TY - JOUR TI - Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences AU - Pouyet, Fanny AU - Aeschbacher, Simon AU - Thiéry, Alexandre AU - Excoffier, Laurent A2 - Veeramah, Krishna A2 - Wittkopp, Patricia J A2 - Gronau, Ilan VL - 7 PY - 2018 DA - 2018/08/20 SP - e36317 C1 - eLife 2018;7:e36317 DO - 10.7554/eLife.36317 UR - https://doi.org/10.7554/eLife.36317 AB - 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. KW - genomic diversity KW - background selection KW - GC-biased gene conversion KW - recombination KW - demography JF - eLife SN - 2050-084X PB - eLife Sciences Publications, Ltd ER -