DOI: 10.5061/dryad.r7fs8
title: Data from: Modeling human population separation history using physically phased genomes

description: Phased haplotype sequences are a key component in many population genetic
 analyses since variation in haplotypes reflects the action of
 recombination, selection, and changes in population size. In humans,
 haplotypes are typically estimated from unphased sequence or genotyping
 data using statistical models applied to large reference panels. To assess
 the importance of correct haplotype phase on population history inference,
 we performed fosmid pool sequencing and resolved phased haplotypes of five
 individuals from diverse African populations (including Yoruba, Esan,
 Gambia, Maasai, and Mende). We physically phased 98% of heterozygous SNPs
 into haplotype-resolved blocks, obtaining a block N50 of 1 Mbp. We
 combined these data with additional phased genomes from San, Mbuti,
 Gujarati and CEPH European populations and analyzed population size and
 separation history using the Pairwise Sequentially Markovian Coalescent
 (PSMC) and Multiple Sequentially Markovian Coalescent (MSMC) models. We
 find that statistically phased haplotypes yield a more recent split-time
 estimation compared with experimentally phased haplotypes. To better
 interpret patterns of cross-population coalescence, we implemented an
 approximate Bayesian computation (ABC) approach to estimate population
 split times and migration rates by fitting the distribution of coalescent
 times inferred between two haplotypes, one from each population, to a
 standard Isolation-with-Migration model. We inferred that the separation
 between hunter-gather populations and other populations happened around
 120,000 to 140,000 years ago with gene flow continuing until 30,000 to
 40,000 years ago; separation between west African and out of African
 populations happened around 70,000 to 80,000 years ago, while the
 separation between Maasai and out of African populations happened around
 50,000 years ago.
description: Phased haplotpyes --
 callable regionsThe .tar archive
 contains phasing information for each sample. The files *.mask.bed.gz,
 indicate the genomic regions for each sample deemed to be callable. Files
 are based on the GRCh37 reference genome assembly. This release contains
 phased data generated by Song et al. as well as reprocessing of previously
 published data (samples NA20847 (KITZMAN et al. 2011), HGDP01029 and
 HGDP00456 (MEYER et al. 2012)). Please see Song et al. 2016 for more
 information. The following files are included:
 HG02799.fosmid.phased.vcf.gz, HG02799.mask.bed.gz,
 HG03108.fosmid.phased.vcf.gz, HG03108.mask.bed.gz,
 HG03428.fosmid.phased.vcf.gz, HG03428.mask.bed.gz,
 HGDP00456.fosmid.phased.vcf.gz, HGDP00456.mask.bed.gz,
 HGDP01029.fosmid.phased.vcf.gz, HGDP01029.mask.bed.gz,
 NA12878.fosmid.phased.vcf.gz, NA12878.mask.bed.gz,
 NA19240.fosmid.phased.vcf.gz, NA19240.mask.bed.gz,
 NA20847.fosmid.phased.vcf.gz, NA20847.mask.bed.gz,
 NA21302.fosmid.phased.vcf.gz, NA21302.mask.bed.gz.callable-regions.tarFosmid Phased HaplotypesThe .tar archive contains phasing information for each sample. The files *.mask.bed.gz indicate the genomic regions for each sample deemed to be callable. Files are based on the GRCh37 reference genome assembly. This release contains phased data generated by Song et al. as well as reprocessing of previously published data (samples NA20847 (KITZMAN et al. 2011), HGDP01029 and HGDP00456 (MEYER et al. 2012)). Please see Song et al. 2016 for more information. The following files are included: HG02799.fosmid.phased.vcf.gz, HG02799.mask.bed.gz, HG03108.fosmid.phased.vcf.gz, HG03108.mask.bed.gz, HG03428.fosmid.phased.vcf.gz, HG03428.mask.bed.gz, HGDP00456.fosmid.phased.vcf.gz, HGDP00456.mask.bed.gz, HGDP01029.fosmid.phased.vcf.gz, HGDP01029.mask.bed.gz, NA12878.fosmid.phased.vcf.gz, NA12878.mask.bed.gz, NA19240.fosmid.phased.vcf.gz, NA19240.mask.bed.gz, NA20847.fosmid.phased.vcf.gz, NA20847.mask.bed.gz, NA21302.fosmid.phased.vcf.gz, NA21302.mask.bed.gz.phased-haplotpyes.tar