Data from: Low coverage genomic data resolve the population divergence and gene flow history of an Australian rain forest fig wasp

Population divergence and gene flow are key processes in evolution and
ecology. Model-based analysis of genome-wide datasets allows
discrimination between alternative scenarios for these processes even in
non-model taxa. We used two complementary approaches (one based on the
blockwise site frequency spectrum (bSFS), the second on the Pairwise
Sequentially Markovian Coalescent (PSMC)) to infer the divergence history
of a fig wasp, Pleistodontes nigriventris. Pleistodontes nigriventris and
its fig tree mutualist Ficus watkinsiana are restricted to rain forest
patches along the eastern coast of Australia, and are separated into
northern and southern populations by two dry forest corridors (the
Burdekin and St. Lawrence Gaps). We generated whole genome sequence data
for two haploid males per population and used the bSFS approach to infer
the timing of divergence between northern and southern populations of P.
nigriventris, and to discriminate between alternative isolation with
migration (IM) and instantaneous admixture (ADM) models of post divergence
gene flow. Pleistodontes nigriventris has low genetic diversity (π =
0.0008), to our knowledge one of the lowest estimates reported for a
sexually reproducing arthropod. We find strongest support for an ADM model
in which the two populations diverged ca. 196kya in the late Pleistocene,
with almost 25% of northern lineages introduced from the south during an
admixture event ca. 57kya. This divergence history is highly concordant
with individual population demographies inferred from each pair of haploid
males using PSMC. Our analysis illustrates the inferences possible with
genome-level data for small population samples of tiny, non-model
organisms and adds to a growing body of knowledge on the population
structure of Australian rain forest taxa.