Introgression makes waves in inferred histories of effective population size

TL;DR

This study uses simulations to show that introgression and gene flow from ancient, divergent populations can create wave-like patterns in inferred human effective population size histories, affecting interpretations of human evolution.

Contribution

It demonstrates how introgression from ancient populations influences the inferred effective population size, explaining the observed wave patterns in human genetic history.

Findings

Introgression causes wave-like patterns in population size inference.

The timing and size of waves reflect ancient population divergence and gene flow strength.

Small amounts of ancient gene flow can significantly impact population size estimates.

Abstract

Human populations have a complex history of introgression and of changing population size. Human genetic variation has been affected by both these processes, so that inference of past population size depends upon the pattern of gene flow and introgression among past populations. One remarkable aspect of human population history as inferred from genetics is a consistent "wave" of larger effective population size, prior to the bottlenecks and expansions of the last 100,000 years. Here I carry out a series of simulations to investigate how introgression and gene flow from genetically divergent ancestral populations affect the inference of ancestral effective population size. Both introgression and gene flow from an extinct, genetically divergent population consistently produce a wave in the history of inferred effective population size. The time and amplitude of the wave reflect the time of origin of the genetically divergent ancestral populations and the strength of introgression or gene flow. These results demonstrate that even small fractions of introgression or gene flow from ancient populations may have large effects on the inference of effective population size.