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1000 Genomes Pilot Data Suggests Recent Selective Sweeps Rare in Human Lineage

By Andrea Anderson

NEW YORK (GenomeWeb News) – Classic selective sweeps have played a relatively minor role in recent human adaptation, according to a study appearing online today in Science.

An international research team did computational analyses of nearly 200 human genomes sequenced for the pilot phase of the 1000 Genomes Project, focusing on genetic diversity patterns in functionally important parts of the genome. Overall, they reported, most of these diversity patterns did not fit those predicted by classic selective sweep models, suggesting selective sweeps have not been the main driver of human evolution over the past 250,000 years or so.

For the past decade, researchers have largely assumed that classical selective sweeps were the central mode of adaptation in humans and other organisms, co-senior author Guy Sella, an ecology, systems, and behavior researcher at the University of Jerusalem, told GenomeWeb Daily News.

The new work argues against this notion, implying that other modes of adaptation have had a larger influence on evolution in the human lineage. Based on their data, those involved in the study speculate that some human adaptations may have instead arisen through changes to many genes — a pattern comparable to those identified for several complex human diseases.

"It could be that adaptation was a polygenic phenomenon," Sella said. "Rather than having a single change of large effect at one gene, you had many, smaller changes contributing from many genes."

The classic selective sweep model describes situations in which particularly advantageous mutations pop up in the genome and quickly spread to become 'fixed' within a given population, the researchers explained. Such adaptations can be picked up in the genome, in part, because they leave a telltale pattern of reduced genetic variation at associated sites in the genome sequence.

"If you have a mutation that has a beneficial effect, upon appearance it would be positively selected and, therefore, it would spread very quickly through the population," Sella explained. "In so doing, it would carry with it part of the genome around it. As a result of that, once the sweep is completed, you would have a region of depleted genetic variation."

In an effort to get a better handle on the prevalence of such sweeps in human history, the team scoured 179 human genomes representing individuals from four populations, using computational methods to scrutinize genetic diversity patterns in parts of the genome that are thought to be functionally important.

"We looked at changes to the human genome that are likely to be functional," Sella explained. "And we asked, 'Do we see the signatures of a classical selective sweep?'"

When the team looked at protein-coding sequences, for instance, they found that the genetic variants expected to have functional consequences showed similar diversity levels as variants that don't seem to alter function — a pattern that doesn't jive with classic selective sweep models.

"We compared the patterns of variations around these two types of [non-synonymous and synonymous] changes," Sella said. "We didn't see any difference, which is not what we would expect to see if selective sweeps were pervasive."

Given the dearth of evidence for selective sweeps in their initial analysis, the researchers then turned their attention to looking at the frequency of these sweeps in the human lineage.

Although there are a few well-documented examples of such selective sweeps in humans, Sella noted, the team's analysis suggests that they occur infrequently. "At the moment, we have a handful of these very beautiful examples [of classic selective sweeps in the human genome]. And we will no doubt find a few more," he said. "But according to our study we're not likely to find many more such examples."

Nevertheless, the team explained, a lack of widespread selective sweeps does not point to a shortage of adaptations in humans. Rather, the results imply that many of these changes have occurred via other mechanism.

"This is not to say that there has been little adaptation on the human lineage," Sella said. "It just says that the pervasive mode of adaptation on the human lineage was not the classical selective sweep."

Consequently, those involved in the study say researchers should carefully consider other possible adaptive methods in their efforts to understand adaptation and phenotypic differences between human populations. For instance, they explained, it's possible that a slew of changes occurring across the genome have helped fuel human adaptation.

"Our findings suggest that recent human adaptation has not taken place through the arrival and spread of single changes of large effect, but through shifts of frequency in many places of the genome," co-senior author Mary Przeworski, a human genetics, ecology, and evolution researcher at the University of Chicago, said in a statement. "It suggests that human adaptation, like most common human diseases, has a complex genetic architecture."