Link between sea and land animals found

Discussion in 'Biology & Genetics' started by KennyJC, Apr 6, 2006.

  1. valich Registered Senior Member

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    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."
     
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  3. valich Registered Senior Member

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    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.
     
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  5. Hercules Rockefeller Beatings will continue until morale improves. Moderator

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    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”.
     
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  7. Walter L. Wagner Cosmic Truth Seeker Valued Senior Member

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    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).
     
  8. valich Registered Senior Member

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    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 proposal

    "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
     
  9. valich Registered Senior Member

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  10. valich Registered Senior Member

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    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.

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    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.

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    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.
     
  11. valich Registered Senior Member

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    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.

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    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.

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    “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
     
  12. valich Registered Senior Member

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    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.

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    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

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    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
     
  13. Walter L. Wagner Cosmic Truth Seeker Valued Senior Member

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    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?
     
  14. valich Registered Senior Member

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    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
     
  15. Walter L. Wagner Cosmic Truth Seeker Valued Senior Member

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    2,540
    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.
     
  16. valich Registered Senior Member

    Messages:
    3,501
    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
     
  17. valich Registered Senior Member

    Messages:
    3,501
    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
     
  18. valich Registered Senior Member

    Messages:
    3,501
    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?
     
  19. Walter L. Wagner Cosmic Truth Seeker Valued Senior Member

    Messages:
    2,540
    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.
     
  20. CharonZ Registered Senior Member

    Messages:
    786
    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.
     
  21. valich Registered Senior Member

    Messages:
    3,501
    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.
     
  22. Walter L. Wagner Cosmic Truth Seeker Valued Senior Member

    Messages:
    2,540
    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.
     
  23. valich Registered Senior Member

    Messages:
    3,501
    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
     

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