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

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, up till recently, not been computational feasible. Here we capitalize on important recent advances in gene-genealogy reconstruction and develop methods to use thousands of trees to estimate time-varying 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 the 1001 Genomes dataset of over one thousand Arabidopsis thaliana genomes sampled across a wide geographic extent. We detect a very high dispersal rate in the recent past, especially longitudinally, and use inferred ancestor locations to visualize many examples of recent long-distance dispersal and admixture. We also use inferred ancestor locations to identify the origin and ancestry of the North American expansion and to depict alternative geographic ancestries stemming from multiple glacial refugia. Our method highlights the huge amount of information about past dispersal events and population movements contained in genome-wide genealogies.

Efficient ancestry and mutation simulation with msprime 1.0

“…Given such inferred ancestry, many exciting applications become possible. For example, Osmond and Coop (2021) developed a method to estimate the location of genetic ancestors based on inferred trees, and other uses are sure to follow. Since the inferred genetic ancestry becomes the input for other downstream inferences, it is vitally important that these primary inferences are thoroughly validated, with the detailed properties of the inferred ancestries cataloged and understood.…”

A unified genealogy of modern and ancient genomes

“…We use a naive, non-parametric approach to gain insight into the geographic location of ancestral haplotypes based on the known locations of sampled genomes. We note that while the relationships between genealogies and spatial structure has been an active area of research in both phylogenetics and population genetics for many years (191)(192)(193)(194)(195)(196), and a recent, more sophisticated method uses marginal trees in genome-wide genealogies (197), such approaches typically ignore recombination.…”

Genetic similarity versus genetic ancestry groups as sample descriptors in human genetics

“…Other approaches to ancestry have been laid out where a person's ancestry could be reported for various different time epochs, which would remove the need for the implicit choice of time-period. Or we could imagine tracing genetic ancestors back across geographical space over the generations, which would allow a more continuous view of ancestry (Osmond and Coop, 2021;Wohns et al, 2022). Such approaches may well be useful for population geneticists and genetic anthropologists interested in human history.…”