Data from: Testing models of speciation from genome sequences: divergence and asymmetric admixture in Island Southeast Asian Sus species during the Plio-Pleistocene climatic fluctuations

In many temperate regions, ice ages promoted range contractions into
refugia resulting in divergence (and potentially speciation), while warmer
periods led to range expansions and hybridization. However, the impact
these climatic oscillations had in many parts of the tropics remains
elusive. Here, we investigate this issue using genome sequences of three
pig (Sus) species, two of which are found on islands of the Sunda-shelf
shallow seas in Island Southeast Asia (ISEA). A previous study revealed
signatures of inter-specific admixture between these Sus species (Frantz
et al. (2013) Genome sequencing reveals fine scale diversification and
reticulation history during speciation in Sus. Genome biology, 14, R107).
However, the timing, directionality and extent of this admixture remain
unknown. Here we use a likelihood based model comparison to more finely
resolve this admixture history and test whether it was mediated by humans
or occurred naturally. Our analyses suggest that inter-specific admixture
between Sunda-shelf species was most likely asymmetric and occurred long
before the arrival of humans in the region. More precisely, we show that
these species diverged during the late Pliocene but around 23% of their
genomes have been affected by admixture during the later Pleistocene
climatic transition. In addition, we show that our method provides a
significant improvement over D-statistics which are uninformative about
the direction of admixture.