Ancient genomes reveal natural selection in action

http://www.eurekalert.org/pub_releases/2015-11/hms-agr112015.php

Public Release: 23-Nov-2015
Ancient genomes reveal natural selection in action
Study tracks gene changes during the introduction of farming in Europe
Harvard Medical School

The introduction of agriculture into Europe about 8,500 years ago changed the way people lived right down to their DNA.

Until recently, scientists could try to understand the way humans adapted genetically to changes that occurred thousands of years ago only by looking at DNA variation in today's populations. But our modern genomes contain mere echoes of the past that can't be connected to specific events.

Now, an international team reports in Nature that researchers can see how natural selection happened by analyzing ancient human DNA.

"It allows us to put a time and date on selection and to directly associate selection with specific environmental changes, in this case the development of agriculture and the expansion of the first farmers into Europe," said Iain Mathieson, a research fellow in genetics at Harvard Medical School and first author of the study.

By taking advantage of better DNA extraction techniques and amassing what is to date the largest collection of genome-wide datasets from ancient human remains, the team was able to identify specific genes that changed during and after the transition from hunting and gathering to farming.

Many of the variants occurred on or near genes that have been associated with height, the ability to digest lactose in adulthood, fatty acid metabolism, vitamin D levels, light skin pigmentation and blue eye color. Two variants appear on genes that have been linked to higher risk of celiac disease but that may have been important in adapting to an early agricultural diet.

Other variants were located on immune-associated genes, which made sense because "the Neolithic period involved an increase in population density, with people living close to one another and to domesticated animals," said Wolfgang Haak, one of three senior authors of the study, a research fellow at the University of Adelaide and group leader in molecular anthropology at the Max Planck Institute for the Science of Human History.

"Although that finding did not come fully as a surprise," he added, "it was great to see the selection happening in 'real time.'"

The work also supports the idea that Europe's first farmers came from ancient Anatolia, in what is now Turkey, and fills in more details about how ancient groups mixed and migrated.

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"In the past year, we've had a super-exponential rise in the number of ancient samples we can study on a genome scale," said Reich, who is also an associate member of the Broad Institute of Harvard and MIT and a Howard Hughes Medical Investigator. "In September 2014, we had 10 individuals. In this study, we have 230."

The DNA came from the remains of people who lived between 3,000 and 8,500 years ago at different sites across what is now Europe, Siberia and Turkey. That time span provided snapshots of genetic variation before, during and after the agricultural revolution in Europe.

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Members of the team used several technological advances to obtain and analyze the new genetic material. For example, they exploited a method pioneered by Pinhasi's laboratory to extract DNA from a remarkably rich source: a portion of the dense, pyramid-shaped petrous bone that houses the internal auditory organs. In some cases, the bone yielded 700 times more human DNA than could be obtained from other bones, including teeth.

"That changed everything," said Pinhasi. "Higher-quality DNA meant we could analyze many more positions on the genome, perform more complex tests and simulations, and start systematically studying allele frequency across populations."

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