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.

Aim  We aim to propose validated, spatially explicit hypotheses for the late Quaternary distribution of the Brazilian Atlantic forest, and thereby provide a framework for integrating analyses of species and genetic diversity in the region.Location  The Atlantic forest, stretching along the Brazilian coast.Methods  We model the spatial range of the forest under three climatic scenarios (current climate, 6000 and 21,000 years ago) with BIOCLIM and MAXENT. Historically stable areas or refugia are identified as the set of grid cells for which forest presence is inferred in all models and time projections. To validate inferred refugia, we test whether our models are matched by the current distribution of the forest and by fossil pollen data. We then investigate whether the location of inferred forest refugia is consistent with current patterns of species endemism and existing phylogeographical data.Results  Forest models agree with pollen records and predict a large area of historical forest stability in the central corridor (Bahia), as well as a smaller refuge (Pernambuco) along the Brazilian coast, matching current centres of endemism in multiple taxa and mtDNA diversity patterns in a subset of the species examined. Less historical stability is predicted in coastal areas south of the Doce river, which agrees with most phylogeographical studies in that region. Yet some widely distributed taxa show high endemism in the southern Atlantic forest. This may be due to limitations of the modelling approach, differences in ecology and dispersal capability, historical processes not contemplated by the current study or inadequacy of the available test data sets.Main conclusions  Palaeoclimatic models predict the presence of historical forest refugia in the Atlantic rain forest and suggest spatial variation in persistence of forests through the Pleistocene, predicting patterns of biodiversity in several local taxa. The results point to the need for further studies to document genetic and species endemism in the relatively poorly known and highly impacted areas of Atlantic rain forests of north‐eastern Brazil.

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.

Many biodiversity hotspots are located in montane regions, especially in the tropics. A possible explanation for this pattern is that the narrow thermal tolerances of tropical species and greater climatic stratification of tropical mountains create more opportunities for climate-associated parapatric or allopatric speciation in the tropics relative to the temperate zone. However, it is unclear whether a general relationship exists among latitude, climatic zonation and the ecology of speciation. Recent taxon-specific studies obtained different results regarding the role of climate in speciation in tropical versus temperate areas. Here, we quantify overlap in the climatic distributions of 93 pairs of sister species of mammals, birds, amphibians and reptiles restricted to either the New World tropics or to the Northern temperate zone. We show that elevational ranges of tropical-and temperate-zone species do not differ from one another, yet the temperature range experienced by species in the temperate zone is greater than for those in the tropics. Moreover, tropical sister species tend to exhibit greater similarity in their climatic distributions than temperate sister species. This pattern suggests that evolutionary conservatism in the thermal niches of tropical taxa, coupled with the greater thermal zonation of tropical mountains, may result in increased opportunities for allopatric isolation, speciation and the accumulation of species in tropical montane regions. Our study exemplifies the power of combining phylogenetic and spatial datasets of global climatic variation to explore evolutionary (rather than purely ecological) explanations for the high biodiversity of tropical montane regions.

High-resolution, easily accessible paleoclimate data are essential for environmental, evolutionary, and ecological studies. The availability of bioclimatic layers derived from climatic simulations representing conditions of the Late Pleistocene and Holocene has revolutionized the study of species responses to Late Quaternary climate change. Yet, integrative studies of the impacts of climate change in the Early Pleistocene and Pliocene – periods in which recent speciation events are known to concentrate – have been hindered by the limited availability of downloadable, user-friendly climatic descriptors. Here we present PaleoClim, a free database of downscaled paleoclimate outputs at 2.5-minute resolution (~5 km at equator) that includes surface temperature and precipitation estimates from snapshot-style climate model simulations using HadCM3, a version of the UK Met Office Hadley Centre General Circulation Model. As of now, the database contains climatic data for three key time periods spanning from 3.3 to 0.787 million years ago: the Marine Isotope Stage 19 (MIS19) in the Pleistocene (~787 ka), the mid-Pliocene Warm Period (~3.264–3.025 Ma), and MIS M2 in the Late Pliocene (~3.3 Ma).

