flagellum" http://www.talkdesign.org/faqs/flagellum.html

"Evolving the Bacterial Flagellum Through Mutation and Cooption: Part VI....Homology, Design, Analogy, Beginnings....." http://www.idthink.net/biot/flag6/index.html

"Sequencing of Flagellin Genes from Natrialba magadii Provides New Insight into Evolutionary Aspects of Archaeal Flagellins" http://www.bionewsonline.com/o/q/inna_serganova_2002_318.htm

"There are two competing groups of models for the origin of the eukaryotic flagellum (referred to as a cilium below to distinguish it from its bacterial counterpart)....The only real point in favor of the symbiotic hypothesis is that there apparently actually are eukaryotes that use symbiotic spirochetes as their motility organelles....The homology of tubulin to the bacterial replication/cytoskeletal protein FtsZ would seem to clinch the case against Margulis, as FtsZ is apparently found native in archaebacteria, providing an endogenous ancestor to tubulin (as opposed to Margulis' hypothesis, that an archaebacterium acquired tubulin from a symbiotic spirochete).
the archaeal flagellum appears to grow at the base rather than the tip, and is about 15 nanometers (nm) in diameter rather than 20.

Sequence comparison indicates that the archaeal flagellum is homologous to Type IV pili (pili are filamentous structures outside the cell). Interestingly, some type IV pili can retract. Pilus retraction provides the driving force for a different form of bacterial motility called "twitching" or "social gliding" which allows baterial cells to crawl along a surface. Thus type IV pili can, in different bacteria, promote either swimming or crawling.Type IV pili are asembled through the Type II transport system. So far, no species of bacteria is known to use its type IV pili for both swimming and crawling." http://www.aseannewsnetwork.de/articles/content/e/ev/evolution_of_flagella.html

Mol Biol Evol, 2003 Jul, 20(7), 1098 - 112 Epub 2003 May 30.
"The molecular evolution of catalatic hydroperoxidases: evidence for multiple lateral transfer of genes between prokaryota and from bacteria into eukaryota; Klotz MG et al.; The past decade has produced an increasing number of reports on horizontal gene transfer between prokaryotic organisms . Only recently, with the flood of available whole genome sequence data and a renewed intensity of the debate about the universal tree of life, a very few reports on lateral gene transfer (LGT) from prokaryotes into the Eukaryota have been published . We have investigated and report here on the molecular evolution of the gene families that encode catalatic hydroperoxidases . We have found that this process included not only frequent horizontal gene transfer among prokaryotes but also several lateral gene transfer events between bacteria and fungi and between bacteria and the protistan ancestor of the alga/plant lineage." http://www.bionewsonline.com/r/2/prokaryote_c.htm

"Flagellar determinants of bacterial sensitivity to c-phage. Bacteriophage c is known to infect motile strains of enteric bacteria by adsorbing randomly along the length of a flagellar filament and then injecting its DNA into the bacterial cell at the filament base. Here, we provide evidence for a “nut and bolt” model for translocation of phage along the filament: the tail fiber of c fits the grooves formed by helical rows of flagellin monomers, and active flagellar rotation forces the phage to follow the grooves as a nut follows the threads of a bolt." http://www.mansfield.ohio-state.edu/~sabedon/ab_all.htm

"Variations on the classical flagellum, such as different lateral and polar flagella on the same cell, and the periplasmic flagella of spirochaetes. Motility is also conferred by flagella in the domain Archaea, yet these structures bear little similarity to their bacterial counterparts. Rather, archaeal flagella demonstrate similarity to another bacterial motility apparatus, type IV pili. Additional structures involved in bacterial motility include the junctional pore complex and the ratchet structure involved in gliding motility, and the unique contractile cytoskeleton of Spiroplasma....Insight into how changes in the arrangement of the flagellin subunits assembled in the filament lead to a switch in bacterial motility, from swimming to tumbling, has been obtained from flagellin crystals....An intriguing aspect of the polar/lateral flagellation systems in various Vibrio species is that the polar flagellum is sheathed (possibly an extension of the cell membrane) and driven by a sodium ion gradient, while the lateral flagella are unsheathed and driven by a proton gradient.

