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Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences.


ABSTRACT: Disentangling the effect on genomic diversity of natural selection from that of demography is notoriously difficult, but necessary to properly reconstruct the history of species. Here, we use high-quality human genomic data to show that purifying selection at linked sites (i.e. background selection, BGS) and GC-biased gene conversion (gBGC) together affect as much as 95% of the variants of our genome. We find that the magnitude and relative importance of BGS and gBGC are largely determined by variation in recombination rate and base composition. Importantly, synonymous sites and non-transcribed regions are also affected, albeit to different degrees. Their use for demographic inference can lead to strong biases. However, by conditioning on genomic regions with recombination rates above 1.5 cM/Mb and mutation types (C?G, A?T), we identify a set of SNPs that is mostly unaffected by BGS or gBGC, and that avoids these biases in the reconstruction of human history.

SUBMITTER: Pouyet F 

PROVIDER: S-EPMC6177262 | biostudies-literature | 2018 Aug

REPOSITORIES: biostudies-literature

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Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences.

Pouyet Fanny F   Aeschbacher Simon S   Thiéry Alexandre A   Excoffier Laurent L  

eLife 20180823


Disentangling the effect on genomic diversity of natural selection from that of demography is notoriously difficult, but necessary to properly reconstruct the history of species. Here, we use high-quality human genomic data to show that purifying selection at linked sites (i.e. background selection, BGS) and GC-biased gene conversion (gBGC) together affect as much as 95% of the variants of our genome. We find that the magnitude and relative importance of BGS and gBGC are largely determined by va  ...[more]

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