Demographic inference for spatially heterogeneous populations using long shared haplotypes

Forien, Raphaël, Harald Ringbauer and Graham Coop

Theoretical Population Biology, 2024, vol. 159, issue C, 108-124

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.

Keywords: Population genetics; Spatial Λ-Fleming–Viot process; Spatial coalescent; Segments of shared haplotypes; Skew Brownian motion; Isolation by distance (search for similar items in EconPapers)
Date: 2024
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Persistent link: https://EconPapers.repec.org/RePEc:eee:thpobi:v:159:y:2024:i:c:p:108-124

DOI: 10.1016/j.tpb.2024.03.002

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