DOI: 10.5061/dryad.466mn
title: Data from: Spotted stream frog diversification at the Australasian faunal zone interface, mainland versus island comparisons, and a test of the Philippine ‘dual-umbilicus’ hypothesis

description: Aim: We utilize comprehensive geographical sampling and a new, multilocus
 dataset to re-examine the biogeography of spotted stream frogs throughout
 Southeast Asia. We compare patterns of diversification among stream frog
 populations on land-bridge islands and oceanic islands and we reevaluate a
 previous ‘dual-invasion’ hypothesis for the origins of several endemic
 Philippine taxa. Location: Southeast Asia, Sundaland, and the Philippines.
 Methods: Stream frogs were collected and sequenced for two mitochondrial
 and two nuclear gene regions. We used summary statistics and phylogenetic
 networks to characterize the geographic distribution of genetic variation.
 Phylogenetic relationships and ancestral biogeographic ranges were
 estimated using Bayesian and likelihood methods. Finally, we used the
 preferred topology and trees from the posterior distribution of the
 Bayesian analyses to evaluate a previous biogeographic ‘dual-invasion’
 topological hypothesis. Results: In contrast to expectations, we found
 evidence of highly divergent, demographically stable, and geographically
 regionalized lineages (including currently unrecognized putative species)
 in the land-bridge island clade, but minimally divergent, widespread and
 clinally distributed (with evidence of recent demographic expansion)
 populations in adjacent oceanic island populations. Novel phylogenetic
 relationships depart from previous studies and our data strongly reject
 the previously published ‘dual-invasion’ topological hypothesis. Main:
 conclusions Our results join a new body of literature suggesting that the
 biogeographic distribution of species diversity on mainland areas and
 continental shelf islands may harbor high levels of unrecognized diversity
 in conspicuous vertebrate groups, whereas adjacent oceanic island
 archipelagos can and do support naturally occurring widespread species or
 minimally divergent clades. Although increased sampling coupled with more
 sophisticated methods indicate that the original individual identities of
 species previously hypothesized to be involved in the ‘dual-invasion’
 scenario may have been incorrect, this mechanism for faunal exchange
 between the archipelago and adjacent mainland undoubtedly has contributed
 to the accumulation of endemic vertebrate diversity in the Philippines.
description: Concatenated Sequence
 Alignment FileThis is the sequence
 alignment file used in phylogenetic analyses for our study. The gene
 alignments have been concatenated into a single alignment, and the
 character block descriptions are provided at the bottom of the sequence
 alignment.Brown.etal_Alignment.nexBayesian Majority Rule Consensus TopologyThis is the majority rule consensus topology resulting from Bayesian analyses in the program MrBayes. The file is provided in Newick tree format.Bayesian_50PercentMajority.treMaximum Likelihood Bootstrap TopologyThis is the bootstrap topology resulting from Maximum Likelihood analyses in the program RAxML.RAxML_Topology.tre