UT Arlington genome biologist reports on surprising evolutionary
Kleuskes & Moos
"ARLINGTON - About 8 percent of human genetic material comes from a
virus and not from our ancestors, according to an article by
University of Texas at Arlington biology professor C�dric Feschotte
published in the Jan. 7, 2010 issue of Nature magazine."
http://www.uta.edu/ucomm/mediarelations/press/2010/01/genome-biologist-reports.php
How does this fit into the classic systematics of clades*) and, more
interesting creationist "kinds"? On the former it should have a
profound effect, but the latter seemsto be completely obliterated by
it.
*) if it's an incorrect term, remember i'm no biologist, but set me
right, anyway.
Ernest Major
<76afa63d-0301-4efa...@j4g2000yqe.googlegroups.com>,
Kleuskes & Moos <kle...@xs4all.nl> writes
>This seems relevant and interesting...
>
>"ARLINGTON - About 8 percent of human genetic material comes from a
>virus and not from our ancestors, according to an article by
>University of Texas at Arlington biology professor C�dric Feschotte
>published in the Jan. 7, 2010 issue of Nature magazine."
>
>http://www.uta.edu/ucomm/mediarelations/press/2010/01/genome-biologist-r
>eports.php
>
It has been known for some time that some of the human genome was
composed of sequences of viral origin. That is the endogenous
retroviruses (ERVs) that you may have noticed people mentioning here.
Recently in Nature a paper has reported that viruses belonging to
another group (bornaviruses) have been found to have been inserted into
the genomes of various mammals, including the common ancestors of a
considerable clade of primates. (Because the paper is paywalled I don't
know exactly what clade - it's something between great apes on the one
hand, and all apes and old world monkeys on the other. Yet another bit
of evidence for common descent.)
Professor Feschotte has written a News and Views ("executive summary")
article on this paper for Nature, wherein he mentions in passing that 8%
of the human genome is of viral origin. (That's about all that's on this
side of the paywall.) For some reason, his institution thought that this
was worthy of a press release.
If you google for bornavirus you'll find various blogs discussing the
contents of the actual paper.
>How does this fit into the classic systematics of clades*) and, more
>interesting creationist "kinds"? On the former it should have a
>profound effect, but the latter seemsto be completely obliterated by
>it.
>
The presence of a sequence of viral origin at a particular location in
the genome is a derived trait. There is some risk of complications from
insertional hotspots, but usually it is a shared derived trait. Within
the clade sharing that trait sequence variation of that stretch of DNA
can be used to estimate the phylogeny in the same way as other bits of
DNA. I'd guess that it's more useful that retrotransposons, which copy
themselves all over the genome, so identifying homologs is more
difficult.
Parasite phylogenies often parallel host phylogenies, so comparison
between bornavirus sequence in different clades (identified by the
sequence being in different places in the genome) gives a weak
indication of the relationships of the host genomes. Because of the
imperfect correlation of host and parasite phylogenies, and any
confounding effects of the interaction between different rates of codon
change in "wild" and endogenous virus sequences combined with different
dates of insertion, one should be at the least cautious of drawing
conclusions based on this on its own.
>
>*) if it's an incorrect term, remember i'm no biologist, but set me
>right, anyway.
>
--
alias Ernest Major
John Harshman
> This seems relevant and interesting...
>
> "ARLINGTON - About 8 percent of human genetic material comes from a
> virus and not from our ancestors, according to an article by
> University of Texas at Arlington biology professor C�dric Feschotte
> published in the Jan. 7, 2010 issue of Nature magazine."
>
> http://www.uta.edu/ucomm/mediarelations/press/2010/01/genome-biologist-reports.php
>
> How does this fit into the classic systematics of clades*) and, more
> interesting creationist "kinds"?
This is hardly new information. He's talking about endogenous
retroviruses and various sequences that descend from them. Occasionally
a retrovirus will even carry a little genetic material from one species
to another. But it doesn't disguise the overall pattern, each insertion
being separate. In fact, it helps us discern the pattern, because
particular retroviral insertions are events that happen at some
particular time, on some particular branch of the tree, and are
inherited by any descendants. As such, it can act as a marker of phylogeny.
