  Secondary contact between divergent populations or incipient species may
result in the exchange and introgression of genomic material. We develop a
simple DNA sequence measure, called Gmin, which is designed to identify genomic
regions experiencing introgression in a secondary contact model. Gmin is
defined as the ratio of the minimum between-population number of nucleotide
differences to the average number of between-population differences. One
advantage of Gmin is that it is computationally inexpensive relative to
model-based methods for detecting gene flow and it scales easily to the level
of whole-genome analysis. We compare the sensitivity and specificity of Gmin to
those of the widely used index of population differentiation, Fst, and suggest
a simple statistical test for identifying genomic outliers. Extensive computer
simulations demonstrate that Gmin has both greater sensitivity and specificity
for detecting recent introgression than does Fst. Furthermore, we find that the
sensitivity of Gmin is robust with respect to both the population mutation and
recombination rates. Finally, a scan of Gmin across the X chromosome of
Drosophila melanogaster identifies candidate regions of introgression between
sub-Saharan African and cosmopolitan populations that were previously missed by
other methods. These results show that Gmin is a biologically straightforward,
yet powerful, alternative to Fst, as well as to more computationally intensive
model-based methods for detecting gene flow.

Populations and Evolution