Data from: Modeling human population separation history using physically phased genomes

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.