IBD-based estimation of X chromosome effective population size with application to sex-specific demographic history

Effective population size ( N e ) in the recent past can be estimated through analysis of identity-by-descent (IBD) segments. Several methods have been developed for estimating N e from autosomal IBD segments, but no such effort has been made with X chromosome IBD segments. In this work, we propose a method to estimate the X chromosome effective population size from X chromosome IBD segments. We show how to use the estimated autosome N e and X chromosome N e to estimate female and male effective population sizes. We demonstrate the accuracy of our autosome and X chromosome N e estimation with simulated data, and we show that pronounced differences in female and male effective population size can be detected. In analysis of UK Biobank and the TOPMed project data, we obtain results that are consistent with equal female and male effective population sizes in the UK White British and UK Indian populations and in an African American population.