Peter Ruest wrote:
>
>I have studied the Johnson & Coffin paper. It looks really relevant to
>my question. I have just a minor reservation lingering. Only two of the
>six proviruses they studied behaved exactly as expected, while in
>several cases they had to invoke gene conversions (or lack of true
>homology) to explain their deviant gene trees. They were surprised by
>the high frequency of such conversion, saying this "probably reflects
>the likelihood of conversion among any repeated, nuclear DNA sequences".
>They also emphasized the "evidence for high frequency of recombination
>involving ERV sequences". What are the implications of this? Doesn't
>this weaken the evidence for non-selected sequence similarities between
>human and chimp?
>
>There is a more recent paper from the same lab: Hughes J.F., Coffin J.M.
>Evidence for genomic rearrangements mediated by human endogenous
>retroviruses during primate evolution. Nature Genetics 29 (2001),
>487-489. Again, they find that recombination events involving HERVs "may
>have been extremely frequent during the course of primate evolution".
>Curiously, in all 23 new cases they investigated, they never found both
>of the predicted reciprocal products of recombination. What's the
>implication for the evidence of common ancestry between human and chimp?
>
>I have not yet been able to look at the Zhang & Rosenberg paper, as the
>full text is not available online to non-subscribers, and the library I
>frequent had not yet received any 2002 issue of PNAS by March 20! I'll
>get to it later I hope.
>
Peter
Peter,
I don't have time right now to respond in any detail, and it has been
awhile since I read the paper. However, I will say that what I think
is most compelling about this sort of evidence is not just the fact
that these mobile elements are not (usually) selected for, but that
they insert in a quasi-random way. Since they have 3 x 10^9 possible
locations to insert, each insertion can be treated as a unique event.
It is just not plausible that the same element can insert at the same
site independently in different species. It is true that many
insertions may be obscured later by gene conversion, recombination or
deletion, but with nearly half the primate genome composed of
transposable element relics, there are still thousands of instances
that are clear. There is at least one example where a particular
retrovirus is present in one copy in the whole genome, at the same
place in human and ape genomes.
Got to go now.
Blessed Easter,
Preston G.
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