Eight thousand years of natural selection in Europe

Ancient DNA makes it possible to observe natural selection directly by looking for parts of the genome that changed rapidly over time. By sequencing the genomes of ancient Europeans who lived during the past eight thousand years, we find selection on genes associated with diet, pigmentation and immunity, likely driven by the transition to an agricultural lifestyle in new environments at this time.

HFSP Long-Term Fellow Iain Mathieson and colleagues
authored on Thu, 26 November 2015

Natural selection is one of the major forces shaping our genomes. We want to find parts of our genome that have been selected to understand how our ancestors adapted to new diets, diseases, and environments, and also how those adaptations affect us today. Selection has left distinctive patterns in the genomes of present-day people, but those patterns can be obscured by other processes and are very difficult to link to specific historical events. Ancient DNA provides a solution to this problem – by allowing us to watch the frequencies of different alleles change over time and actually see the process of evolution as it happened.

The skeleton of an Anatolian Neolithic individual – one of the samples investigated in this study
Photo credit: Songül Alpaslan-Roodenberg

In this study, we looked at 230 ancient genomes from Europe, including the first European farmers, their ancestors from Anatolia, and the hunter-gatherers who preceded them. We found selection at genes related to diet, pigmentation and immunity – painting a picture of people adapting to settled agricultural life at high latitudes. Important dietary traits under selection include lactase persistence–the ability to digest milk as an adult–and fatty acid metabolism. Light skin pigmentation was likely advantageous as a way of avoiding vitamin D deficiency, and selection on immune related genes likely reflects new diseases that people were exposed to as they moved into denser communities in close proximity to domesticated animals.

Many traits have more complex genetic causes, for example height, which is controlled by many hundreds or even thousands of sites across the genome. Each of these sites has a very small effect but, by analyzing them all simultaneously, we can detect selection on these complex traits as well. In particular, we find that there were at least two independent episodes of selection on height – one for decreased height in early Iberian farmers, and one for increased height in populations living on the Steppe in the Bronze Age. One important question for future research is to quantify how much of the present-day variation in this and other complex traits is driven by historical natural selection.

Reference

Genome-wide patterns of selection in 230 ancient Eurasians. Iain Mathieson, Iosif Lazaridis, Nadin Rohland, Swapan Mallick, Nick Patterson, Songül Alpaslan Roodenberg, Eadaoin Harney, Kristin Stewardson, Daniel Fernandes, Mario Novak, Kendra Sirak, Cristina Gamba, Eppie R. Jones, Bastien Llamas, Stanislav Dryomov, Joseph Pickrell, Juan Luís Arsuaga, José María Bermúdez de Castro, Eudald Carbonell, Fokke Gerritsen, Aleksandr Khokhlov, Pavel Kuznetsov, Marina Lozano, Harald Meller, Oleg Mochalov, Vyacheslav Moiseyev, Manuel A. Rojo Guerra, Jacob Roodenberg, Josep Maria Vergès, Johannes Krause, Alan Cooper, Kurt W. Alt, Dorcas Brown, David Anthony, Carles Lalueza-Fox, Wolfgang Haak*, Ron Pinhasi* & David Reich*. Nature; Advanced online publication doi:10.1038/nature16152.

Link to Nature article

Farming's in their DNA (video link)