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Thread: Rhesus Monkey Wrench in the Nested Hierarchy?

  1. #1 Rhesus Monkey Wrench in the Nested Hierarchy? 
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    One of the evidences for common ancestry of humans and chimpanzees is 'shared ERVs', (the same endogenous retrovirus in humans as in chimpanzees). A potential falsification of that evidence would be matching ERVs that violated the nested hierarchy of species; In other words, if an ERV in the human genome had a match in a species other than chimpanzees, our closest biological relative. In other words, a common ancestor from the time before the common ancestor of humans and chimps would have had the ERV insertion and among its descendants a branch would split off away from the branch of the chimpanzee-human ancestor, so that the chimpanzee-human common ancesor branch should be carrying that ERV. Therefore, any ERV in any other primate that matches an ERV in humans must be in the chimpanzee genome also.

    The tree collapses if either the human or the chimpanzee has an ERV matching that of some other primate, since if humans and chimpanzees allegedly share a common ancestor, how is it that the chimpanzee or the human is missing that ERV.

    Ah, but not so fast. The proponents of common ancestry may not be so quick to give up this device.

    It turns out the Rhesus monkey (Rhesus Macaque/Macaca mulatta), has a closer matching ERV-K with humans differing greatly from chimpanzees.
    http://www.sciencedaily.com/releases...1009212538.htm
    "The study by Romano and colleagues being published this week on PLoS Onerevealed that human ERV-K had a similar demographic signature to that of the rhesus monkey, both differing greatly from that of the chimpanzee."
    However, the difference between the Rhesus-Human ERV-K from that of the chimpanzee ERV was explained away as a matter of demographics and:
    "The data suggested that the humans and rhesus have been purging ERV-K copies from their genomes while the chimpanzee ERV-K population kept the signature of increasing numbers of ERV-K amplification in the genome of ancestral primates during the last 20 million years."

    Here is the main article from PLoS ONE: (well not all of it, just a teeny snippet)
    http://www.plosone.org/article/info%...l.pone.0001026
    "Nevertheless, the elevated dispersal of both Homo and Macaca compared to Pan may be an important factor that could explain the similarities in the demographic histories of HERV-K and RhERV-K.
    Unlike HERV-K and RhERV-K, the chimpanzee ERV-K demographic signal was characterized by a far larger effective population size. Assuming that host dynamics impacts on ERV-K numbers, the recent flat curve of Pan skyline after 6 MYBP agrees with the lack of evidence for severe bottlenecks in the Pan lineage and a 3.2 times larger effective ancestral population size. The latter could have facilitated the maintenance of a higher number of integrated elements observed in the chimpanzee genome, because of a weaker effect of genetic drift, although the wide HPD values caution against over-interpretation."

    OK, this is dissappointing. It appeared the bar had been met, a violation of the nested hierarchy. But its hard to get a slam dunk in the evolution/creation debate.

    Neo.


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  3. #2 Re: Rhesus Monkey Wrench in the Nested Hierarchy? 
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    Quote Originally Posted by Neocon_Voter
    One of the evidences for common ancestry of humans and chimpanzees is 'shared ERVs', (the same endogenous retrovirus in humans as in chimpanzees).
    only if the retrovirus was acquired prior to the split between the human and the chimp lineage - any retroviruses acquired at a later stage don't tell you anything about common ancestry


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  4. #3  
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    I am afraid I don't follow.

    Does the argument rest on the assumption that primates undergo the same approximate rates and types of evolutionary change? This is a no-starter at the outset. For example, one of the biggest differences between human and chimp genomes is the number and location of deletions, inversions, and insertions in their respective genomes --- and as these are rather gross structural events, which bring new areas of the chromosomes into proximity - they all increase the likelihood of additional mutational events at the ends of the translocated sites. In short, since different types of primates have undergone different gross structural genomic changes, one cannot take the absence of an HERV in chimps as meaningful, particularly without contextual sequence analysis.

    http://www.genome.org/cgi/content/abstract/15/10/1344

    Related articles:

    http://scholar.google.com/scholar?q=...-8&oi=scholart

    More to the point, what precisely is your argument? (Dare I assume you thought the rhesus result evidenced creationism????)
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  5. #4 Re: Rhesus Monkey Wrench in the Nested Hierarchy? 
    Forum Cosmic Wizard spuriousmonkey's Avatar
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    Quote Originally Posted by Neocon_Voter
    One of the evidences for common ancestry of humans and chimpanzees is 'shared ERVs', (the same endogenous retrovirus in humans as in chimpanzees). A potential falsification of that evidence would be matching ERVs that violated the nested hierarchy of species; In other words, if an ERV in the human genome had a match in a species other than chimpanzees, our closest biological relative. In other words, a common ancestor from the time before the common ancestor of humans and chimps would have had the ERV insertion and among its descendants a branch would split off away from the branch of the chimpanzee-human ancestor, so that the chimpanzee-human common ancesor branch should be carrying that ERV. Therefore, any ERV in any other primate that matches an ERV in humans must be in the chimpanzee genome also.
    I think you misread the article in question.

    The PloS article does not compare genetical identity of the ERV-K's

    In fact:
    As no RhERV-K orthologue was closely related to those in either the chimpanzee or human genomes, all RhERV-K proviruses appear to have arisen by active transposition rather than chromosomal duplication. In contrast, Pan and Homo share several ERV-K, and exhibit many closely related elements that most likely originated by chromosomal duplications and rearrangement events (e.g., CERV-K32, CERV-K31, CERV-K34; CERV-K26, 27 and 28 on the Y chromosome).
    The sequence of Rhesus ERV-K is much different from human and chimp, while chimp and human are more similar.
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  6. #5  
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    Quote Originally Posted by free radical
    I am afraid I don't follow.

