Estimating dispersal rates and locating genetic ancestors with genome-wide genealogies
- University of Toronto, Canada
- 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}.
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Relate-inferred genealogies for 66 longread Arabidopsis thaliana genomesZenodo, doi:10.5281/zenodo.5099656.
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Towards telomere-to-telomere assemblies of Arabidopsis thaliana genomes: CLR vs HiFi readsNational Center for Biotechnology Information.
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ddAraThal4 (thale cress)National Center for Biotechnology Information.
Article and author information
Author details
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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Estimating dispersal rates and locating genetic ancestors with genome-wide genealogies
eLife 13:e72177.
https://doi.org/10.7554/eLife.72177
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