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Demographic inference for spatially heterogeneous populations using long shared haplotypes

Author

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  • Forien, Raphaël
  • Ringbauer, Harald
  • Coop, Graham

Abstract

We introduce a modified spatial Λ-Fleming–Viot process to model the ancestry of individuals in a population occupying a continuous spatial habitat divided into two areas by a sharp discontinuity of the dispersal rate and effective population density. We derive an analytical formula for the expected number of shared haplotype segments between two individuals depending on their sampling locations. This formula involves the transition density of a skew diffusion which appears as a scaling limit of the ancestral lineages of individuals in this model. We then show that this formula can be used to infer the dispersal parameters and the effective population density of both regions, using a composite likelihood approach, and we demonstrate the efficiency of this method on a range of simulated data sets.

Suggested Citation

  • Forien, Raphaël & Ringbauer, Harald & Coop, Graham, 2024. "Demographic inference for spatially heterogeneous populations using long shared haplotypes," Theoretical Population Biology, Elsevier, vol. 159(C), pages 108-124.
    • Handle: RePEc:eee:thpobi:v:159:y:2024:i:c:p:108-124
    DOI: 10.1016/j.tpb.2024.03.002
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    References listed on IDEAS

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    1. Guindon, Stéphane & Guo, Hongbin & Welch, David, 2016. "Demographic inference under the coalescent in a spatial continuum," Theoretical Population Biology, Elsevier, vol. 111(C), pages 43-50.
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