65 Statistical inference using identity-by-descent segments

Oregon Convention Center 

If two haplotypes share the same alleles for an extended gene tract, these haplotypes are likely to derive identical-by-descent (IBD) from a recent common ancestor. The length distribution of IBD segments can be informative about recent demographic changes and strong positive selection. The data is correlated via unobserved ancestral tree and recombination processes, which commonly presents challenges to the derivation of theoretical results in population genetics. Under interpretable regularity conditions, we show that the proportion of detectable IBD segments at locus (IBD rate) is normally distributed for large sample size and large scaled population size. We use efficient and exact simulations to study the non-normality of the IBD rate in finite samples and its implications to downstream statistical inference. Specifically, we discuss our suite of IBD-based statistical methods designed to detect selection and estimate selection coefficients. We indicate that genome-wide scans and selection coefficient estimation based on the IBD rate may be subject to slightly conservative Type 1 error control and loose confidence intervals. Using samples of predominant European ancestry from the TOPMed project, we apply our methods to model recent adaptive evolution at the LCT gene.

adaptive evolution

recent relatedness

coalescent models

parametric bootstrap

population genetics 

Section on Statistics in Genomics and Genetics