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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.

Many tropical organisms show large genetic differences among populations, yet the prevalent drivers of the underlying divergence processes are incompletely understood. We explored the effect of several habitat and natural history features (body size, macrohabitat, microhabitat, reproduction site, climatic heterogeneity, and topography) on population genetic divergence in tropical amphibians, based on a data set of 2680 DNA sequences of the mitochondrial cytochrome b gene in 39 widely distributed frog species from Brazil, Central America, Cuba, and Madagascar. Generalized linear models were implemented in an information-theoretic framework to evaluate the effects of the six predictors on genetic divergence among populations, measured as spatially corrected pairwise distances. Results indicate that topographic complexity and macrohabitat preferences have a strong effect on population divergence with species specialized to forest habitat and/or from topographically complex regions showing higher phylogeographic structure. This relationship changed after accounting for phylogenetic relatedness among taxa rendering macrohabitat preferences as the most important feature shaping genetic divergence. The remaining predictors showed negligible effects on the observed genetic divergence. A similar analysis performed using the population-scaled mutation rate (Θ) as response variable showed little effect of the predictors. Our results demonstrate greater evolutionary independence among populations of anurans from forested regions versus species from open habitats. This pattern may result from lower vagility and stringency in reproductive requirements of rainforest species. Conversely, open landscapes may offer ephemeral and unstable breeding sites suitable for vagile generalist species, resulting in reduced intraspecific divergence. Our results predict that, for a given period of time, there should be a higher chance of speciation in tropical anurans living in forests than in species adapted to open habitats.

Intraspecific communication in frogs plays an important role in the recognition of conspecifics in general and of potential rivals or mates in particular and therefore with relevant consequences for pre-zygotic reproductive isolation. We investigate intraspecific communication in Hylodes japi, an endemic Brazilian torrent frog with territorial males and an elaborate courtship behavior. We describe its repertoire of acoustic signals as well as one of the most complex repertoires of visual displays known in anurans, including five new visual displays. Previously unknown in frogs, we also describe a bimodal inter-sexual communication system where the female stimulates the male to emit a courtship call. As another novelty for frogs, we show that in addition to choosing which limb to signal with, males choose which of their two vocal sacs will be used for visual signaling. We explain how and why this is accomplished. Control of inflation also provides additional evidence that vocal sac movement and color must be important for visual communication, even while producing sound. Through the current knowledge on visual signaling in Neotropical torrent frogs (i.e. hylodids), we discuss and highlight the behavioral diversity in the family Hylodidae. Our findings indicate that communication in species of Hylodes is undoubtedly more sophisticated than we expected and that visual communication in anurans is more widespread than previously thought. This is especially true in tropical regions, most likely due to the higher number of species and phylogenetic groups and/or to ecological factors, such as higher microhabitat diversity.

Anurans are a highly diverse group in the Atlantic Forest hotspot (AF), yet distribution patterns and species richness gradients are not randomly distributed throughout the biome. Thus, we explore how anuran species are distributed in this complex and biodiverse hotspot, and hypothesize that this group can be distinguished by different cohesive regions. We used range maps of 497 species to obtain a presence/absence data grid, resolved to 50×50 km grain size, which was submitted to k-means clustering with v-fold cross-validation to determine the biogeographic regions. We also explored the extent to which current environmental variables, topography, and floristic structure of the AF are expected to identify the cluster patterns recognized by the k-means clustering. The biogeographic patterns found for amphibians are broadly congruent with ecoregions identified in the AF, but their edges, and sometimes the whole extent of some clusters, present much less resolved pattern compared to previous classification. We also identified that climate, topography, and vegetation structure of the AF explained a high percentage of variance of the cluster patterns identified, but the magnitude of the regression coefficients shifted regarding their importance in explaining the variance for each cluster. Specifically, we propose that the anuran fauna of the AF can be split into four biogeographic regions: a) less diverse and widely-ranged species that predominantly occur in the inland semideciduous forests; b) northern small-ranged species that presumably evolved within the Pleistocene forest refugia; c) highly diverse and small-ranged species from the southeastern Brazilian mountain chain and its adjacent semideciduous forest; and d) southern species from the Araucaria forest. Finally, the high congruence among the cluster patterns and previous eco-regions identified for the AF suggests that preserving the underlying habitat structure helps to preserve the historical and ecological signals that underlie the geographic distribution of AF anurans.

