Inferring human population size and separation history from multiple genome sequences

By Stephan Schiffels, Richard Durbin. Nature Genetics, 2014

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The availability of complete human genome sequences from populations across the world has given rise to new population genetic inference methods that explicitly model ancestral relationships under recombination and mutation. So far, application of these methods to evolutionary history more recent than 20,000–30,000 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) analyzes 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 recent as 2,000 years ago, including the bottleneck in the peopling of the Americas and separations within Africa, East Asia and Europe.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/7f8849ecb0ff39af244687cd267c2e931309dea2

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Citations in the corpus

1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana (2016, methodology): “Moreover, while relicts show strong IBD on all geographic scales, non-relicts have a similarly clear pattern only over short distances (Figure 3D), as expected if they had spread rapidly to occupy their (A) Coalescence rates over time for pairs of individuals from different ADMIXTURE groups, inferre”
Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes (2015, methodology): “Furthermore, methods based on the SMC approximation [17, 18] have been tested using SMC simulations out of necessity, making it difficult to assess the impact of the approximation on accuracy.”
Robust and scalable inference of population history from hundreds of unphased whole-genomes (2016, methodology): “We note that these findings are somewhat at odds with the simulation results reported by Schiffels and Durbin 24 , which seem to have been generated with error-free data.”
HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies (2017, background): “Reconstructing individual haplotypes has important implications for understanding human genetic variation, interpretation of variants in disease, and reconstructing human population history (Tewhey et al. 2011; Glusman et al. 2014; Schiffels and Durbin 2014; Snyder et al. 2015).”
Efficient ancestry and mutation simulation with msprime 1.0 (2021, background): “…in population genetics use the distribution of coalescence rates be-tween pairs of lineages to infer effective population sizes over time (Li and Durbin 2011; Sheehan et al. 2013; Schiffels and Durbin 2014) or split times and subsequent migration rates between populations (Wang et al. 2020).”
A genomic history of Aboriginal Australia (2016, result): “…of Pama-126 Nyungan speakers and Highland Papuans diverged  37 kya (95% CI 25-40 kya, Figure 4a, S07), which is in close agreement with results of an MSMC analysis (Figure 4b, S08), a method estimating cross coalescence rates between pairs of populations based on individuals’ haplotypes 49 .”
Visualizing spatial population structure with estimated effective migration surfaces (2014, background): “It is possible that the pairwise sequentially Markov coalescent [50], extended to deal with pairs of individuals [51], could also provide useful alternative distance matrices which could be visualized as an EEMS.”