Inferring recent demography from isolation by distance of long shared sequence blocks Journal Article

Author(s): Ringbauer, Harald; Coop, Graham; Barton, Nicholas H
Article Title: Inferring recent demography from isolation by distance of long shared sequence blocks
Affiliation IST Austria
Abstract: Recently it has become feasible to detect long blocks of nearly identical sequence shared between pairs of genomes. These IBD blocks are direct traces of recent coalescence events and, as such, contain ample signal to infer recent demography. Here, we examine sharing of such blocks in two-dimensional populations with local migration. Using a diffusion approximation to trace genetic ancestry, we derive analytical formulae for patterns of isolation by distance of IBD blocks, which can also incorporate recent population density changes. We introduce an inference scheme that uses a composite likelihood approach to fit these formulae. We then extensively evaluate our theory and inference method on a range of scenarios using simulated data. We first validate the diffusion approximation by showing that the theoretical results closely match the simulated block sharing patterns. We then demonstrate that our inference scheme can accurately and robustly infer dispersal rate and effective density, as well as bounds on recent dynamics of population density. To demonstrate an application, we use our estimation scheme to explore the fit of a diffusion model to Eastern European samples in the POPRES data set. We show that ancestry diffusing with a rate of σ ≈ 50–100 km/√gen during the last centuries, combined with accelerating population growth, can explain the observed exponential decay of block sharing with increasing pairwise sample distance.
Keywords: isolation by distance; identity by descent; effective population size; Demographic Inference; Dispersal Rate
Journal Title: Genetics
Volume: 205
Issue 3
ISSN: 0016-6731
Publisher: Genetics Society of America  
Date Published: 2017-03-01
Start Page: 1335
End Page: 1351
DOI: 10.1534/genetics.116.196220
Notes: We thank Melinda Pickup, Himani Sachdeva, Tiago Paixao, Srdjan Sarikas, Julia Huber and members of the Coop lab for helpful comments on previous drafts of this article. We thank the two anonymous reviewers for helpful feedback. The research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement number 250152 (N.B.).
Open access: yes (repository)
IST Austria Authors
  1. Nick Barton
    252 Barton