Biodiversity hotspots, representing regions with high species endemism and conservation threat, have been mapped globally. Yet, biodiversity distribution data from within hotspots are too sparse for effective conservation in the face of rapid environmental change. Using frogs as indicators, ecological niche models under paleoclimates, and simultaneous Bayesian analyses of multispecies molecular data, we compare alternative hypotheses of assemblage-scale response to late Quaternary climate change. This reveals a hotspot within the Brazilian Atlantic forest hotspot. We show that the southern Atlantic forest was climatically unstable relative to the central region, which served as a large climatic refugium for neotropical species in the late Pleistocene. This sets new priorities for conservation in Brazil and establishes a validated approach to biodiversity prediction in other understudied, species-rich regions.

A molecular phylogeny was reconstructed for 26 recognized genera of the Gymnophthalmidae using a total of 2379 bp of mitochondrial (12S, 16s and ND4) and nuclear (18s and c-mos) DNA sequences. We performed maximum parsimony (MP) and maximum likelihood (ML) analyses, and data partitions were analysed separately and in combination under MP. ML analyses were carried out only on the combined sequences for computational simplicity. Robustness for the recovered nodes was assessed with bootstrap and partitioned Bremer support (PBS) analyses. The total molecular evidence provided a better-resolved hypothesis than did separate analysis of individual partitions, and the PBS analysis indicates congruence among independent partitions for support of some internal nodes. Based on this hypothesis, a new classification for the family is proposed. Alopoglossus, the sister group of all the other Gymnophthalmidae was allocated to a new subfamily Alopoglossinae, and Rhachisaums (a new genus for Anotosaura brachylepis) to the new Rhachisaurinae. Two tribes are recognized within the subfamily Gymnophthalminae: Heterodactylini and Gymnophthalmini, and two others within Cercosaurinae (Ecpleopini and Cercosaurini). Some ecological and evolutionary implications of the phylogenetic hypothesis are considered, including the independent occurrence of limb reduction, body elongation, and other characters associated with fossoriality.

Phylogeographic endemism, the degree to which the history of recently evolved lineages is spatially restricted, reflects fundamental evolutionary processes such as cryptic divergence, adaptation and biological responses to environmental heterogeneity. Attempts to explain the extraordinary diversity of the tropics, which often includes deep phylogeographic structure, frequently invoke interactions of climate variability across space, time and topography. To evaluate historical versus contemporary drivers of phylogeographic endemism in a tropical system, we analyse the effects of current and past climatic variation on the genetic diversity of 25 vertebrates in the Brazilian Atlantic rainforest. We identify two divergent bioclimatic domains within the forest and high turnover around the Rio Doce. Independent modelling of these domains demonstrates that endemism patterns are subject to different climatic drivers. Past climate dynamics, specifically areas of relative stability, predict phylogeographic endemism in the north. Conversely, contemporary climatic heterogeneity better explains endemism in the south. These results accord with recent speleothem and fossil pollen studies, suggesting that climatic variability through the last 250 kyr impacted the northern and the southern forests differently. Incorporating sub-regional differences in climate dynamics will enhance our ability to understand those processes shaping high phylogeographic and species endemism, in the Neotropics and beyond.

No abstract

The relative influence of Neogene geomorphological events and Quaternary climatic changes as causal mechanisms on Neotropical diversification remains largely speculative, as most divergence timing inferences are based on a single locus and have limited taxonomic or geographic sampling. To investigate these influences, we use a multilocus (two mitochondrial and 11 nuclear genes) range-wide sampling of Phyllopezus pollicaris, a gecko complex widely distributed across the poorly studied South American 'dry diagonal' biomes. Our approach couples traditional and model-based phylogeography with geospatial methods, and demonstrates Miocene diversification and limited influence of Pleistocene climatic fluctuations on P. pollicaris. Phylogeographic structure and distribution models highlight that persistence across multiple isolated regions shaped the diversification of this species complex.Approximate Bayesian computation supports hypotheses of allopatric and ecological/sympatric speciation between lineages that largely coincide with genetic clusters associated with Chaco, Cerrado, and Caatinga, standing for complex diversification between the 'dry diagonal' biomes. We recover extremely high genetic diversity and suggest that eight well-supported clades may be valid species, with direct implications for taxonomy and conservation assessments. These patterns exemplify how low-vagility species complexes, characterized by strong genetic structure and pre-Pleistocene divergence histories, represent ideal radiations to investigate broad biogeographic histories of associated biomes.

Phylogenetic analyses based on mtDNA cytochrome b were performed in 42 lizards of the Gymnodactylus darwinii complex from three regions within Brazil's Atlantic Forest. Mainland regions and continental shelf islands in the south-eastern range and mainland areas from the north-east were sampled. The criteria of maximum parsimony (MP), maximum likelihood (ML) and Bayesian methods were explored, with the robustness for nodes assessed by bootstrapping (MP and ML) and posterior probabilities (Bayesian searches). By all methods, three distinctive phylogroups were recovered: a south-eastern clade (SE) and two clades from northern regions (NE 1 and NE 2 ). The pattern of genetic structure of the major clades coincided with the presence of river systems in the Atlantic Forest, and based on corrected genetic distances between those clades, divergence times were tentatively estimated using mtDNA rates calibrated for squamate reptiles. The putative role of Atlantic Forest rivers in generating differentiation is discussed. We present a hypothesis of species limits for G. darwinii , based on concordant lines of evidence including cytogenetic and mtDNA analyses. Two chromosome races (cytotype A, 2n = 38; and cytotype B, 2n = 40) had distributions concordant with clades SE and NE 1 + NE 2 , respectively. These races are interpreted to be full species on the basis of a number of empirical criteria.

No abstract

Aim For many taxa, inaccuracy of species boundaries and distributions hampers inferences about diversity and evolution. This is particularly true in the Neotropics where prevalence of cryptic species has often been demonstrated. The frog genus Adenomera is suspected to harbour many more species than the 16 currently recognized. These small terrestrial species occur in Amazonia, Atlantic Forest (AF), and in the open formations of the Dry Diagonal (DD: Chaco, Cerrado and Caatinga). This widespread and taxonomically complex taxon provides a good opportunity to (1) test species boundaries, and (2) investigate historical connectivity between Amazonia and the AF and associated patterns of diversification.Location Tropical South America east of the Andes.Methods We used molecular data (four loci) to estimate phylogenetic relationships among 320 Adenomera samples. These results were integrated with other lines of evidence to propose a conservative species delineation. We subsequently used an extended dataset (seven loci) and investigated ancestral area distributions, dispersal-vicariance events, and the temporal pattern of diversification within Adenomera. ResultsOur conservative delineation identified 31 Confirmed Candidate Species (four remaining unconfirmed) representing a 94% increase in species richness. The biogeographical analysis suggested an Amazonian origin of Adenomera with as many as three dispersals to the DD and one to the AF during the Miocene. These dispersals were associated with habitat shifts from forest towards open habitats. Main conclusionsThe DD played a major role in the history of Adenomera in limiting dispersal and favouring diversification of open-habitat lineages. Moreover, a forest bridge during the Miocene Climatic Optimum may have permitted dispersal from Amazonia towards the AF and subsequent diversification. Uncovering species boundaries and distributions might drastically change inferences based on currently perceived distribution patterns.