Data from: A new method to scan genomes for introgression in a secondary contact model

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 in a genomic window to the average number of
between-population differences. Although it is conceptually simple, 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.