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

article Inferring recent demography from isolation by distance of long shared sequence blocks published yes Harald Ringbauer author 417FCFF4-F248-11E8-B48F-1D18A9856A870000-0002-4884-9682 Graham Coop author Nicholas H Barton author 4880FE40-F248-11E8-B48F-1D18A9856A870000-0002-8548-5240 NiBa department Limits to selection in biology and in evolutionary computation project 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. Genetics Society of America2017 eng Genetics 0016-6731 00039580720002310.1534/genetics.116.196220 20531335 - 1351 https://research-explorer.ista.ac.at/record/200 H. Ringbauer, G. Coop, N.H. Barton, Genetics 205 (2017) 1335–1351. Ringbauer, Harald, Graham Coop, and Nicholas H Barton. “Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.” Genetics. Genetics Society of America, 2017. <a href="https://doi.org/10.1534/genetics.116.196220">https://doi.org/10.1534/genetics.116.196220</a>. Ringbauer, Harald, et al. “Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.” Genetics, vol. 205, no. 3, Genetics Society of America, 2017, pp. 1335–51, doi:<a href="https://doi.org/10.1534/genetics.116.196220">10.1534/genetics.116.196220</a>. Ringbauer H, Coop G, Barton NH. 2017. Inferring recent demography from isolation by distance of long shared sequence blocks. Genetics. 205(3), 1335–1351. H. Ringbauer, G. Coop, and N. H. Barton, “Inferring recent demography from isolation by distance of long shared sequence blocks,” Genetics, vol. 205, no. 3. Genetics Society of America, pp. 1335–1351, 2017. Ringbauer, H., Coop, G., & Barton, N. H. (2017). Inferring recent demography from isolation by distance of long shared sequence blocks. Genetics. Genetics Society of America. <a href="https://doi.org/10.1534/genetics.116.196220">https://doi.org/10.1534/genetics.116.196220</a> Ringbauer H, Coop G, Barton NH. Inferring recent demography from isolation by distance of long shared sequence blocks. Genetics. 2017;205(3):1335-1351. doi:<a href="https://doi.org/10.1534/genetics.116.196220">10.1534/genetics.116.196220</a> 10742018-12-11T11:50:00Z2025-07-10T11:49:56Z