title: Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.
abstract: Recently it has become feasible to detect long blocks of nearly identical sequence shared between pairs of genomes. These identity-by-descent (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 formulas 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 formulas. 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 Population Reference Sample data set. We show that ancestry diffusing with a rate of [Formula: see text] during the last centuries, combined with accelerating population growth, can explain the observed exponential decay of block sharing with increasing pairwise sample distance.
authors.affiliation: Institute of Science and Technology Austria, A-3400 Klosterneuburg, Austria hringbauer@ist.ac.at.
authors.forename: Harald
authors.identifier: 0000-0002-4884-9682
authors.initials: H
authors.lastname: Ringbauer
authors.affiliation: Department of Evolution and Ecology, University of California, Davis, California 95616.|Center for Population Biology, University of California, Davis, California 95616.
authors.forename: Graham
authors.identifier: 0000-0001-8431-0302
authors.initials: G
authors.lastname: Coop
authors.affiliation: Institute of Science and Technology Austria, A-3400 Klosterneuburg, Austria hringbauer@ist.ac.at.
authors.forename: Nicholas H
authors.identifier: 0000-0002-8548-5240
authors.initials: NH
authors.lastname: Barton
mesh_terms: D005060:Europe; D019143:Evolution, Molecular; D015894:Genome, Human; D063426:Human Migration; D006801:Humans; D008957:Models, Genetic; D010375:Pedigree; D011110:Polymorphism, Genetic; D044465:White People / Q000235:genetics*
keywords: demographic inference; dispersal rate; effective population size; identity by descent; isolation by distance