Defining species when there is gene flow

Whatever one’s definition of species, it is generally expected that individuals of the same species should be genetically more similar to each other than they are to individuals of another species. Here we show that in the presence of cross-species gene flow, this expectation may be incorrect. We use the multispecies coalescent model with migration or introgression to study the impact of gene flow on genetic differences within and between species and highlight a surprising but plausible scenario in which different population sizes and asymmetrical migration rates cause a genetic sequence to be on average more closely related to a sequence from another species than to a sequence from the same species. Our results highlight the extraordinary impact that even a small amount of gene flow may have on the genetic history of the species. We suggest that contrasting long-term migration rate and short-term hybridization rate, both of which can be estimated using genetic data, may be a powerful a...