Joel,
I read your posts at the ASA site about whole genome
duplication. Bravo! I'd like to share them with
Stephen Jones at his blog site. He is a "progressive
creationist" (a creationistic I.D.ist) named Stephen
Jones who used to run a yahoo group called
CreationEvolutionDesign, and now he has a blog. He is
pretty outspoken, but seems to be able to read and
comprehend and at least listen to pro-evolutionary
arguments and evidence. The subject of whole genome
duplication came up and I sent him the following
information. You may be interested in his reply to me
as well:
http://creationevolutiondesign.blogspot.com/2006/05/massive-
duplication-of-genes-may-solve.html
STEPHEN JONES: Harvard botanist and Neo-Darwinism
co-founder G. Ledyard Stebbins pointed out that
"polyploidy has contributed little to progressive
evolution"
ED: Stebbins wrote that way back in 1971. Since then
geneticists have learned much more about duplications
of individual chromosomes, and also about duplications
of ENTIRE GENOMES. And no, the animals in such cases
do not die from such a massive mutation. In fact two
similar species of zebrafish live today, one with
nearly twice the genetic material of the other, though
many of the duplicated genes are pseuodgenes in the
species whose ancestors underwent the duplication.
For instance, CONTRA STEBBINS,
in 1998 a "Computational Genetics Discussion Group:
Genome Duplication" wrote on the web:
"Whole genome duplication appears to be an important
evolutionary mechanism (Ohno, 1970).
"Despite the rarity of whole-genome duplications, we
have observational evidence for several of them:
"Saccharomyces cerevisiae (yeast) duplicated about
10^8 years ago.
"Vertebrates underwent 2 duplications some 2*10^8
years ago.
"More recent genome duplications have occurred in some
vertebrate lines such as frogs, the salmoniform fish
and zebrafish.
"Particularly prevalent in plants (i.e. several
occurences in the cereal lineage)."
~~~~~~~~~~
"In 1999 Holland [a professor] lists understanding
‘the importance of gene duplication in the evolution
of development’ as one of the two most important
questions in evolutionary developmental biology at the
end of the 20th century.
"This statement reflects the particular interest in
duplications in developmental genes, but also the
general interest in evolution by gene duplications."
~~~~~~~~~~~~~~~~
Since then, "unmistakable" evidence for "whole genome
duplication" in the vertebrate line of evolutionary
changes has been found:
Two rounds of whole genome duplication in the
ancestral vertebrate.
PLoS Biol. 2005 Oct;3(10):e314. Epub 2005 Sep 6.
Related Articles, Links
ABSTRACT
<...> UNMISTAKABLE EVIDENCE OF TWO DISTINCT GENOME
DUPLICATION EVENTS EARLY IN VERTEBRATE EVOLUTION
indicated by clear patterns of four-way paralogous
regions covering a large part of the human genome. Our
results highlight the potential for these large-scale
genomic events to have driven the evolutionary success
of the vertebrate lineage.
Definition of *PARALOGOUS GENES*: "Two genes or
clusters of genes at different chromosomal locations
in the same organism that have structural similarities
indicating that they derived from a common ancestral
gene and have since diverged from the parent copy by
mutation and selection or drift."
~~~~~~~~~~~~
Genome duplication in the teleost fish Tetraodon
nigroviridis reveals the early vertebrate
proto-karyotype.
Nature. 2004 Oct 21;431(7011):916-7.
ABSTRACT
<...> ANALYSIS OF THE TETRADON AND HUMAN GENOMES SHOWS
THAT WHOLE-GENOME DUPLICATION OCCURRED IN THE TELEOST
FISH LINEAGE, SUBSEQUENT TO ITS DIVERGENCE FROM
MAMMALS. The analysis also makes it possible to infer
the basic structure of the ancestral bony vertebrate
genome" <...>
~~~~~~~~
Excerpts from: GENE DUPLICATIONS AND VERTEBRATE
PHYLOGENY by James Cotton (circa 2001)
"Theoretical studies have shown that gene duplications
may be relatively likely to lead to new gene
functions, and to increase the fitness of genomes in
which they occur. Walsh (1995) presents a population
genetic model suggesting that, for large populations,
‘new gene function, rather than pseudogene formation,
is the expected fate of most duplicated genes’, which
would make gene duplication an impressively powerful
mechanism for the evolution of novel biochemistry and
novel developmental processes. Specifically, new
functions are likely to evolve where rS >> 1, where S
= 4Nes and Ne is the effective population size, S is
the selection coefficient and r is the ratio of
advantageous to other mutations. This model is likely
to underestimate the rate of evolution of new gene
functions, principally because it assumes that all
nonadvantageous mutations are neutral, where in
reality many will be more or less deleterious. Ohta
(1989) admits that ‘gene duplication could well have
been the primary mechanism for the evolution of
complexity in higher organisms’, and presents models
for the origin of ‘gene families with diverse
functions’, concluding that natural selection should
favour those genomes with more favourable mutations
occurring in duplicated genes, so there should be
selective pressure favouring mechanisms of gene
duplication. Ohta has also presented a number of other
simulation studies on the evolution of large gene
families (Batson and Ohta, 1992; Ohta 1987, 1988a,
1988b), which broadly support the likelihood of this
model in molecular evolution. Empirical studies (such
as Nadeau and Sankoff, 1997) largely suggest that the
evolution of new functions is even more common than
theoretical studies suggest, but there are a number of
difficulties with the empirical work (Wagner, 1998).
"The very existence of families of paralogous genes
also provides powerful evidence for the importance of
gene duplications, so data like those shown in figure
2 seem to confirm that gene duplications have indeed
played a very powerful role in shaping genomes.
Although, as discussed later, much interest has
focused on gene duplications in vertebrates, there is
substantial evidence (e.g. Brenner et al., 1995; Wolfe
and Shields, 1997) that gene duplications have also
been important in other organisms, such as in the
evolution of cell-to-cell communication pathways in
the first multicellular animals (Suga et al., 1999.
Ono et al, 1999). It is also important to note here
that a number of potential mechanisms for gene
duplication have been suggested, ranging from unequal
crossing-over, which will lead to duplication of a
relatively small stretch of DNA, to polyploidisation,
which will lead to duplication of the entire genome."
--- Joel Cannon <jcannon@jcannon.washjeff.edu> wrote:
> 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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Received on Sun Jul 23 23:28:22 2006
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