Data from: Colonization of the Tibetan Plateau by the homoploid hybrid pine Pinus densata

Pinus densata is an intriguingly successful homoploid hybrid species that
occupies vast areas of the southeastern Tibetan Plateau in which neither
of its parental species are present, but the colonization processes
involved are poorly understood. To shed light on how this species
colonized and became established on the plateau, we surveyed paternally
inherited chloroplast (cp) and maternally inherited mitochondrial (mt) DNA
variation within and among 54 populations of P. densata and its putative
parental species throughout their respective ranges. Strong spatial
genetic structure of both cp and mtDNA were detected in P. densata
populations. Mitotypes specific to P. densata were likely generated by
complex recombination events. A putative ancestral hybrid zone in the
northeastern periphery of P. densata was identified, and we propose that
the species then colonized the plateau by migrating westwards. Along the
colonization route, consecutive bottlenecks and surfing of rare alleles
caused a significant reduction of genetic diversity and strong population
differentiation. The direction and intensity of introgression from
parental species varied among geographic regions. In western parts of its
range the species seems to have been isolated from seed and pollen flow
from its parent species for a long time. The observed spatial distribution
of genetic diversity in P. densata also appears to reflect the persistence
of this species on the plateau during the last glaciation. Our results
indicate that both ancient and contemporary population dynamics have
contributed to the spatial distribution of genetic diversity in P.
densata, which accordingly reflects its evolutionary history.