Inferring human population size and separation history from multiple genome sequences

Abstract

The availability of complete human genome sequences from populations across the world has given rise to new population genetic inference methods that explicitly model their ancestral relationship under recombination and mutation. So far, application of these methods to evolutionary history more recent than 20-30 thousand years ago and to population separations has been limited. Here we present a new method that overcomes these shortcomings. The Multiple Sequentially Markovian Coalescent (MSMC) analyses the observed pattern of mutations in multiple individuals, focusing on the first coalescence between any two individuals. Results from applying MSMC to genome sequences from nine populations across the world suggest that the genetic separation of non-African ancestors from African Yoruban ancestors started long before 50,000 years ago, and give information about human population history as recently as 2,000 years ago, including the bottleneck in the peopling of the Americas, and separations within Africa, East Asia and Europe.

The empirical case against the ‘demographic turn’ in Palaeolithic archaeology

“…Furthermore, population estimates obtained in a recent multi-locus study [22] give rise to a different set of mismatches to those obtained by Powell et al [5] (figure 2). For example, the new population estimates suggest that the 'package' arrived in Europe when population size was at a historic low.…”

Inferring species divergence times using pairwise sequential Markovian coalescent modelling and low-coverage genomic data

“…Pairwise sequentially Markovian coalescent (PSMC) [8] and multiple sequentially Markovian coalescent (MSMC) [9] are two new computational approaches that are capable of estimating the demographic history of a lineage from genome-scale data. Both PSMC and MSMC infer fluctuations in ancestral effective population size (N e ) from either a single genome (PSMC) or from multiple genomes sampled from the same population (MSMC).…”

“…In addition to inferring changes in effective population size over time, PSMC and MSMC have been used to estimate divergence times between species [8][9][10][11][12][13]. The most common approach has been to first infer PSMC plots for each species separately and then to overlay these plots.…”

“…This approach does not, however, account for the possibility of demographic processes other than complete divergence, such as population structure or that the two lineages might have the same effective size owing to chance [8]. The second approach, which we investigate further here, uses phased data, which has either been the X chromosomes of male individuals [8], or from multiple whole genomes drawn from high-quality human datasets [9]. These phased data are used to create artificial F 1 hybrid genomes comprising one chromosome from each of the two lineages whose divergence time is to be inferred, and plots are generated from these artificial hybrid genomes.…”

A Spatial Framework for Understanding Population Structure and Admixture.

“…little or no geographic structure). There has been considerable recent progress in this area, using a variety of summaries such as the allele frequency spectrum [1][2][3], or approximations to the coalescent applied to sequence data [4][5][6].…”