DOI: 10.5061/dryad.t76fk80
title: Data from: Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences

description: 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.
description: Main
 READMEThis dryad page provides
 the data and the source code for the figures in " Background
 selection and biased gene conversion affect more than 95% of the human
 genome and bias demographic inferences " by Pouyet F,* Aeschbacher
 S*, Thiery A and Excoffier L. * first co-authors It contains as compressed
 files: -- 1 -- Genotype tables and annotations from 1000G and SGDP data
 1000G_genot-table.zip SGDP_genotypetable-annotation.zip with README files
 that describe the data and how to use them. -- 2 -- the R scripts to
 perform the figures of INDA figures_INDA_Rscripts.zip -- 3 -- the
 confidence intervals of the estimates as well as the source code to
 estimate them confidenceIntervals.zip -- 4 -- the scripts (R and python)
 to make the SFS figures as well as estimate confidence intervals and
 compute the SFS figures_data_SFS_Rscripts.zip -- 5 -- the setting
 parameters for FastSimCoal demographic inferences Supplementary file -
 settings files for demographi ... -- 6 -- the scripts for SLiM simulations
 and analyses (bash and R code) + a table with parameters used in the SLiM
 simulations (.csv) + the scripts and raw data that I used to make the
 figures (.txt and .R) si_files_SA.tar.gz Extra READMEs describe the files
 and how to launch them to compute the statistics or to make the
 figures.SGDP_genotypetable-annotationIt contains as compressed files: - Genotype tables and annotations from SGDP see the file README_columns genotypeTables README files describe the files and how to launch them.Supplementary file - settings files for demographic inferencesconfidence IntervalsFiles with 95% CIconfidenceIntervals.zipsi_files_SA.tarSLiM simulationsfigures_DAFi_RScripts1000G.extraData_distanceHotspotPhastconsAnnotations of distance to hotspots and distance to conserved elements (phastcons) in centimorgans for 1000G data.1000G_genot-tableContains as a compressed file the genotype table with annotation for 1000G data. Please see the README file for further description and information on how to make the figures. Author: Fanny Pouyet1000G_Nb_DerAll_byPopFiles from which the SFS are computed. Author: Fanny Pouyetfigures_data_SFS_RscriptsFiles to make figures of SFS and scripts to compute the SFS too. The SFS are done from files in "1000G_Nb_derAll.zip". For further details, see README fileregions.YRIrecomb1p5Regions from hg19 with recombination rate above 1.5cM/Mb (using YRI recombination map - see the publication). Mutations in these regions that are GC-conservative (A to T, T to A, G to C and C to G) can be considered as neutral for demographic inferences.regions.YRIrecomb1p5.nophastConsElements46wayPrimates100bpSame as "regions.YRIrecomb1p5.bed" + the removal of regions close to conserved elements (see Fig1S9 and Fig2S4 for the impact of conserved elements on DAFi and on the SFS). For this file, the removed regions are less than 100bp from conserved elements.