Estimating dispersal rates and locating genetic ancestors with genome-wide genealogies

  1. Matthew Osmond  Is a corresponding author
  2. Graham Coop  Is a corresponding author
  1. University of Toronto, Canada
  2. University of California, Davis, United States

Abstract

Spatial patterns in genetic diversity are shaped by individuals dispersing from their parents and larger-scale population movements. It has long been appreciated that these patterns of movement shape the underlying genealogies along the genome leading to geographic patterns of isolation by distance in contemporary population genetic data. However, extracting the enormous amount of information contained in genealogies along recombining sequences has, until recently, not been computationally feasible. Here we capitalize on important recent advances in genome-wide gene-genealogy reconstruction and develop methods to use thousands of trees to estimate per-generation dispersal rates and to locate the genetic ancestors of a sample back through time. We take a likelihood approach in continuous space using a simple approximate model (branching Brownian motion) as our prior distribution of spatial genealogies. After testing our method with simulations we apply it to Arabidopsis thaliana. We estimate a dispersal rate of roughly 60km2 per generation, slightly higher across latitude than across longitude, potentially reflecting a northward post-glacial expansion. Locating ancestors allows us to visualize major geographic movements, alternative geographic histories, and admixture. Our method highlights the huge amount of information about past dispersal events and population movements contained in genome-wide genealogies.

Data availability

All code used to perform the analyses in this study can be found at \url{https://github.com/mmosmond/spacetrees-ms}. More information on how to run our method, \texttt{spacetrees}, is available at \url{https://github.com/osmond-lab/spacetrees}.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Matthew Osmond

    Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
    For correspondence
    mm.osmond@utoronto.ca
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6170-8182
  2. Graham Coop

    Center for Population Biology, University of California, Davis, Davis, United States
    For correspondence
    gmcoop@ucdavis.edu
    Competing interests
    Graham Coop, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8431-0302

Funding

Natural Sciences and Engineering Research Council of Canada (RGPIN-2021-03207)

  • Matthew Osmond

Natural Sciences and Engineering Research Council of Canada (DGECR-2021-00114)

  • Matthew Osmond

Banting Research Foundation

  • Matthew Osmond

National Institute of General Medical Sciences (R01 GM108779)

  • Graham Coop

National Institute of General Medical Sciences (R35 GM136290)

  • Graham Coop

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

© 2024, Osmond & Coop

This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

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  1. Matthew Osmond
  2. Graham Coop
(2024)
Estimating dispersal rates and locating genetic ancestors with genome-wide genealogies
eLife 13:e72177.
https://doi.org/10.7554/eLife.72177

Share this article

https://doi.org/10.7554/eLife.72177

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