AimMapping Amazonian biodiversity accurately is a major challenge for integrated conservation strategies and to study its origins. However, species boundaries and their respective distribution are notoriously inaccurate in this region. Here, we generated a georeferenced database of short mtDNA sequences from Amazonian frogs, revised the species richness and the delimitation of bioregions of the Eastern Guiana Shield and estimated endemism within these bioregions. LocationAmazonia, with a focus on the Eastern Guiana Shield. Taxon studiedAmphibia: Anura. MethodsWe used an extensive DNA-based sampling of anuran amphibians of Amazonia using nextgeneration sequencing to delimit Operational Taxonomic Units (OTU) and their distribution. We analysed this database to infer bioregions using Latent Dirichlet Allocation modelling. We then compared endemism within these bioregions based on our results and the current IUCN database, and inferred environmental variables that contributed the most to the biogeographic pattern. ResultsThe recognized anuran species richness within the focal area increased from 440 species currently listed by the IUCN Red List to as much as 876 OTUs with our dataset. We recovered eight bioregions, among which three lie within the Eastern Guiana Shield. We estimated that up to 82% of the OTUs found in this area are endemic, a figure three times higher than the previous estimate (28%). Environmental features related to seasonal precipitations are identified as playing an important role in shaping Amazonian amphibian bioregions. Main conclusionsOur results have major implications for defining future conservation priorities of this vast area given that endemism in most Amazonian bioregions is vastly underestimated, and might therefore hide a large portion of threatened species. Moreover, these findings raise concern about meta-analyses based on public databases within Amazonia dealing with poorly known groups.

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Gymnophthalmus represents a challenging group for systematics of microteiid lizards. Due to scarcity of exemplars and molecular data, the taxonomy of the genus has been unstable, and six of its eight species are considered part of a poorly-delimited complex of unisexual and bisexual species. Unnamed populations of red-tailed Gymnophthalmus from savanna enclaves in Amazon, similar to G. vanzoi but with differences in color pattern, have been noted in the literature. Here, we used molecular and morphological data to test the taxonomic status of the Central Amazonian red-tailed Gymnophthalmus (G. sp.). Our molecular analysis recovered a close relationship between G. vanzoi and G. sp. from Central Amazon, with minimal divergence. Samples were similar in scale counts but presented significant variation in color pattern and morphometry. Despite the geographic isolation, individuals of both populations cannot be fully differentiated based on morphology. Thus, our results suggest that G. vanzoi has a wider distribution, including the Central Amazonian red-tailed Gymnophthalmus and likely morphologically similar populations from other enclaves of Amazonian savannas, which may have been isolated recently. Based on our comparative analysis, we highlight some characters proved useful for differentiating Brazilian Gymnophthalmus and discuss some prospects for the taxonomy of the genus.

The Cercosaurini tribe stands out from other Gymnophthalmidae lizards for including several species with morphological adaptations to aquatic lifestyle (“Crocodile‐Like Morphology” – CLM). Recent molecular phylogenies of Cercosaurini demonstrated the paraphyly of CLM species, implicitly suggesting that adaptations to the aquatic life evolved more than once. However, CLM species have remained poorly sampled, and a number of uncertainties persist, such as the monophyly of Neusticurus and the placement of Potamites apodemus within the tribe. Based on a more extensive molecular and morphological data set, we propose a phylogenetic hypothesis for Neusticurus and investigate, for the first time, the phylogenetic position of P. apodemus. We recovered a monophyletic Neusticurus clade; however, Neusticurus rudis as currently understood was recovered as paraphyletic, with two lineages that also show consistent morphological diagnosis; as a result, we resurrect and provide a taxonomic redescription of Neusticurus surinamensis Müller, . Moreover, because P. apodemus was recovered as sister to all other Echinosaura, we propose a new combination for this species (Echinosaura apodema). We also review the distribution of Neusticurus species, offering a comprehensive view of their biogeography. Lastly, our ancestral character reconstruction and dating analyses indicate that the CLM phenotype evolved four times independently during Cercosaurini′s evolutionary history. We hypothesize that the CLM phenotype and subsequent adaptation to aquatic life may be linked to the development of the Pebas Lake in western Amazonia during the Miocene.

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In the last decades, a remarkable fauna of psammophilous and fossorial squamates was discovered in sandy habitats of the semiarid Caatinga of northeast Brazil. Despite the increasing accumulation of genetic data from this unique fauna, an incomplete knowledge of its diversity still hampers a better understanding of its origins and diversification. The fossorial lizard genus Calyptommatus (Gymnophthalmidae) is endemic to sandy habitats of the Caatinga, being currently represented by four allopatric species. In this study, we used morphological and molecular data to assess population-level variation in Calyptommatus. We found a new morphotype of Calyptommatus from the state of Bahia, Brazil, readily distinguished from congeners by the presence of a frontal scale. Morphological, nuDNA and geographic data support the recognition of a new species herein described as Calyptommatus frontalis sp. nov. Nevertheless, genetic data revealed mito-nuclear+morphology discordance, with populations with frontal scales distributed in three distantly related mtDNA clades, suggesting either potential historical and/or current introgressions or incomplete lineage sorting. Further data are needed to clarify the status of the two other mtDNA clades displaying a frontal scale.

Major historical landscape changes have left significant signatures on species diversification. However, how these changes have affected the build-up and maintenance of Amazonia’s megadiversity continues to be debated. Here, we addressed this issue by focusing on the evolutionary history of a pan-Amazonian toad genus that has diversified throughout the Neogene (Amazophrynella). Based on a comprehensive spatial and taxonomic sampling (286 samples, all nominal species), we delimited operational taxonomic units (OTUs) from mitochondrial DNA sequences. We delimited 35 OTUs, among which 13 correspond to nominal species, suggesting a vast underestimation of species richness. Next, we inferred time-calibrated phylogenetic relationships among OTUs based on complete mitogenomic data, which confirmed an ancient divergence between two major clades distributed in eastern and western Amazonia, respectively. Ancestral area reconstruction analyses suggest that the Andean foothills and the Brazilian Shield region represent the ancient core areas for their diversification. These two clades, probably isolated from one other by lacustrine ecosystems in western Amazonia during the Miocene, display a pattern of northward and eastward dispersals throughout the Miocene‒Pliocene. Given the ecological association of Amazophrynella with non-flooded forests, our results reinforce the perception that ancient Amazonian landscape changes had a major impact on the diversification of terrestrial vertebrates.