[asa] Whole Genome Duplication

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.

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