  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.
