Data from: Genealogy and demographic history of a widespread amphibian throughout Indochina

Relatively little is known about spatial patterns of cryptic diversity in
tropical species and the processes that generate them. Few studies examine
the geographic distribution of genetic lineages in Southeast Asia, an area
hypothesized to harbor substantial cryptic diversity. We investigated the
evolutionary history of Asian tree frogs of the Polypedates leucomystax
complex (n = 172) based on 1800 bp of the mtDNA genes ND 1 and cytochrome
b and tested hypotheses pertaining to climate, geology and dispersal
patterns. Analyses revealed substantial genetic diversity and lineage
divergence throughout the region with evidence for widespread sympatric
lineages and a general north versus south clustering. Relaxed molecular
clock analysis and tests for demographic expansion identified an initial
cladogenesis during the Miocene with subsequent Plio–Pleistocene
diversification, which corresponded to periods of increased aridity and
the onset of monsoonal weather systems, respectively. Rates of
diversification were relatively constant until the Early Pleistocene when
rates increased exponentially. We found equivocal evidence for both
isolation-by-distance and a potential role of some landscape features as
partial barriers to dispersal. Finally, our analyses showed that
divergence between insular and mainland populations occurred before Homo
sapiens colonized Southeast Asia suggesting that historical human-mediated
dispersal did not drive insular diversification. Our results suggested
that demographic expansion in the Late Pleistocene resulted in widespread
sympatric lineages in the P. leucomystax complex throughout southern China
and Indochina, and further clarified the evolutionary history of lineages
within P. leucomystax.