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Sequential Markov coalescent algorithms for population models with demographic structure.

Artikel i vetenskaplig tidskrift
Författare Anders Eriksson
B. Mahjani
Bernhard Mehlig
Publicerad i Theoretical population biology
Volym 76
Nummer/häfte 2
Sidor 84-91
ISSN 1096-0325
Publiceringsår 2009
Publicerad vid Institutionen för fysik (GU)
Sidor 84-91
Språk en
Länkar dx.doi.org/10.1016/j.tpb.2009.05.00...
Ämnesord Algorithms, Demography, Humans, Markov Chains, Models, Theoretical, Recombination, Genetic
Ämneskategorier Biologiska vetenskaper

Sammanfattning

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 by 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. These quantities characterise the linkage between the two loci in question. 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 correlations may be significantly underestimated. We explain why this is the case.

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