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Perhaps the most unusual case of bacterial flagellation is that of the spirochaetes. Here flagella are located in the periplasm between the outer membrane sheath and cell cylinder, subterminally attached to one end of the cell cylinder. The number of periplasmic flagella and whether the flagella overlap at the centre of the cell varies among species. The flagella function by rotating within the periplasmic space. Unlike some other bacteria in which flagellation depends on environmental changes, the spirochaete periplasmic flagella are expressed throughout the cell's life-cycle and are believed to have vital skeletal and motility functions. Due to their continuous presence, the complex regulatory controls observed for motility gene expression in many bacteria seem to be absent in at least certain spirochaetes.

Spirochaete periplasmic flagella are compositionally some of the most complex yet described. They are comprised of FlaA sheath proteins and usually multiple (two to four) FlaB core proteins. The FlaA proteins are made with a leader peptide and are likely secreted via a sec-dependent pathway into the periplasm before assembly onto the flagellar filament. FlaA proteins bear no sequence similarity to the FlaB proteins which make up the filament proper. The FlaB proteins have N- and C-terminal sequence similarity to other bacterial flagellins and are not processed at their N terminus. They are presumed to be secreted through the hollow basal body–hook structure via the type III mechanism found for other bacterial flagellins.
The spirochaete flagellar motion is driven by the proton-motive force (PMF) and the cellular movement depends on asymmetrical rotation of the two ends of the cell. In other words, when the periplasmic flagella located at either end of the spirochaete are rotating in the same direction the cells do not swim. One of the interesting aspects to be determined for spirochaete motility is how the cell controls the rotation of the flagella at the opposite ends of the cell so that both structures rotate in opposite directions. Since some unique motility genes are believed to exist in spirochaetes it has been speculated that some of these might be present to address this problem.

Fundamental differences between archaeal and bacterial flagella have become obvious from analysis of complete genome sequences of many flagellated archaea. Genes encoding bacterial proteins involved in structure or assembly of flagella have not been reported in archaeal genomes. If archaeal flagella have an anchoring structure it appears to be composed of proteins that are archaea-specific. Even the archaeal flagellins, which compose the major portion of the flagellar filament, lack sequence similarity to bacterial flagellins. In several ways they appear more similar to type IV pilins which themselves form a structure involved in other forms of motility, such as twitching motility (see below). There is sequence similarity between type IV pilins and archaeal flagellins over the first 50 aa, which are extremely hydrophobic. In addition, both type IV pilins and archaeal flagellins are made as preproteins with short positively charged leader peptides. These proteins are processed by specific leader peptidases, distinct from the leader peptidase I equivalent. Mutations in the leader peptidase in either system prevent the assembly of a detectable structure. In the case of the archaeal flagellum this strongly suggests that the assembly mechanism is distinct from the bacterial one involving a type III secretion mechanism with flagellins that lack leader peptides.

In archaea, only one major gene cluster involving up to 12 genes has been reported to be involved with flagellation. Mutations in a number of these genes result in nonflagellated cells. Recently the gene encoding a preflagellin peptidase has been reported. In Methanococcus jannaschii it is part of the large gene cluster involved in flagellation but in other Methanococcus species it is located quite removed from the flagellin gene cluster. All flagellated archaeal species have three conserved genes, termed flaHIJ, located near the genes for the flagellins. Interestingly, FlaI is a homologue of TadA, an ATPase involved in type IV pilus production in Actinobacillus, while FlaJ is similar to TadB, a multitopic membrane protein needed in the same system. In archaea, there are always multiple (2–6) flagellin genes present (Sulfolobus solfataricus appears to be an exception). Thus far the only components of the archaeal flagellum identified are the flagellins themselves, where it appears that the multiple flagellins are all present as structural components of the assembled flagellum. Recent work indicated that the hook protein might in fact be a minor flagellin, FlaB3 in the case of Methanococcus voltae. The flagellins are often, perhaps even universally, posttranslationally modified, usually by glycosylation although only in the case of halobacteria have the associated carbohydrate moieties been determined. Flagellin glycosylation may be necessary for proper flagellar assembly.

