Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences
- University of Bern, Switzerland
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.
Data availability
All data generated and script to analyse them is provided on the dryad repository: http://dx.doi.org/10.5061/dryad.t76fk80
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Data from: Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferencesAvailable at Dryad Digital Repository under a CC0 Public Domain Dedication.
Article and author information
Author details
Funding
Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (310030B-166605)
- Laurent Excoffier
University of Berkeley (Visiting Miller Professorship)
- Laurent Excoffier
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Krishna Veeramah, Stony Brook University, United States
Publication history
- Received: March 1, 2018
- Accepted: August 17, 2018
- Accepted Manuscript published: August 20, 2018 (version 1)
- Accepted Manuscript updated: August 23, 2018 (version 2)
- Version of Record published: October 9, 2018 (version 3)
Copyright
© 2018, Pouyet et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences
eLife 7:e36317.
https://doi.org/10.7554/eLife.36317
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