Data from: Distinguishing migration from isolation using genes with intragenic recombination: detecting introgression in the Drosophila simulans species complex

Background: Determining the presence or absence of gene flow between
populations is the target of some statistical methods in population
genetics. Until recently, these methods either avoided the use of
recombining genes, or treated recombination as a nuisance parameter.
However, genes with recombination contribute additional information for
the detection of gene flow (i.e. through linkage disequilibrium). Methods:
We present three summary statistics based on the spatial arrangement of
fixed differences, and shared and exclusive polymorphisms that are
sensitive to the presence and direction of gene flow. Power and false
positive rate for tests based on these statistics are studied by
simulation. Results: The application of these tests to populations from
the Drosophila simulans species complex yielded results consistent with
migration between D. simulans and its two endemic sister species D.
mauritiana and D. sechellia, and between populations D. mauritiana on the
islands of the Mauritius and Rodrigues. Conclusions: We demonstrate the
sensitivity of the developed statistics to the presence and direction of
gene flow, and characterize their power as a function of differentiation
level and recombination rate. The properties of these statistics make them
especially suitable for analyzing high-throughput sequencing data or for
their integration within the approximate Bayesian computation framework.