Re: The Chimpanzee Genome

In "Who Was Adam," published in 2005, Rana includes a chapter called "What
About Chimpanzees." He concludes:

"Although human and chimpanzee genomes display great similarity, that
similarity has been magnified to some extent by research
methodology. Researchers are starting to uncover significant
differences. Results of large-scale comparisons must be considered
preliminary, as it's not yet clear what genetic differences mean in terms of
anatomical and behavioral characteristics. However, greater clarity will
likely come as research progresses. Already the newly recognized genetic
differences between humans and chimpanzees complicate the picture for
biologists who view the high degree of genetic similarity between humans and
chimpanzees as proof of shared ancestry. If 99 percent genetic similarity
represents a close evolutionary connection, what does the more recently
measured 86.7 percent genetic similarity mean?"

On 3/2/06, Janice Matchett <janmatch@earthlink.net> wrote:
>
> As an aside, does anyone know if Fazale R. Rana, Ph.D. has had any
comment
> about the information published in 2005 (see commentary about it below)
> since the 2001 article "Humans and Chimps Differ" in Hugh Ross'
Connections
> 2001 - Volume 3, Number 3 posted here?:
> http://www.reasons.org/resources/connections/2001v3n3/index.shtml
>
> I haven't been able to find anything. ~ Janice
>
> Thursday, September 01, 2005
>
> The chimpanzee genomePZ Myers • 17 Comments
>
http://64.233.179.104/search?q=cache:SvBbphfO81oJ:pharyngula.org/index/weblog/comments/the_chimpanzee_genome/+Has+a+genome-wide+comparison+of+humans%E2%80%99+and+chimps%E2%80%99+DNA+ever+been+made%3F&hl=en&gl=us&ct=clnk&cd=1
>
> I finished reading the chimpanzee genome paper last night, and it is not
an
> easily digestible piece of work. It's fairly technical genetics, and it's
> actually a bit of a hodge-podge, as you might expect given the multitude
of
> authors and the immensity of the project.
>
> In many places where the results were particularly interesting, the
authors
> also got very cautious and tentative, and quite rightly so:
>
> this is just the first step in a very difficult research program, and
there
> aren't any simple, clear answers to be expected…not yet, if ever.
>
> I'm not even going to try to present a narrative summary of the work. The
> best I can do is dole out some little tidbits that I thought were
> interesting.
>
> The sequence as a whole was obtained from a single specimen of Pan
> troglodytes. However, they also analyzed sequences from four other West
> African and three Central African chimps.
>
> Humans and chimps are much more alike than different. 29% of our proteins
> are identical, and the average protein differs by only two amino acids.
The
> genome wide nucleotide divergence rate is 1.23% (it's higher in the Y
> chromosome, which seems to be a special case­see John Hawks).
>
> While single nucleotides are different in 1.23% of the genome, 3% differs
> because of insertions and deletions; that is, largish chunks of DNA that
are
> missing in one species relative to the other, or that have been added in
> one. The authors estimate that there have been about 5 million insertions
> and deletions in the combined chimp and human lineages in the last 5-7
> million years since they diverged.
>
> Most of the differences are the result of the fixation of neutral or
> slightly deleterious alleles.
>
> One common question is which differences are important; which genetic
> changes are responsible for the obvious differences between chimps and
> humans? Of the 13,454 human-chimp gene orthologues they examined, they
> identified 585 that have a high level on non-synonymous sequence changes,
> and examined their function, where known.
>
> If you were hoping for an obvious 'big brain' or 'hairy-limb' gene, you
> will be disappointed. What they found were genes involved in:
>
> immune responses, for instance against malaria and tuberculosis
>
> reproduction, protamines and semenogelins
>
> olfaction
>
> That's what's important, humbling as it may be.
>
> A search by functional category for relative acceleration in the rate of
> non-synonymous substitutions did find one interesting difference: humans
> have a greater than expected difference in genes involved in transcription
> factor activity. This includes some homeotic genes.
>
> This suggests that there may have been important changes in developmental
> regulatory genes in the human lineage, but because the absolute number of
> nucleotide changes is small, the authors suggest some caution about
> overinterpreting this at this point.
>
> 36 human genes are not present at all in the chimp, and and additional 17
> are partially deleted.
>
> There are also genes present in chimps that are missing or damaged in
> humans, but deficiencies in the gene models for chimps makes them more
> difficult to quantify.
>
> One very interesting example is caspase-12, an important enzyme in
> apoptosis, which triggers cell death in response to problems in calcium
> levels.
>
> Humans have a damaged copy of the gene, while that of chimps and mice is
> intact. Loss of function in mice leads to a failure of amyloid-induced
> neuronal cell death; this may be a gene that contributes to Alzheimer's
> disease in humans.
>
> Another interesting analysis was to compare human alleles associated with
> disease to the chimp orthologues. As it turns out, some alleles we
consider
> 'bad', or disease-related, are the wild-type forms. For example, a form of
> the gene called PPARG that has a proline at position 12 is associated with
a
> greater risk of type 2 diabetes in humans, but is the most common allele
in
> chimps. That suggests that the diabetes-resistant form of PPARG is the
> recent adaptation, and that we may be seeing the ongoing spread of this
> allele in our population.
>
> The authors identified evidence of selective sweeps in human history.
> Alleles that are selectively successful can rise rapidly in frequency in a
> population. Because recombination in any one region is relatively rare,
when
> that allele becomes fixed, the other alleles that happen to be in the gene
> locations around it will also be fixed in the population. This process
> reduces diversity and also increases the frequency of a whole set of
> hitchhiking alleles in that same region.
>
> Comparison with the chimpanzee genome as a baseline allowed the authors
to
> pick out 6 regions in the human genome that exhibit all the signs of
having
> been subject to a selective sweep within the last quarter million years.
One
> of these regions contains both the FOXP2 gene, involved in speech, and the
> CFTR gene which, when defective, is responsible for cystic fibrosis.
..."
> [snip]
>
> NOTE: Pharyngula has moved to
> http://scienceblogs.com/pharyngula/
>
>
>
>
Received on Thu Mar 2 11:52:13 2006