The Mascarene ridged frog, Ptychadena mascareniensis, is a species complex that includes numerous lineages occurring mostly in humid savannas and open forests of mainland Africa, Madagascar, the Seychelles, and the Mascarene Islands. Sampling across this broad distribution presents an opportunity to examine the genetic differentiation within this complex and to investigate how the evolution of bioclimatic niches may have shaped current biogeographic patterns. Using model-based phylogenetic methods and molecular-clock dating, we constructed a time-calibrated molecular phylogenetic hypothesis for the group based on mitochondrial 16S rRNA and cytochrome b (cytb) genes and the nuclear RAG1 gene from 173 individuals. Haplotype networks were reconstructed and species boundaries were investigated using three species-delimitation approaches: Bayesian generalized mixed Yule-coalescent model (bGMYC), the Poisson Tree Process model (PTP) and a cluster algorithm (SpeciesIdentifier). Estimates of similarity in bioclimatic niche were calculated from species-distribution models (maxent) and multivariate statistics (Principal Component Analysis, Discriminant Function Analysis). Ancestral-area reconstructions were performed on the phylogeny using probabilistic approaches implemented in BioGeoBEARS. We detected high levels of genetic differentiation yielding ten distinct lineages or operational taxonomic units, and Central Africa was found to be a diversity hotspot for these frogs. Most speciation events took place throughout the Miocene, including "out-of-Africa" overseas dispersal events to Madagascar in the East and to São Tomé in the West. Bioclimatic niche was remarkably well conserved, with most species tolerating similar temperature and rainfall conditions common to the Central African region. The P. mascareniensis complex provides insights into how bioclimatic niche shaped the current biogeographic patterns with niche conservatism being exhibited by the Central African radiation and niche divergence shaping populations in West Africa and Madagascar. Central Africa, including the Albertine Rift region, has been an important center of diversification for this species complex.

African Amphibian Conservation Research Group Unit for Environmental Sciences and Management North West University Potchefstroom 2520 South Africa; South African Institute for Aquatic Biodiversity Somerset Street Grahamstown 6139 South Africa

Centre de Recherche en Sciences Naturelles Département de Biologie Lwiro The Democratic Republic of the Congo

Department of Biological Sciences University of Cincinnati 820F Rieveschl Hall Cincinnati OH 45221 USA

Department of Biological Sciences University of Texas at El Paso 500 W University Ave El Paso TX 79968 USA

Department of Biological Sciences University of Texas at El Paso 500 W University Ave El Paso TX 79968 USA; Department of Biology Tidewater Community College 120 Campus Dr Portsmouth VA 23701 USA

Department of Biology University of Copenhagen Copenhagen Denmark

Department of Comparative Anatomy Institute of Zoology Jagiellonian University Gronostajowa 9 30 387 Kraków Poland

Division of Evolutionary Biology Zoological Institute Technical University of Braunschweig Mendelssohnstraße 4 38106 Braunschweig Germany

Fakultät für Biologie Universität Bielefeld Abt Biologiedidaktik Universitätsstraße 25 33615 Bielefeld Germany

Harvey Ecological 35 Carbis Road Pietermaritzburg 3201 KwaZulu Natal South Africa

Institute of Integrated Sciences Department of Biology University of Koblenz Landau Universitätsstraße 1 56070 Koblenz Germany

Institute of Vertebrate Biology Czech Academy of Sciences 603 65 Brno Czech Republic; National Museum Department of Zoology 19300 Prague Czech Republic

Museum für Naturkunde Leibniz Institute for Evolution and Biodiversity Science Invalidenstrasse 43 10115 Berlin Germany

Museum für Naturkunde Leibniz Institute for Evolution and Biodiversity Science Invalidenstrasse 43 10115 Berlin Germany; Joint Experimental Molecular Unit Royal Belgian Institute of Natural Sciences Rue Vautier 29 1000 Brussels Belgium

Museum für Naturkunde Leibniz Institute for Evolution and Biodiversity Science Invalidenstrasse 43 10115 Berlin Germany; Wildlife Ecology and Management University of Freiburg Tennenbacher Str 4 79106 Freiburg Germany

Museum of Comparative Zoology Harvard University Cambridge MA 02138 USA

Trier University Department of Biogeography 54286 Trier Germany

University of Basel Biogeography Research Group Department of Environmental Sciences Klingelbergstrasse 27 Basel 4056 Switzerland

University of the Western Cape Biodiversity and Conservation Biology Private Bag X17 Bellville 7535 South Africa

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