Ratchet Structure: Members of the Cytophaga–Flavobacterium group of bacteria appear to glide by a yet different mechanism. Here it seems motility at a rate of 2–10 µm s-1 is the result of the movement of cell surface components. This has been readily demonstrated through the use of latex beads which can be observed to move along the surface of cells in complex paths. One proposed model for gliding in Flavobacterium johnsoniae and related organisms is specific motility proteins anchored in the cytoplasmic and outer membrane. Movement of the cytoplasmic proteins may be driven by the PMF and their interaction with the outer-membrane proteins in a ratcheting mechanism may propel the cells forward. The outer-membrane proteins may be anchored to the peptidoglycan, forming tracks. Several genes have been implicated in gliding motility in F. johnsoniae including three (gldA, gldF and gldG) whose products may form an ATP transporter required for movement. The exact function of any of these proteins in gliding is unknown. Another possibility is that gliding in this organism is due to slime extrusion and subsequent uptake with the gld gene products forming the transporter for import or export.

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From: "Prokaryotic Motility Structures," by Sonia L. Bardy, Sandy Y. M. Ng and Ken F. Jarrell, Department of Microbiology and Immunology, Queen's University, Kingston, ON, Canada K7L 3N6. Microbiology 149 (2003), 295-304; DOI 10.1099/mic.0.25948-0. http://mic.sgmjournals.org/cgi/content/full/149/2/295

Walter: You're referring to where it says "there is now increasing evidence that genes normally found in alpha-proteo bacteria are also present in the nucleus of amitochondriate prostists and that mitochondria were present much earlier than previously thought, but have now been lost from some early eukaryotes (Roger, 1999)" "Reconstructing Early Events in Eukaryotic Evolution," by A. J. Roger, 1999: http://www.botany.ubc.ca/keeling/BIOL332/Papers/Roger99.pdf.
or html version at: http://72.14.203.104/search?q=cache:aX198Fdbs9gJ:www.botany.ubc.ca/keeling/BIOL332/Papers/Roger99.pdf+Reconstructing+early+events+in+eukaryo tic+evolution&hl=en&gl=us&ct=clnk&cd=1

You also state: "I suspect that the ingestion and endosybiosis of one type into a larger cell, allowed the now internally-situated bacteria to evolve into a cellular nucleus, but how that occurred, and how it developed larger ribosomes, etc. for DNA transcription compared to the bacterial/mitochondrial ribosomes, etc. is certainly not yet clear to me."

What about the "RNA-World"? Basal to all eukaryotes, eubacteria, and archaea. You can start with any simple life-form of RNA and then it became engulfed in a simple enclosed membrane structure - a plasma membrane.

Valich:

As to your last post - yes, I was referring to the a-mitochondriate protists referenced by the quoted author (Roger, 1999), though I reached it through my originally posted web-page, not the ones you've posted.

And yes, likely RNA preceded DNA for genetic coding. As I recall, though, the mitochondria and the eu-bacteria and the archaea all have ribosomes much smaller than those for the eukaryotes, and they are made of two major sub-units, and they are all comparably sized, compared to the much larger ribosomes utilized for gene transcription by the eukaryotic nucleus (as determined by centrifugal units of mass). However, we now see the RNA used as both the t-RNA, as well as I believe incorporated into the ribosomes, and how such a change from a presumptively more primitive cell utilizing RNA genetic coding to the DNA based genetic coding of extant archaea, eu-bacterial, eukaryotes, etc. is also not known to me.

Somewhere I read that the spindle apparatus were believed by some to be derived from endosymbiots, but I really know very little about that, too. Under the microscope, they suddenly seem to 'appear' whenever a cell begins to undergo mitosis or meiosis, though clearly they must be there all along, though what causes them to become conspicous under the light microscope is also not known to me.

