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

Pouyet, Fanny; Aeschbacher, Simon; Thiéry, Alexandre Benoit Xavier; Excoffier, Laurent (2018). Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences. eLife, 7, pp. 1-21. eLife Sciences Publications 10.7554/eLife.36317

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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.

Item Type:

Journal Article (Original Article)

Division/Institute:

08 Faculty of Science > Department of Biology > Institute of Ecology and Evolution (IEE)

UniBE Contributor:

Pouyet, Fanny Anne-Laure; Aeschbacher, Simon; Thiéry, Alexandre Benoit Xavier and Excoffier, Laurent

Subjects:

500 Science > 570 Life sciences; biology

ISSN:

2050-084X

Publisher:

eLife Sciences Publications

Language:

English

Submitter:

Susanne Holenstein

Date Deposited:

08 Nov 2018 09:30

Last Modified:

08 Nov 2018 09:30

Publisher DOI:

10.7554/eLife.36317

BORIS DOI:

10.7892/boris.120988

URI:

https://boris.unibe.ch/id/eprint/120988

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