Evidence of evolutionary selection found in 544 genes

September 16, 2008 By Bill Steele

(PhysOrg.com) -- By comparing the genomes of humans and five other mammals, Cornell researchers have identified 544 genes that have been shaped by positive selection over millions of years of evolution.

"To our knowledge this is the largest and most comprehensive analysis of positive selection to date," write the researchers in the Aug. 1 issue of the journal PLoS Genetics, reporting on research mainly funded by the National Science Foundation. Natural selection (favorable traits becoming more common over successive generations) that tends to favor new forms of genes is known as positive selection.

Previously, the Cornell group compared the genomes of humans, chimpanzees and the Rhesus macaque. By extending the analysis to mice, rats and dogs, the researchers were able to find "stronger signals" of change by going back up to 80 million years on the evolutionary tree. Other studies have found signatures of positive selection using population genetics methods -- comparing genomes across many members of the same species -- but those focus on changes over just the last tens of thousands of years.

The researchers -- including Adam Siepel, Cornell assistant professor, and Carlos Bustamante, Cornell associate professor, both of biological statistics and computational biology; and Cornell postdoctoral researchers Carolin Kosiol and Tomas Vinar -- used a high-performance computer cluster at the Cornell Center for Advanced Computing to study 16,500 human genes that are also found, with some differences, in at least two of the other five species.

Over time, random changes can occur in the genetic code that replace one of the amino acids in a protein with another. Sometimes these changes have no effect on the function of the protein. But if the change alters the function of the protein and the change is beneficial -- if, for example, it protects against a disease that is common in a certain time and place -- individuals with the new version of the gene will be more likely to survive than others, and the new version will gradually replace the old one in an evolving population.

Siepel's group used the unimportant changes as a sort of clock to show how much change would be expected over evolutionary time. If a gene showed significantly more change than expected by random chance it was predicted to be under positive selection.

Many of the positively selected genes found in rodents involved immunity and defense, including defense against bacteria and viruses, suggesting an evolutionary "arms race" with pathogens. Responses to wounding and inflammation were also common.

The largest group of positively selected genes in primates involved sensory inputs -- including perceptions of taste, color and pain. "The conventional wisdom is that we should see major changes in the brain-related genes," Siepel noted. "We didn't find a signal for that, but did find inputs to the central nervous system." Perhaps, the researchers speculated, changes in sensory input drove changes in the brain.

The study supports the idea that positive selection is important in evolution, Siepel said. Theorists have argued over the relative importance of positive selection versus "neutral drift," where random changes simply happen with no positive or negative result. He noted that positive selection was found mainly in genes that are not expressed in as many tissues as others. "Genes with more specialized purposes may have more freedom for adaptation," he explained.

The researchers also found evidence that many changes seem to have occurred in spurts over short periods of time. For example, they found genes that were not under selection in lower mammals, then came under selection in primates, then were lost in humans. Whether evolution has been continuous or episodic has also been a subject of much debate among biologists.

Provided by Cornell University

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DonR
Sep 16, 2008

Rank: 4.3 / 5 (8)
I'm now 32 and very much looking forward to the possibility that we'll see the end of fantastic, deistic rubbish, due to discoveries such as this, in my lifetime.
LucFerris
Sep 16, 2008

Rank: 3 / 5 (7)
The prejudicial problem with that statement, DonR, is that faith driven beliefs are not as much rubbish as they are a fundamental part of the culture of humanity. Organized religion was there to control the thoughts of the masses in order to make civilization possible. Science and the exploratory spirit of humans, while oftentimes flying in the face of dogma, would have never been given a foothold without the power and protection of religion. Now, science is poised to remove these controls and allow humanity to flourish with untethered creative and innovative thought. You must not forget, DonR, that the basic idea of evolution hinges on the fact of positive selection. This happens in human culture as well, just look at how much better prepared our silly government is when faced with impending weather phenomena. Cultural evolution is not an accident, it is the destiny of mankind. Humanity is approaching the cusp of a new re-evolution. The so-called Age of Aquarius is coming, so humans will need the patience and wisdom of the literati of the world on our side. The Human Revolution is happening. Stories like these are proof of it. But evolution does not just happen in one's lifetime without determination, and, above all, education. Only when a person wants to learn truths, can that person let go of his fantastic beliefs. I put it in your hands, DonR, to make this happen.
Arikin
Sep 16, 2008

Rank: 2 / 5 (9)
By religion you sound like you mean the institutes/churches run by imperfect humans closely involved with politics. Please separate that from the creationism that this article is related to.

But I do not see how positive selection rules out creationism. According to creationism an all knowing being created life. If this being is all knowing wouldn't that being know that positive selection is required for any long term survival in our world of so many food chains and interaction of species?

This article just shows that the all knowing being of creationism knew what they were doing. We just get the pleasure of discovering all the details :-)
Dinotron
Sep 16, 2008

Rank: 3.7 / 5 (6)
and who created the all knowing bearded one in the sky?
Keys1337
Sep 17, 2008

Rank: 3.7 / 5 (6)
and who created the all knowing bearded one in the sky?
The mustachioed one of course
seanpu
Sep 17, 2008

Rank: 3 / 5 (4)
"Whether evolution has been continuous or episodic has also been a subject of much debate among biologists."

Its pretty obvious from any biologists perspective that evolution shows the behavior of being both 'gradual, continuous refinement across generations' (aka Darwinism), and 'episodic and spontaneous innovations' caused by horizontal gene transfer methods (aka cosmic ancestry and panspermia www.panspermia.org ).
Scuba_jeff
Sep 17, 2008

Rank: 3.7 / 5 (3)
listen , if the was an all powerful all knowing omnipoent being ( call it god or as I prefer zeus) why did'nt he/she/it get it right the first time. It seems to me that the should be no evidence of anything else in my dna but human. no vestigle tails; or fetal gills. He/shee must have done something right when he made the dinosaurs- they live for 65 million years-- couldt he step in and deflect the astreroid ?
nano999
Sep 19, 2008

Rank: 5 / 5 (1)
Malachi 2:3 Behold, I will corrupt your seed, and spread dung upon your faces

Why does a supreme being feel the need to spread poop upon our faces? Scat fetish?
DrRobMiller
May 19, 2009

Rank: not rated yet
Can anyone explain to me how DNA obtained all of the information it contains including the epigentic and chromosomal topography info?
Rank 4.4 /5 (46 votes)
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