Anthropogenic habitat disturbances often create discontinuity between the multiple classes of natural habitats that many species need to complete their life cycles. This process, termed habitat split , is common across Neotropical landscapes and negatively impacts several classes of vertebrates and invertebrates. For instance, habitat split—often arising from habitat loss and fragmentation—exposes aquatic-breeding amphibians to risky migrations through disturbed environments as they move between natural terrestrial habitats and aquatic breeding sites, contributing to population declines. In contrast, terrestrial-breeding amphibians should not be impacted by this form of habitat split because they may spend their entire life cycle in the same terrestrial habitat. We used available field data and natural history information to develop Individual-Based Models (IBM) that account for seasonal migrations to quantify the impact of different levels of habitat split on population survival of Brazilian amphibians. Our IBM results align with our observed field data, indicating a disproportionate decline in the occurrence and population abundances of migrating aquatic-breeding amphibians compared to non-migratory terrestrial-breeding amphibians in regions with high habitat split. An intermediate dispersal optimum for aquatic-breeding frogs was suggested by our IBM, indicating that long-distance dispersal might not always be advantageous for population persistence, likely due to tradeoffs between reproduction and migration risk. Our spatial model framework factoring breeding migration could be applied widely across ecoregions of interest and help inform targeted habitat restoration strategies to curb localized amphibian declines and extinctions.

Satellite DNAs (satDNAs) play a crucial role in understanding chromosomal evolution and the differentiation of sex chromosomes across diverse taxa, particularly when high karyotypic diversity occurs. The Physalaemus cuvieri–Physalaemus ephippifer species complex comprises at least seven divergent lineages, each exhibiting specific karyotypic signatures. The group composed of Ph. ephippifer, Lineage 1B of ‘Ph. cuvieri’ (L1B), and a lineage resulting from their secondary contact is especially intriguing due to varying degrees of sex chromosome heteromorphism. In this study, we characterized the satellitome of Ph. ephippifer in order to identify novel satDNAs that may provide insights into chromosomal evolution, particularly concerning sex chromosomes. We identified 62 satDNAs in Ph. ephippifer, collectively accounting for approximately 10% of the genome. Notably, nine satDNA families were shared with species from distantly related clades, raising questions about their potential roles in anurans genomes. Among the seven satDNAs mapped via fluorescent in situ hybridization, PepSat3 emerged as a strong candidate for the centromeric sequence in this group. Additionally, PepSat11 and PepSat24 provided evidence supporting a translocation involving both arms of the W chromosome in Ph. ephippifer. Furthermore, a syntenic block composed of PepSat3, PcP190, and PepSat11 suggested an inversion event during the divergence of Ph. ephippifer and L1B. The variation in signal patterns of satDNAs associated with nucleolar organizer regions (NORs) highlights the complexity of NOR evolution in this species complex, which exhibits substantial diversity in this genomic region. Additionally, our findings for PepSat30-350 emphasize the importance of validating the sex-biased abundance of satDNAs.

Most amphibian species have biphasic life histories and undergo an ontogenetic shift from aquatic to terrestrial habitats. In deforested landscapes, streams and forest fragments are frequently disjunct, jeopardizing the life cycle of forest-associated amphibians with aquatic larvae. We tested the impact of habitat split--defined as human-induced disconnection between habitats used by different life-history stages of a species--on four forest-associated amphibian species in a severely fragmented landscape of the Brazilian Atlantic Forest. We surveyed amphibians in forest fragments with and without streams (referred to as wet and dry fragments, respectively), including the adjacent grass-field matrix. Our comparison of capture rates in dry fragments and nearby streams in the matrix allowed us to evaluate the number of individuals that engaged in high-risk migrations through nonforested habitats. Adult amphibians moved from dry fragments to matrix streams at the beginning of the rainy season, reproduced, and returned at the end of the breeding period. Juveniles of the year moved to dry fragments along with adults. These risky reproductive migrations through nonforested habitats that expose individuals to dehydration, predation, and other hazards may cause population declines in dry fragments. Indeed, capture rates were significantly lower in dry fragments compared with wet fragments. Declining amphibians would strongly benefit from investments in the conservation and restoration of riparian vegetation and corridors linking breeding and nonbreeding areas.

