Genome-wide patterns of selection in 230 ancient Eurasians

By I. Mathieson, Iosif Lazaridis, N. Rohland, Swapan Mallick, Nick Patterson, S. A. Roodenberg, Éadaoin Harney, Kristin Stewardson, D. Fernandes, M. Novak and 28 more. Nature, 2015

1,336 citations recorded by the source corpus.

Ancient DNA makes it possible to observe natural selection directly by analysing samples from populations before, during and after adaptation events. Here we report a genome-wide scan for selection using ancient DNA, capitalizing on the largest ancient DNA data set yet assembled: 230 West Eurasians who lived between 6500 and 300 bc, including 163 with newly reported data. The new samples include, to our knowledge, the first genome-wide ancient DNA from Anatolian Neolithic farmers, whose genetic material we obtained by extracting from petrous bones, and who we show were members of the population that was the source of Europe’s first farmers. We also report a transect of the steppe region in Samara between 5600 and 300 bc, which allows us to identify admixture into the steppe from at least two external sources. We detect selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height.

Subfields: Genetics

View Paper: https://www.semanticscholar.org/paper/fb48d03b320fc6c6aa0188fc169630258225a80b

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In Genetics

Citations in the corpus

From the field to the laboratory: Controlling DNA contamination in human ancient DNA research in the high-throughput sequencing era (2017, neutral): “…assays can be complete mitochondrial genomes (Brotherton et al. 2013; Llamas et al. 2016; Posth et al. 2016), genome-wide SNPs (Haak et al. 2015; Mathieson et al. 2015; Fu et al. 2016), exomes (Castellano et al. 2014), chromosomes (Fu, Meyer, et al. 2013), or complete genomes (Carpenter et al.…”
pong: fast analysis and visualization of latent clusters in population genetic data (2015, methodology): “In this article, we focus on the population-genetic application of mixed-membership models, and refer to this application as clustering inference; see Novembre (2014) for a review of multiple population-genetic clustering inference methods, including STRUCTURE.”
Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016, background): “Even lactose tolerance, assumed to be associated with pastoralism, appears to have been absent in early European farmers, being found in only 10 % of Bronze Age Europeans and increasing dramatically in just the past 3000 years [32, 44] (Fig.”
Signals of polygenic adaptation on height have been overestimated due to uncorrected population structure in genome-wide association studies (2018, neutral): “581 [6] Mathieson I et al.”
Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions (2016, neutral): “A second set of methods for reduced representation uses restriction enzymes to isolate small pieces of DNA (such as restriction-associated digest sequencing [RAD-seq] or genotyping by sequencing [GBS; reviewed in Puritz et al. 2014 b ; Andrews et al. 2016]; table A2).”
Tread Lightly Interpreting Polygenic Tests of Selection (2018, background): “…over 20 years, directional selection has been acting to increase the mean body size,yetbodysizeshaveactuallybeendecreasing, likelybecause of compensating effects in which recent changes in climatic conditions have led to slower growth rates and in turn lower average body sizes (Ozgul et al. 2009).”