Demographic inference for spatially heterogeneous populations using long shared haplotypes.

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  • Author(s): Forien R;Forien R; Ringbauer H; Ringbauer H; Coop G; Coop G
  • Source:
    Theoretical population biology [Theor Popul Biol] 2024 Oct; Vol. 159, pp. 108-124. Date of Electronic Publication: 2024 Mar 16.
  • Publication Type:
    Journal Article
  • Language:
    English
  • Additional Information
    • Source:
      Publisher: Academic Press Country of Publication: United States NLM ID: 0256422 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1096-0325 (Electronic) Linking ISSN: 00405809 NLM ISO Abbreviation: Theor Popul Biol Subsets: MEDLINE
    • Publication Information:
      Original Publication: New York, Academic Press.
    • Subject Terms:
      Haplotypes* ; Genetics, Population*; Humans ; Population Density ; Population Dynamics ; Demography/methods ; Models, Genetic ; Likelihood Functions
    • 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.
      Competing Interests: Declaration of competing interest The authors declare that they have no competing interest relating to the content of this manuscript.
      (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)
    • Comments:
      Update of: bioRxiv. 2023 Jun 13:2023.06.13.544589. doi: 10.1101/2023.06.13.544589. (PMID: 37398501)
    • Contributed Indexing:
      Keywords: Isolation by distance; Population genetics; Segments of shared haplotypes; Skew Brownian motion; Spatial coalescent; Spatial Λ-Fleming–Viot process
    • Publication Date:
      Date Created: 20240316 Date Completed: 20240915 Latest Revision: 20240915
    • Publication Date:
      20240916
    • Accession Number:
      10.1016/j.tpb.2024.03.002
    • Accession Number:
      38492811