Data from: Demography and speciation history of the homoploid hybrid pine Pinus densata on the Tibetan Plateau

Pinus densata is an ecologically successful homoploid hybrid that inhabits
vast areas of heterogeneous terrain on the southeastern Tibetan Plateau as
a result of multiple waves of colonization. Its region of origin, route of
colonization onto the plateau and the directions of introgression with its
parental species have previously been defined, but little is known about
the isolation and divergence history of its populations. In this study, we
surveyed nucleotide polymorphism over eight nuclear loci in 19
representative populations of P. densata and its parental species. Using
this information and coalescence simulations, we assessed the historical
changes in its population size, gene flow, and divergence in time and
space. The results indicate a late Miocene origin for P. densata
associated with the recent uplift of southeastern Tibet. The subsequent
differentiation between geographical regions of this species began in the
late Pliocene and was induced by regional topographic changes and
Pleistocene glaciations. The ancestral P. densata population had a large
effective population size but the central and western populations were
established by limited founders, suggesting that there were severe
bottlenecks during the westward migration out of the ancestral hybrid
zone. After separating from their ancestral populations, population
expansion occurred in all geographic regions especially in the western
range. Gene flow in P. densata was restricted to geographically
neighboring populations, resulting in significant differentiation between
regional groups. The new information on the divergence and demographic
history of P. densata reported herein enhances our understanding of its
speciation process on the Tibetan Plateau.