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The rainforest biome of eastern Madagascar is renowned for its extraordinary biodiversity and restricted distribution ranges of many species, whereas the arid western region of the island is relatively species poor. We provide insight into the biogeography of western Madagascar by analyzing a multilocus phylogeographic dataset assembled for an amphibian, the widespread Malagasy bullfrog, Laliostoma labrosum. We find no cryptic species in L. labrosum (maximum 1.1% pairwise genetic distance between individuals in the 16S rRNA gene) attributable to considerable gene flow at the regional level as shown by genetic admixture in both mtDNA and three nuclear loci, especially in central Madagascar. Low breeding site fidelity, viewed as an adaptation to the unreliability of standing pools of freshwater in dry and seasonal environments, and a ubiquitous distribution within its range may underlie overall low genetic differentiation. Moreover, reductions in population size associated with periods of high aridity in western Madagascar may have purged DNA variation in this species. The mtDNA gene tree revealed seven major phylogroups within this species, five of which show mostly non-overlapping distributions. The nested positions of the northern and central mtDNA phylogroups imply a southwestern origin for all extant mtDNA lineages in L. labrosum. The current phylogeography of this species and paleo-distributions of major mtDNA lineages suggest five potential refugia in northern, western and southwestern Madagascar, likely the result of Pleistocene range fragmentation during drier and cooler climates. Lineage sorting in mtDNA and nuclear loci highlighted a main phylogeographic break between populations north and south of the Sambirano region, suggesting a role of the coastal Sambirano rainforest as a barrier to gene flow. Paleo-species distribution models and dispersal networks suggest that the persistence of some refugial populations was mainly determined by high population connectivity through space and time. (C) 2015 Elsevier Inc. All rights reserved.