Re: In the news: Cornell finds natural selection in humans


John Harshman wrote:
> Ron O wrote:
>
> > John Wilkins wrote:
> >
> >>http://www.eurekalert.org/pub_releases/2005-10/cuns-cfn102105.php
> >>
> >>ITHACA, N.Y. -- The most detailed analysis to date of how humans differ from
> >>one another at the DNA level shows strong evidence that natural selection has
> >>shaped the recent evolution of our species, according to researchers from
> >>Cornell University, Celera Genomics and Celera Diagnostics.
> >>In a study published in the Oct. 20 issue of the journal Nature, Cornell
> >>scientists analyzed 11,624 genes, comparing how genes vary not only among 39
> >>humans but also between the humans and a chimpanzee, whose DNA is 99 percent
> >>identical to humans.
> >>
> >>The comparisons within and between species suggest that about 9 percent of
> >>genes that show some variability within humans or differences between humans
> >>and chimpanzees have evolved too rapidly to be explained simply by chance. The
> >>study suggests that positive Darwinian natural selection -- in which some
> >>forms of a gene are favored because they increase the probability of survival
> >>or reproduction -- is responsible for the increased rate of evolution. Since
> >>genes are blueprints for proteins, positive selection causes changes in the
> >>amino acid sequence of the protein for which the gene codes.
> >>
> >>"Our study suggests that natural selection has played an important role in
> >>patterning the human genome," said the paper's lead author, Carlos Bustamante,
> >>assistant professor of biological statistics and computational biology at Cornell.
> >>
> >>The Cornell/Celera team found that genes involved in immune function, sperm
> >>and egg production, sensory perception and transcription factors (proteins
> >>that control which genes are turned on or off) have been particularly affected
> >>by positive selection and show rapid evolution in the last 5 million years,
> >>when humans shared a common ancestor with chimps.
> >>
> >>Likewise, the researchers found that approximately 13 percent of the genes
> >>that may vary show evidence of slightly deleterious or harmful mutations in
> >>human populations; these include genes involved in determining the basic
> >>structure of cells and muscles as well as genes that control traffic in and
> >>out of the cell. These mutations are subject to weak negative selection,
> >>according to the study. In general, negative selection eliminates from the
> >>population very harmful changes to proteins that kill or stop reproduction.
> >>But mutations that have led to slightly deleterious versions of the gene --
> >>mutations that may cause disease or only slightly reduce the average number of
> >>children left by those that carried the mutation -- can by chance become quite
> >>common in the population.
> >>
> >>The authors also found a correlation between genes predicted to be under
> >>negative selection and genes implicated in certain hereditary diseases. For
> >>example, among the genes the researchers predicted to be under negative
> >>selection are those involved in muscular dystrophy and in Usher syndrome, the
> >>most common cause of congenital blindness and deafness in developed countries.
> >>
> >>"We have a long way to go before we can predict from looking at sequences,
> >>which mutations in which genes and under which environmental conditions can
> >>ultimately lead to disease. This is a first step in identifying the classes of
> >>genes that appear to be particularly vulnerable to these types of changes,"
> >>said Bustamante.
> >>
> >>A team from Celera initiated the project and sequenced more than 20,000 genes
> >>in 39 humans and a chimpanzee. By comparing the DNA sequences of the 39 human
> >>subjects across the 20,000 genes, the Celera researchers identified DNA sites
> >>in the genome where individuals in the sample differed from one another. The
> >>chimpanzee sequence was then used to identify which form of the gene was the
> >>original ancestral form and which was the derived or new type. The original
> >>goal of the project was to identify novel amino acid variants that could then
> >>be tested for association with human disease in subsequent studies. The
> >>Cornell researchers became involved at the analysis stage in order to make
> >>predictions about what types of changes are most likely to be functionally
> >>important.
> >>
> >>[For Larry Moran ;-)]
> >>--
> >>John S. Wilkins, Postdoctoral Research Fellow, Biohumanities Project
> >>University of Queensland - Blog: evolvethought.blogspot.com
> >>"Darwin's theory has no more to do with philosophy than any other
> >>hypothesis in natural science." Tractatus 4.1122
> >
> >
> > What they need to do is the same study on chimps that have a shrinking
> > population instead of an expanding population where founder effects
> > could become significant.
>
> Founder effects in a rapidly expanding population? Just the opposite,
> really. Alleles would have a reduced chance of being lost, even if they
> were slightly deleterious under normal conditions. Anyway, that would
> not explain less than expected variation at particular loci; only a
> selective sweep would explain that.

I wasn't talking about the obvious indications of selection, but just
the notion that increased variation means selection.

>
> > Of course chimps could have the opposite
> > problem of founder effects becoming more significant because of their
> > shrinking populations. Selection could have relaxed for humans for
> > many genes. The question is how we differ from other species that may
> > have a more normal population dynamic. But what is normal? If
> > allopatric speciation is the most likely type of speciation event.
>
> Let's not confuse allopatric with peripatric. The latter incorporates a
> bottleneck of sorts. The former doesn't, or doesn't have to. If a large
> population splits exactly in half, that's still allopatric speciation.

Doesn't matter to me since it is a subset of allopatric speciation
events.

>
> > All
> > populations may do this during the course of their expansion and
> > evolution. It may be the fuel for new speciation events, but on the
> > whole most of these "selective" changes don't make it into the next
> > speciation event or our molecular data would be much different for the
> > comparisons between species. If populations are cauldrons of change
> > speciation events appear to be conservative. The great variation
> > within an established species isn't transferred to the new species. If
> > it were, just think what our DNA data would look like. Instead of a
> > 5:1 replacement to silent amiino acid substitution ratio it would be
> > closer to 1:1 between species.
>
> Let's also not confuse speciation with the mere passage of time. Most
> variants will disappear from a population over time just by neutral
> drift, and slightly deleterious mutations can reach a detectable
> frequency before disappearing. No "speciation event" required. And you
> mean 1:5, presumably.

I did mean 1:5. That is what you expect (loss of neutral and
detrimental variation over time. So why is there so much variation?
It could be selection, but it could also be relaxed selection and
population expansion. Even if these things are slightly detrimental,
they could still increase in frequency due to population expansion and
founder effects.

Ron Okmoto

.

Relevant Pages

  • In the news: Cornell finds natural selection in humans
    ... N.Y. -- The most detailed analysis to date of how humans differ from ... one another at the DNA level shows strong evidence that natural selection has ... scientists analyzed 11,624 genes, comparing how genes vary not only among 39 ...
    (talk.origins)
  • Re: In the news: Cornell finds natural selection in humans
    ... N.Y. -- The most detailed analysis to date of how humans differ from ... > one another at the DNA level shows strong evidence that natural selection has ... > scientists analyzed 11,624 genes, comparing how genes vary not only among 39 ...
    (talk.origins)
  • Re: Atheists support evolution because evolution supports their
    ... But scientists have now found that chimps are ... more evolved than humans are, ... selection in chimpanzee evolution than in human evolution". ... just that more genes underwent selection in chimps than ...
    (talk.origins)
  • Re: One Good Thing Abou Dumbledore Being Gay
    ... plants applies, as such, to humans. ... selection" means very different things for humans on the one hand ... There's no difference at all - it's all about survival of genes. ... that don't have any kids of their own; it's about your genes surviving ...
    (alt.fan.harry-potter)
  • Re: The root of all evil? - Dawkins Documentary
    ... selection not being a very common phenomenon, ... Dawkins himself refers to genes are 'selfish cooperators'. ... what the biochemical nature of life itself and how it might have begun. ... parasitical is one manner in which a meme can operate, ...
    (talk.origins)