Sequential Markov coalescent algorithms for population models with demographic structure

Details Sequential Markov coalescent algorithms for population models with demographic structure Sequential Markov coalescent algorithms for population models with demographic structure

2009-01-19

arxiv.org/abs/0901.2867v1

Biology

Quantitative Biology

Populations and Evolution

10 pages, 7 figures

Scientific paper

We analyse sequential Markov coalescent algorithms for populations with demographic structure: for a bottleneck model, a population-divergence model, and for a two-island model with migration. The sequential Markov coalescent method is an approximation to the coalescent suggested by McVean and Cardin, and Marjoram and Wall. Within this algorithm we compute, for two individuals randomly sampled from the population, the correlation between times to the most recent common ancestor and the linkage probability corresponding to two different loci with recombination rate R between them. We find that the sequential Markov coalescent method approximates the coalescent well in general in models with demographic structure. An exception is the case where individuals are sampled from populations separated by reduced gene flow. In this situation, the gene-history correlations may be significantly underestimated. We explain why this is the case.

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