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

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.