Determining how ecological and evolutionary processes produce spatial variation in local species richness remains an unresolved challenge. Using mountains as a model system, we outline an integrative research approach to evaluate the influence of ecological and evolutionary mechanisms on the generation and maintenance of patterns of species richness along and among elevational gradients. Biodiversity scientists interested in patterns of species richness typically start by documenting patterns of species richness at regional and local scales, and based on their knowledge of the taxon, and the environmental and historical characteristics of a mountain region, they then ask whether diversity–environment relationships, if they exist, are explained mostly by ecological or evolutionary hypotheses. The final step, and perhaps most challenging one, is to tease apart the relative influence of ecological and evolutionary mechanisms. We propose that elucidating the relative influence of ecological and evolutionary mechanisms can be achieved by taking advantage of the replicated settings afforded by mountains, combined with targeted experiments along elevational gradients. This approach will not only identify potential mechanisms that drive patterns of species richness, but also allow scientists to generate more robust hypotheses about which factors generate and maintain local diversity.

Aim  We use novel data on the occurrence of the amphibian chytrid fungus Batrachochytrium dendrobatidis in Costa Rica to model its potential distribution in that country. Location  Lowland and montane areas of Costa Rica. Methods  We use published and new data on the presence of B. dendrobatidis on 647 amphibians (35 species). Screening was performed through histological techniques by which 156 sites were surveyed. Of these, 21 were found to have the amphibian chytrid. Maxent, a presence‐only distribution modelling technique, was used to create 100 predictions of B. dendrobatidis occurrence, of which the most accurate 10 (based on area under the receiver‐operating characteristic curve) were chosen to create a composite distribution model. This approach increased confidence in model predictions, distinguishing areas of high probability of occurrence and low variability across model runs (higher confidence) from those with high probability but high variability (lower confidence). Results  Predicted distribution patterns were not uniform along Costa Rica's mountains, where most amphibian declines have occurred. The pathogen was predicted to occur with greater probability on the Caribbean slopes than on the Pacific slopes. While high temperature seems to constrain the distribution of the pathogen, areas that also have small amounts of rainfall during the driest period of the year were predicted to have low probability of B. dendrobatidis occurrence. Main conclusions  The model predicts that the Santa Elena Peninsula and the Central Valley have low probabilities of B. dendrobatidis occurrence, suggesting that they could function as refuges for amphibians. In such refugial areas, one could expect B. dendrobatidis to be absent, or to be present in low abundance (rendering an epidemic outbreak of chytridiomycosis unlikely). Craugastor ranoides, which belongs to a group of frogs particularly sensitive to chytridiomycosis outbreaks, persists in the hot and seasonally dry Santa Elena Peninsula but disappeared in the nearby colder and more humid Guanacaste Volcanic Chain. This information suggests that climatic refuges, where environmental conditions prevent disease outbreaks, could be an important component in amphibian conservation.

Population declines have previously been reported for at least 31 amphibian species in Brazil, in the families Leptodactylidae (19), Hylidae (7), Centrolenidae (2), Dendrobatidae (2), and Bufonidae (1). In five Brazilian museum collections, we found no entries of new records dating back to at least 15 yr ago for 13 of these species. We suggest that these taxa be studied in more detail to verify their status and to generate basic ecological data. Museum data indicate that the remaining species have been recently found in areas of reported crashes, or elsewhere. Several apparent declines in Brazil can be associated with habitat loss, interspecific interactions, natural fluctuations, or lack of intensive sampling. Personal observations and field data also indicate possible declines in the states of Paraná and Ceará as well as in highlands within the Cerrado biome, in the state of Minas Gerais. Records suggest declines of montane and stream‐associated populations of Brazilian amphibians in apparently pristine habitats. Field work is necessary to confirm these cases and to examine whether factors associated with similar extinctions in other parts of the globe—such as pathogens and climate change—are also related to local disappearances. To clarify pending questions and perhaps circumvent new cases, it is important to invest in short‐ and long‐term field studies, and in the maintenance and expansion of museum collections.