Identity-by-descent-based estimation of the X chromosome effective population size with application to sex-specific demographic history

The effective size of a population (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 the female and male effective population sizes. We demonstrate the accuracy of our autosome and X chromosome N-e estimation with simulated data. We find that the estimated female and male effective population sizes generally reflect the simulated sex-specific effective population sizes across the past 100 generations but that short-term differences between the estimated sex-specific N-e across tens of generations may not reliably indicate true sex-specific differences. We analyzed the effective size of populations represented by samples of sequenced UK White British and UK Indian individuals from the UK Biobank.