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.分型单倍型序列（phased haplotype sequences）是众多群体遗传学分析的核心组成部分，因为单倍型的变异能够反映重组、选择以及种群规模变化的作用效应。在人类研究中，单倍型通常通过应用于大型参考面板的统计模型，由未分型序列或基因分型数据进行推断得到。为了评估准确的单倍型分型对种群历史推断的重要性，我们开展了黏粒池测序，并对来自不同非洲人群（包括约鲁巴人、埃桑人、冈比亚人、马赛人以及门德人）的5名个体的分型单倍型进行了解析。我们将98%的杂合单核苷酸多态性（SNP）物理分型为单倍型解析区块，获得的区块N50长度为1兆碱基对（Mbp）。我们将上述数据与来自桑人、姆布蒂人、古吉拉特人以及CEPH欧洲人群的额外分型基因组数据相结合，利用成对顺序马尔可夫合并（PSMC）与多重顺序马尔可夫合并（MSMC）模型分析了种群规模与种群分化历史。我们发现，相较于实验分型的单倍型，通过统计方法分型的单倍型会得到更为晚近的分化时间估计结果。为了更好地阐释跨种群合并模式，我们采用了近似贝叶斯计算（ABC）方法：通过将两个分别来自不同种群的单倍型之间推断得到的合并时间分布拟合至标准隔离与迁移模型，以此估计种群分化时间与基因流速率。我们推断，狩猎采集人群与其他人群的分化发生在约12万至14万年前，且基因流持续至3万至4万年前；西非人群与走出非洲人群的分化发生在约7万至8万年前，而马赛人与走出非洲人群的分化则发生在约5万年前。