[asa] Re: Whole Genome Duplication .... References

Here are the references for the Whole Genome Duplication discussed in
the post copied below.

Original proposal:

   Kenneth H. Wolfe & Denis C. Shields, Molecular Evidence for an
   ancient duplication of the entire yeast genome, Nature, 387,
   p. 709, 12 June 1997

Papers analyzing connections between S. cerevisiae and species from
pre-WGD branch:

   M. Kellis, et. al., Proof and Evolutionary analysis of ancient gene
   duplication in the yeast Saccharomyces cerevisiae, Nature, 428,
   617-24, 2004.

   F. Dietrich, et. al., The Ashbya gossypii genome as a tool for
   mapping the ancient Saccharamoyces cerevisiae genome, Science, 304,
   304-307, April 9, 2004.

On Wed, Jul 19, 2006 at 02:20:56AM -0400, Joel Cannon wrote:
> The information here may have been previously posted. It was striking
> enough to me to take the time to pass it on anyway. The biologists on
> the list will be able to provide more details or correct mistatements.
>
> I am attending a workshop on quantitative approaches to gene
> regulatory systems. A couple of days ago, I was listening to a talk
> on the evolution of gene regulation. To study this, several research
> groups looked at 4 closely related yeast species which had diverged
> relatively recently (~ 20 million years is my recollection). They
> looked, among other things at the regulatory stuctures and the DNA
> region surrounding orthologs (a gene found in different species which
> has a common origin) and paralogs (two genes in a single species which
> has a common origin). More accurately, they used surrounding regions
> to help to discern orthologs and paralogs. The study found
> significant regions (I believe about 8\%) of ``ancient duplication
> blocks.'' There was a one to one mapping of genome regions among the 4
> close species (for each region in on species there was a corresponding
> region of the genome in the close species).
>
> Based on the patterns of similarity, an evolutionary biologist (K. H.
> Wolfe) argued that in an ancestor of the 4 species a whole set of
> genes had been duplicated (WGD or whole genome duplication) followed
> by rapid evolution and disappearance of one member of each pair. The
> claim was controversial. A number of others argued that there had been
> multiple small duplication events.
>
> The problem was resolved in stunning fashion when two separate groups
> (my notes only record one group's name) sequenced other yeast species
> that descended from common ancestors that existed prior to the proposed
> WGD. Google on ``WGD Eric Lander'' to find the 2004 Nature paper by
> Kellis, Lander, and others to see the results of one of the groups. In
> contrast to the 1 to 1 mapping of the closely related species, the
> researches found that for every region in the species which is not a
> descendent of the WGD (K. Waltii), there are two corresponding
> regions in the WGD descendent (the common S. Cerevisiae). A total of
> 253 blocks of ``doubly conserved synteny'' containing 75\% of the K.
> Waltii and 81\% of the S. Cerevisiae genomes were identified. If you get the
> paper at the website, there is a stunning graphical depiction of the
> mapping.
>
> Another thing the authors of the paper did was to look at the
> subsequent divergence of the paired genes. One biologist had predicted
> that in WGD, one set of genes would preserve the original function and
> the other would diverge (naturally, someone else argued the converse
> --- that divergence would would occur in both sets -- i.e. all genes).
> Based on the analysis, the first appears to have happened. The authors
> found that 17\% of the genes underwent accelerated evolution, defined
> to by amino acid substitution in the duplicated genome at least 50\%
> faster than the genes in K. Waltii. 95\% of these cases occurred in
> only one of the gene paralogues (i.e. one of the pair was stable, one
> was not). Thus it appears that one paralog retained the ancestral
> function, the other was free to evolve more rapidly.
>
> One other interesting point is that the the duplicated descendents'
> metabolism shifted from aerobic respiration to anaerobic respiration
> (fermentation). Thus the alcohol my conservative friends will not
> consume originated in the evolutionary process whose reality they deny.
>
>
> In hopes that others find this as intersting as I did.
> --
>
> ------------------------------------------------------------------------------
> Joel W. Cannon | (724)223-6146
> Physics Department | jcannon@washjeff.edu
> Washington and Jefferson College |
> Washington, PA 15301 |
>
>
>

-- 
------------------------------------------------------------------------------
Joel W. Cannon                   |   (724)223-6146         
Physics Department               |   jcannon@washjeff.edu 
Washington and Jefferson College |      
Washington, PA 15301             |      
                                     
                    
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