What is interesting about all this, as I've indicated before, is that the more me learn and know, the more we learn how little we know. Anyway, any further enlightenment along those lines would likewise be appreciate.

By the by, I suspect that most casual readers of these posts are not following this thread, as they likely don't have the more in-depth background you seem to possess, or the more general background I happen to have, since this is not my major field of study.

I think that the reference on the "Tree of Life - Eukaryote" page that states amitochondriate acquired then lost mitochondria is innacurate. I highly doubt that this sequence of evolutionary events (lost their mitochondria - reduction) ever occurred and it appears that this subject is currently hotly debated. The very prestiguous Woods Hole Oceanographic Institution states that:

"It is now widely accepted that the eukaryotes we call protists are far more diverse in cellular organization than the non-protist eukaryote groups—namely animals, plants and fungi. A variety of heterotrophic protists lack classical mitochondria, inhabiting low- oxygen environments such as the guts and tissues of animals, marine or freshwater sediments, and the lower reaches of stratified water bodies. Over the last two decades these 'amitochondriate' organisms have been of great interest to evolutionary biologists, as some may have diverged before the acquisition of the mitochondrion and consequently represent very early stages in the evolution of the eukaryotic cell. Some amitochondriate groups—particularly the largely parasitic trichomonads, diplomonads, and microsporidia— have indeed tended to form the most basal branches in evolutionary trees of eukaryotes, based on molecular sequence comparisons. However the validity of these deep branches has, of late, been vigorously challenged, as has the contention that these organisms lack any trace of having had mitochondria. To date, almost all of the research into amitchondriate protists has focused on those groups with parasitic members. However surveys of sediments and anoxic water bodies reveal a considerable and drastically understudied diversity of free-living, low-oxygen protists, frequently of unclear affinities. In several instances, electron-microscopical studies indicate the absence of classical mitochondria. Detailed morphological data in concert with molecular phylogenies, covering both free-living and parasitic taxa, are leading us towards a more authoritative state regarding the affinities of the amitochondriate protists and whether any groups remain candidates for being primitively amitochondriate relicts of early eukaryotic evolution.”

From: “The evolutionary importance and affinities of 'amitochondriate' protists,”by Virginia Edgcomb, Andrew Roger, and Alastair Simpson. Woods Hole Oceanographic Institution, University of Sydney, Australia, November 4, 1998. http://www.mbari.org/seminars/1998/nov4_simpson.html

"Phylogenetic evidence is presented that primitively amitochondriate eukaryotes containing the nucleus, cytoskeleton, and endomembrane system may have never existed. Instead, the primary host for the mitochondrial progenitor may have been a chimeric prokaryote, created by fusion between an archaebacterium and a eubacterium, in which eubacterial energy metabolism (glycolysis and fermentation) was retained. A Rickettsia-like intracellular symbiont, suggested to be the last common ancestor of the family Rickettsiaceae and mitochondria, may have penetrated such a host (pro-eukaryote), surrounded by a single membrane, due to tightly membrane-associated phospholipase activity, as do present-day rickettsiae. The relatively rapid evolutionary conversion of the invader into an organelle may have occurred in a safe milieu via numerous, often dramatic, changes involving both partners, which resulted in successful coupling of the host glycolysis and the symbiont respiration. Establishment of a potent energy-generating organelle made it possible, through rapid dramatic changes, to develop genuine eukaryotic elements. Such sequential, or converging, global events could fill the gap between prokaryotes and eukaryotes known as major evolutionary discontinuity."
From: http://content.febsjournal.org/cgi/content/full/270/8/1599

"“We present a testable model for the origin of the nucleus, the membrane-bounded organelle that defines eukaryotes. A chimeric cell evolved via symbiogenesis by syntrophic merger between an archaebacterium and a eubacterium. The archaebacterium, a thermoacidophil resembling extant Thermoplasma, generated hydrogen sulfide to protect the eubacterium, a heterotrophic swimmer comparable to Spirochaeta or Hollandina that oxidized sulfide to sulfur. Selection pressure for speed swimming and oxygen avoidance led to an ancient analogue of the extant cosmopolitan bacterial