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Researchers find clues to evolution by studying genes of living people

(David L. Ryan/Globe Staff)
By Carolyn Y. Johnson
Globe Staff / January 18, 2010

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Scientists seeking to unravel the evolutionary history of human beings are looking not to the past but into the genes of people living today.

Researchers at Harvard University have developed a powerful method for identifying genes that have been favored by evolution and have spread rapidly among the population because of natural selection, the process by which organisms with beneficial traits survive in greater numbers and pass on their genes to more offspring than others.

The hope is the new tool will cast a light on recent changes in human biology and provide insight into modern-day disease, since one of the most powerful evolutionary pressures human beings have faced are pathogens.

“It’s pretty fascinating you can learn about the history of a population just by looking at patterns of variation in present-day populations,’’ said Joshua Akey, a geneticist at the University of Washington who was not involved in the study. “The second important thing is if something is under selection, it’s doing something functionally important,’’ so the new technique should spotlight genes that have been important for human survival, giving scientists new targets to better understand the recent history of human biology and disease.

For years, scientists have known that genetic footprints left behind by evolution can be used to find regions in the genome that have recently spread through the population. But the tools they used were blunt, often spotlighting a swath of genetic material that included many genes. What was not clear when looking at genetic material that had become more common through evolution was which portion of it was advantageous and which parts were merely along for the ride.

“How do you figure out who is the driver and who is the hitchhiker?’’ said Dr. Pardis Sabeti, an assistant professor of organismic and evolutionary biology at Harvard and the senior author of a paper on the method published online earlier this month in the journal Science Express.

To create the tool, lead authors Sharon Grossman and Ilya Shylakhter combined different approaches for finding regions that have become more common because of natural selection. The method narrowed the results, zeroing in on much more specific areas of the genome - finding on average one gene instead of eight.

They showed that the technique would work by checking it on regions known to be under natural selection that contained pigmentation genes. The new method pinpointed the pigmentation genes and mutations known to be associated with eye or skin color, a proof that it was doing what the researchers had hoped.

The team then used the tool on genetic data gathered from 270 people and found intriguing suggestions that natural selection was working on specific genes. For example, the method highlighted a gene in East Asians known to play a role in sensory perception and another that plays a role in blood pressure and weight. While further research will help scientists understand exactly what those genes are doing, and why they might be advantageous, the findings give scientists new targets to examine.

The technique also pointed to areas that regulate genes and to genes associated with disease.

“We see a lot of genes that are important in infectious disease - including malaria, Lassa fever, tuberculosis - and in addition enrichment of immune genes,’’ Sabeti said.

Akey called the technique “powerful, because until you actually identify the gene and the specific mutation, you still have a very incomplete understanding of selection at that region.’’

Sarah Tishkoff, a geneticist at the University of Pennsylvania, wrote in an e-mail that a necessary next step will be to go from identifying areas that have been targets of natural selection to understanding what they do and why they would have been selected.

Recently selected genes may also give insight into modern-day diseases. Genes that may have had beneficial effects on metabolism or immune response 10,000 years ago, for example, might now be risk factors for diseases such as obesity or autoimmune diseases.

For Sabeti, probing recent evolutionary history has had medical repercussions. In 2007, she found a signature of natural selection in a gene involved in Lassa fever infection, a deadly infectious disease that kills many thousands of people each year.

Sabeti is engaged in research to better understand genetic resistance to the disease in Nigeria and the genome of the virus.

But the tool’s greatest opportunity is on the horizon, when it will be unleashed on a massive data set that is being accumulated: the full genomes of 1,000 people from across the world.

Carolyn Y. Johnson can be reached at cjohnson@globe.com.