    Does the argument rest on the assumption that primates undergo the same approximate rates and types of evolutionary change? This is a no-starter at the outset. For example, one of the biggest differences between human and chimp genomes is the number and location of deletions, inversions, and insertions in their respective genomes --- and as these are rather gross structural events, which bring new areas of the chromosomes into proximity - they all increase the likelihood of additional mutational events at the ends of the translocated sites. In short, since different types of primates have undergone different gross structural genomic changes, one cannot take the absence of an HERV in chimps as meaningful, particularly without contextual sequence analysis.

    http://www.genome.org/cgi/content/abstract/15/10/1344

    Related articles:

    http://scholar.google.com/scholar?q=...-8&oi=scholart

    More to the point, what precisely is your argument? (Dare I assume you thought the rhesus result evidenced creationism????)
    No, not at all. (AFAIK, supernatural creationism cannot be proven by humans)
    The evidence in question is the possible prediction of a nested hierarchy.

    If an ERV missing in chimpanzees can be rationalized away with purgings, etc, or if a match between the wrong candidates (say, rhesus and humans) can be explained with transposition (as in, it wasn't an original match, the sequence jumped there from some other integration site), how can the prediction be falsified.

    Neo
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  7. #6 Re: Rhesus Monkey Wrench in the Nested Hierarchy? 
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    Quote Originally Posted by spuriousmonkey
    Quote Originally Posted by Neocon_Voter
    One of the evidences for common ancestry of humans and chimpanzees is 'shared ERVs', (the same endogenous retrovirus in humans as in chimpanzees). A potential falsification of that evidence would be matching ERVs that violated the nested hierarchy of species; In other words, if an ERV in the human genome had a match in a species other than chimpanzees, our closest biological relative. In other words, a common ancestor from the time before the common ancestor of humans and chimps would have had the ERV insertion and among its descendants a branch would split off away from the branch of the chimpanzee-human ancestor, so that the chimpanzee-human common ancesor branch should be carrying that ERV. Therefore, any ERV in any other primate that matches an ERV in humans must be in the chimpanzee genome also.
    I think you misread the article in question.

    The PloS article does not compare genetical identity of the ERV-K's

    In fact:
    As no RhERV-K orthologue was closely related to those in either the chimpanzee or human genomes, all RhERV-K proviruses appear to have arisen by active transposition rather than chromosomal duplication. In contrast, Pan and Homo share several ERV-K, and exhibit many closely related elements that most likely originated by chromosomal duplications and rearrangement events (e.g., CERV-K32, CERV-K31, CERV-K34; CERV-K26, 27 and 28 on the Y chromosome).
    The sequence of Rhesus ERV-K is much different from human and chimp, while chimp and human are more similar.
    You're probably right about that.
    I jumped at the possibility when I read that 3 of the ERVs were shared by all the players:
    "and only three (RhERV-K3, RhERV-K8 and RhERV-K19) were possibly integrated into the common ancestor of all three primates."
    http://www.plosone.org/article/info%...l.pone.0001026

    and that all 106 ERV-K genomes of the study shared the same base pair sequence:
    "A phylogenetic tree (Fig. 1) for a 4130 bp alignment from the conserved domains (the Partial data set) shared by 106 ERV-K genomes, had a topology congruent to those obtained previously for both ERV-K genomic fragments [21] and complete genomes"
    Oh well.

    Neo
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  8. #7  
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    Quote Originally Posted by Neocon_Voter
    Quote Originally Posted by free radical
    I am afraid I don't follow.

    Does the argument rest on the assumption that primates undergo the same approximate rates and types of evolutionary change? This is a no-starter at the outset. For example, one of the biggest differences between human and chimp genomes is the number and location of deletions, inversions, and insertions in their respective genomes --- and as these are rather gross structural events, which bring new areas of the chromosomes into proximity - they all increase the likelihood of additional mutational events at the ends of the translocated sites. In short, since different types of primates have undergone different gross structural genomic changes, one cannot take the absence of an HERV in chimps as meaningful, particularly without contextual sequence analysis.

    http://www.genome.org/cgi/content/abstract/15/10/1344

    Related articles:

    http://scholar.google.com/scholar?q=...-8&oi=scholart

    More to the point, what precisely is your argument? (Dare I assume you thought the rhesus result evidenced creationism????)
    No, not at all. (AFAIK, supernatural creationism cannot be proven by humans)
    The evidence in question is the possible prediction of a nested hierarchy.

    If an ERV missing in chimpanzees can be rationalized away with purgings, etc, or if a match between the wrong candidates (say, rhesus and humans) can be explained with transposition (as in, it wasn't an original match, the sequence jumped there from some other integration site), how can the prediction be falsified.

    Neo
    Presumably the prediction (of presence/absence of ERV events) is sophisticated enough to take the rates of chromosomal rearrangements (etc) into account. ie, the situation is not a strict logic puzzle.

    For example, the prediction should include the probabilities of gross structural events deleting (or inserting) an ERV in a particular species/location; in other words should identify the statistical probabilities of particular outcomes. It is not clear to me that such predictions have been made in this manner (If ERV's are used to argue against descent from common ancestor, for example, they almost certainly have not!)

    Falsification would entail results that do not satisfy reasonable confidence intervals, and such falsification would presumably lead to additional analyses of how genomes change over time.

    (The issue of ERV sequence, as pointed out by spurious monkey, is more telling.)
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