Data from: Did geckos ride the Palawan raft to the Philippines?

AIM: We examine the genetic diversity within the lizard genus Gekko in the
Philippine islands to understand the role of geography and geological
history in shaping species diversity in this group. We test multiple
biogeographical hypotheses of species relationships, including the
recently proposed Palawan Ark hypothesis. LOCATION: Southeast Asia and the
Philippines. METHODS: Samples of all island endemic and widespread
Philippine Gekko species were collected and sequenced for one
mitochondrial gene (NADH dehydrogenase subunit 2) and one nuclear gene
(phosducin). We used maximum likelihood and Bayesian phylogenetic methods
to derive the phylogeny. Divergence time analyses were used to estimate
the time tree of Philippine Gekko to test biogeographical predictions of
species relationships. The phylogenetic trees from the posterior
distribution of the Bayesian analyses were used for testing
biogeographical hypotheses. Haplotype networks were created for the
widespread species Gekko mindorensis to explore genetic variation within
recently divergent clades. RESULTS: Both maximum likelihood and Bayesian
phylogenetic analyses indicated that Philippine Gekko species are a
diverse clade with a long history in the archipelago. Ancestral range
reconstruction and divergence time analyses suggest a Palawan
microcontinental origin for this clade, coinciding with Palawan’s
separation from Asia beginning 30 Ma, with subsequent diversification in
the oceanic Philippine Islands. The widespread species G. mindorensis and
G. monarchus diversified in the late Miocene/early Pliocene and are
potentially complexes of numerous undescribed species. MAIN CONCLUSIONS:
The view of the Philippine islands as a “fringing archipelago” does not
explain the pattern of species diversity in the genus Gekko. Philippine
Gekko species have diversified within the archipelago over millions of
years of isolation, forming a large diverse group of endemic species.
Furthermore, the Philippine radiation of gekkonid lizards demonstrates
biogeographical patterns most consistent with stochastic colonization
followed by in situ diversification. Our results reveal the need to
consider deeper time geological processes and their potential role in the
evolution of some Philippine terrestrial organisms.