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.

Automated summary

The effective size of a population (N-e) can be estimated through analysis of identity-by-descent (IBD) segments, and this study proposes a method to estimate the X chromosome effective population size from X chromosome IBD segments. The accuracy of the estimation is demonstrated using simulated data, and it is found that short-term differences in sex-specific N-e may not reliably indicate true sex-specific differences. The study also analyzes the effective size of UK White British and UK Indian populations using sequenced samples from the UK Biobank.