> On the former it should have a
> profound effect, but the latter seemsto be completely obliterated by
> it.
The effect isn't that profound. I have no idea what a creationist would
consider an explanation, other than "goddidit", of course.
All-seeing-I
> Kleuskes & Moos wrote:
> > This seems relevant and �interesting...
>
> > "ARLINGTON - About 8 percent of human genetic material comes from a
> > virus and not from our ancestors, according to an article by
> > University of Texas at Arlington biology professor C�dric Feschotte
> > published in the Jan. 7, 2010 issue of Nature magazine."
>
>
> > How does this fit into the classic systematics of clades*) and, more
> > interesting creationist "kinds"?
>
> This is hardly new information. He's talking about endogenous
> retroviruses and various sequences that descend from them. Occasionally
> a retrovirus will even carry a little genetic material from one species
> to another. But it doesn't disguise the overall pattern, each insertion
> being separate. In fact, it helps us discern the pattern, because
> particular retroviral insertions are events that happen at some
> particular time, on some particular branch of the tree, and are
> inherited by any descendants. As such, it can act as a marker of phylogeny.
>
> > On the former it should have a
> > profound effect, but the latter seemsto be completely obliterated by
> > it.
>
> The effect isn't that profound. I have no idea what a creationist would
> consider an explanation, other than "goddidit", of course.
>
>
>
> > *) if it's an incorrect term, remember i'm no biologist, but set me
>
> - Show quoted text -
"retrovirus will even carry a little genetic material from one species
to another"
What happens to this genetic material when it is inserted into the new
spcies?
Kleuskes & Moos
> In message
> <76afa63d-0301-4efa-80f2-2a9e0cc3a...@j4g2000yqe.googlegroups.com>,
> Kleuskes & Moos <kleu...@xs4all.nl> writes>This seems relevant and interesting...
>
> >"ARLINGTON - About 8 percent of human genetic material comes from a
> >virus and not from our ancestors, according to an article by
> >University of Texas at Arlington biology professor C�dric Feschotte
> >published in the Jan. 7, 2010 issue of Nature magazine."
>
> >http://www.uta.edu/ucomm/mediarelations/press/2010/01/genome-biologist-r
> >eports.php
>
> Sigh. Press releases.
Sorry. Won't do it again. This one seemed extra interesting though...
Kleuskes & Moos
> In message
> <76afa63d-0301-4efa-80f2-2a9e0cc3a...@j4g2000yqe.googlegroups.com>,
>
> >"ARLINGTON - About 8 percent of human genetic material comes from a
> >virus and not from our ancestors, according to an article by
> >University of Texas at Arlington biology professor C�dric Feschotte
> >published in the Jan. 7, 2010 issue of Nature magazine."
>
> >http://www.uta.edu/ucomm/mediarelations/press/2010/01/genome-biologist-r
> >eports.php
>
> Sigh. Press releases.
But, still... Thanks for your answer. You and Mr Harshman have made a
humble programmer a bit smarter by expounding on some common knowledge
that had not yet reached me...
John Harshman
Usually, nothing. Just sits there as part of the junk DNA. Why?
Ernest Major
<e39c3eb0-082c-46b2...@j24g2000yqa.googlegroups.com>,
criticising the university PR department.
--
alias Ernest Major
Kleuskes & Moos
Does it form a basis for further evolution? I mean, running simple GA-
models frequently resulted in pseudo-random junk evolving into
something "usefull" over (a relatively small amount of) time.
John Harshman
Yes, that happens occasionally. Not just with transplanted genetic
material, but with any bit of junk DNA, whatever its origin. But the way
to bet is that any random piece of junk will remain junk. There being so
much of is, lots of low-probability events do happen, like new or
improved genes arising from within it. You can probably google several
cases.
el cid
I really wonder what you mean by "frequently" above.
I guess for definitions of frequently that mean exceedingly rarely
this would be true for biology. As in, if you introduce a pseudogene
into a new germ-line odds are it will never become anything more
than another bit of junk DNA. I guess transplantation of a truly
novel enzyme might balance some between rare and significant if
you have the right sort of big picture view, though I think 'too
rarely to be significant in the big picture' would probably be
how things work out.