Modeling recent positive selection in Americans of European ancestry

1940 

Contributed Abstract 

Poster 

Seth Temple (1), Ryan Waples (1), Sharon Browning (1)

(1) University of Washington, N/A

Ryan Waples  
University of Washington

Sharon Browning  
University of Washington

Seth Temple  
University of Washington

Seth Temple  
University of Washington

Recent positive selection can result in an excess of long identity-by-descent (IBD) haplotype segments. The methods that we propose address three major objectives in studying selective sweeps: scanning for regions of interest, identifying possible sweeping alleles, and estimating a selection coefficient s. First, we scan for regions of excess IBD rate. Second, we develop a statistic to rank alleles in strong linkage disequilibrium with a putative sweeping allele. We aggregate these scores to estimate the allele frequency of the sweeping allele, even if it is not genotyped. Lastly, we propose an estimator for the selection coefficient and quantify uncertainty using the parametric bootstrap. We apply our methods to study positive selection in European ancestry samples from the TOPMed project. We find numerous loci where IBD rates exceed four standard deviations above the population median. The excess IBD rate at LCT is thirty-five standard deviations above the population median, and our estimates imply strong selection within the past 100 generations. Overall, we present robust and accurate new approaches to study very recent adaptive evolution under mild assumptions.

adaptive evolution|recent relatedness|coalescent models|parametric bootstrap|population genetics|

Section on Statistics in Genomics and Genetics

Miscellaneous