Re: Lateral gene transfer

Steve Clark (ssclark@facstaff.wisc.edu)
Wed, 14 Aug 1996 10:46:16 -0500

Would transposable elements, such as retroviral genomes, intracisternal
particle sequences, etc. qualify?
>
>Question for Joel Duff (or anyone else on the list):
>
>What experimental -- as opposed to post hoc inferential -- evidence
>is there for lateral gene transfer? I'm pretty familiar with the
>literature on phylogenetic claims, i.e., sequence X is sitting where it
>looks rather odd: postulate a lateral transfer. But what "real time"
>(if you will) studies exist showing the acquisition of foreign genes by
>a population or species?
>
>Here's why this matters. I'll cite a nicely provocative paper by
>Schwabe and Warr:
>
> We believe that it is possible to draw up a list of basic
> rules that underline existing molecular evolutionary models:
>
> 1. All theories are monophyletic, meaning that they all
> start with the *Urgene* and the *Urzelle* which have given
> rise to all proteins and all species, respectively.
>
> 2. Complexity evolves mainly through duplications and
> mutations in structural and control genes.
>
> 3. Genes can mutate or remain stable, migrate laterally
> from species to species, spread through a population by
> mechanisms whose operation is not fully understand, evolve
> coordinately, splice, stay silent, and exist as pseudogenes.
>
> 4. Ad hoc arguments can be invented (such as insect vectors
> or viruses) that can transport a gene into places where no
> monophyletic logic could otherwise explain its presence.
>
> This liberal spread of rules, each of which can be observed
> in use by scientists, does not just sound facetious but
> also, in our opinion, robs monophyletic molecular evolution
> of its vulnerability to disproof, and thereby of its
> entitlement to the status of a scientific theory.
>
>(C. Schwabe and G. Warr, _Perspectives in Biology and Medicine_ 27
>[1984]: 465-485)
>
>Actually, Schwabe and Warr tell only half the story, and not even
>the scariest half.
>
>It is standard practice in molecular phylogeny construction to determine
>sequence alignment, the first analytical stage after the raw sequence
>data are obtained, more or less "by eye" -- and then to assess the
>reliability of that alignment by checking the phylogeny it produces. If
>you get a wild phylogeny: well, must be the wrong alignment.
>
>[A recent example of this sort of method, which should make anyone's hair
>stand on end, is Christopher Wills's paper "Topiary Pruning and Weighting
>Reinforce An African Origin for the Human Mitochondrial DNA Tree,"
>_Evolution_ 50 (1996): 977-989. Wills "prunes" (i.e., manipulates) human
>mtDNA sequence data iteratively until he gets the phylogenetic pattern he
>wants, because the starting pattern shows a starburst phylogeny with the
>primate outgroup located "very asymmetrically" from the root of the human
>starburst. Basically Wills tidies up the data until he gets the phylogeny
>he likes.]
>
>Tim Ikeda and I have correspondended a bit about this. (Tim, are you
>there?) But what I really want to know, re this post, is what
>experimental literature exists on lateral transfer.
>
>I'm guessing not much. If that's the case, then we don't really have
>decent grounds for constraining hypotheses of lateral transfer.
>
>Paul Nelson
>University of Chicago
>
>
>
>
>
__________________________________________________________________________
Steven S. Clark, Ph.D. Phone: (608) 263-9137
Associate Professor FAX: (608) 263-4226
Dept. of Human Oncology and email: ssclark@facstaff.wisc.edu
UW Comprehensive Cancer Ctr
University of Wisconsin
Madison, WI 53792

"Universities are full of knowledge; the freshmen bring a little in,
the seniors take none away...the knowledge accumulates." Mark Twain
__________________________________________________________________________