DOI: 10.5061/dryad.7f327q53
title: Data from: Did geckos ride the Palawan raft to the Philippines?

description: 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.
description: Nexus Alignment
 FileAlignment file used,
 character block provided at bottomgekko_final.nexChronogram Tree file 1Chronogram, UCLD_exp0.01, gamma_root, medianheightgekko_final.ucld_exp0.01.gamma_root.clocktree.runs1234.medianh.mrc.treChronogram Tree file 2Chronogram, UCLD_exp0.01, uniform_root, medianheight, mrc tree filegekko_final.ucld_exp0.01.uniform_root.clocktree.runs1234.medianh.mrc.tregekko_final.ucld.gamma100_exp0.01.clocktree.runs1234.medianh.mrcChronogram, UCLD_gamma100_exp0.01, medianheight, mrc tree fileMrBayes Consensus TreeConsensus Tree from Bayesian analysis in MrBayesMrBayes_ConsensusTree.treRAxML Consensus Tree50% majority rule consensus tree from RAxML ML analysisraxml_MRC_50.treGARLI ML TreeML tree from Garli analysissumtrees_ML.treGarli ML Bootstrap Tree50% majority rule consensus tree from Garli analysissumtrees_mrc_0.5.tre