Discordance between mitochondrial and nuclear DNA is common among animals and can be the result of a number of evolutionary processes, including incomplete lineage sorting and introgression. Particularly relevant in contact zones, mitonuclear discordance is expected because the mitochondrial genome is haploid and primarily uniparentally inherited, whereas nuclear loci are evolving at slower rates. In addition, when closely related taxa come together in hybrid zones, the distribution of diagnostic phenotypic characters and their concordance with the mitochondrial or nuclear lineages can also inform on historical and ongoing dynamics within hybrid zones. Overall, genetic and phenotypic discordances provide evidence for evolutionary divergence and processes that maintain boundaries among sister species or lineages. In this study, we characterized patterns of genetic and phenotypic variation in a contact zone between Cycloramphus dubius and Cycloramphus boraceiensis, two sister species of frogs endemic to the Atlantic Coastal Forest of Brazil. We examined genomic‐scale nuclear diversification across 19 populations, encompassing the two parental forms and a contact zone between them. We compared the distribution of genomic DNA variability with that of a mitochondrial locus (16S) and two morphological traits (dorsal tubercles and body size). Our results reveal multiple divergent lineages with ongoing admixture. We detected discordance in patterns of introgression across the three data types. Cycloramphus dubius males are significantly larger than C. boraceiensis males, and we posit that competition among males in the hybrid zone, coupled with mate choice by females, may be one mechanism leading to patterns of introgression observed between the species. We characterized the patterns of genetic and phenotypic variation in a contact zone between Cycloramphus dubius and Cycloramphus boraceiensis, two sister species of frogs endemic to the Atlantic Coastal Forest of Brazil. We detected discordance in patterns of introgression across the three data types. Cycloramphus dubius males are significantly larger than C. boraceiensis males, and we posit that competition among males in the hybrid zone, coupled with mate choice by females may be one mechanism leading to patterns of introgression observed between the species. Photo credit: Leo R. Malagoli.

The genus Scinax currently includes more than 120 species, recovered in two major clades, the S. catharinae and the S. ruber clades. The latter comprises 75 species, most of which remain unassigned to any species groups, while 12 are included in the S. rostratus and S. uruguayus groups. In this paper we present a taxonomic review of the two species currently included in the S. uruguayus group, discussing some putative phenotypic synapomorphies of this group. Although S. pinima and S. uruguayus have been considered as distinct species, this has been based on scant evidence, and several authors doubted of their distinctiveness. Our study of available specimens of S. pinima and S. uruguayus corroborates that both are valid and diagnosable species based on phenotypic evidence. Furthermore, our results show that S. pinima previously known only from its type locality, has a much widespread distribution than previously thought (including the Brazilian states of Paraná, Santa Catarina, and Rio Grande do Sul), which, added to the biological information presented here allows to suggest the removal of this species from the \"Data Deficient\" IUCN Red List category to \"Least Concern\". Also, we describe a new species formerly reported as S. aff. pinima and S. uruguayus from NE Argentina and some localities from the Brazilian State of Rio Grande do Sul. All species are diagnosed and characterized using adult and larval morphology, osteology, vocalizations, cytogenetics, and natural history.

Understanding how environmental filtering and biotic interactions structure communities across elevational and latitudinal gradients is still a matter of debate. To provide insight into their relative importance, we explore the mismatch between three dimensions of biodiversity (taxonomic, functional and phylogenetic), and compare their patterns to null models of random community assembly. We focus on a highly diverse tropical group: the tree frogs (hylids) of the Atlantic Forest of Brazil. For that, we combined geographic distribution data with phylogenetic and trait information for 158 species to produce maps of the three dimensions of diversity. We show that communities of tree frogs of the Hylidae family tend to have high functional richness along the Atlantic Forest, potentially driven by niche partitioning. However, environmental filtering gains importance in extreme environments, both at high elevations and higher latitudes. In these areas of the forest, clustering of both functional and phylogenetic diversity is observed. Trait overdispersion is found in areas of contact between vegetation types, or of adjacent biomes, reflecting the encounter of amphibian species adapted to distinct environmental conditions and landscape configurations. Considering all three dimensions of diversity along with multiple axes of environmental variation allows for a more comprehensive understanding of the processes shaping amphibian community assembly in this biodiversity hotspot.