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Aim Widespread species found in disturbed habitats are often expected to be human commensals. In island systems, this association predicts that dispersal will be mediated by humans. We investigated the biogeographical relationships among populations of a widespread tree skink that inhabits coastal forest and human-cultivated plantations in Southeast Asia. We sought to determine whether populations of the emerald tree skink, Lamprolepis smaragdina, dispersed via mechanisms that were not human-mediated (‘natural’ dispersal) or whether dispersal was mediated by humans. The latter scenario predicts low levels of genetic differentiation across a species' range, coupled with a genetic signature of recent range expansion. Location Southeast Asia, the Philippines, Wallacea and the south-western Pacific. Methods We analysed sequences of mitochondrial DNA from 204 samples collected throughout the range of this species. We use phylogenetic and population genetic methods to distinguish between predicted geographical patterns of genetic variation that might indicate natural or human-mediated dispersal. Results In contrast to predictions derived from similar studies of taxonomy and natural history, we found L. smaragdina to be characterized by highly structured and seemingly geographically stable mitochondrial gene lineages. Main conclusions Our results demonstrate a novel pattern of widespread species distribution, never before observed in vertebrates of the Indo-Australian Archipelago. Although this widespread and highly dispersive species is capable of long-distance dispersal, and has a clear history of over-water dispersal, it exhibits sharp genetic differentiation across its range. Our results suggest that random waif dispersal has been a pervasive ongoing phenomenon throughout the evolutionary history of this species.

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 in order 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.