Inferring human population size and separation history from multiple genome sequences

Inferring human population size and separation history from multiple genome sequences
Stephan Schiffels, Richard Durbin

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.

4 thoughts on “Inferring human population size and separation history from multiple genome sequences

  1. Pingback: Author post: Inferring human population size and separation history from multiple genome sequences | Haldane's Sieve

  2. Thanks for this further development of a very promising approach. I’m looking for a genome scan of human coalescence times similar to your Fig. 1b (labelled c) but on actual data rather than simulated data, and preferably something closer to population coalescence (such as the MRCA of your 8 haplotypes). Does this exist?

    • Hi Michael,

      sorry, I just saw this. MSMC can in principle locally decode the hidden state for you (i.e. the first coalescence time). I don’t at the moment have it implemented in the front end to output this, but it should be no problem to do so. I don’t think I understand what you mean by “closer to the population coalescence”.

  3. Pingback: Most viewed on Haldane’s Sieve: June 2014 | Haldane's Sieve

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