Molecular phylogeny of Neotropical rock frogs reveals a long history of vicariant diversification in the Atlantic forest

Mitonuclear and phenotypic discordance in an Atlantic Forest frog hybrid zone

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.

Shape Evolution in Two Acts: Morphological Diversity of Larval and Adult Neoaustraranan Frogs

Phenotypic traits can evolve independently at different stages of ontogeny, optimizing adaptation to distinct ecological contexts and increasing morphological diversity in species with complex life cycles. Given the relative independence resulting from the profound changes induced by metamorphosis, niche occupation and resource utilization in tadpoles may prompt evolutionary responses that do not necessarily affect the adults. Consequently, diversity patterns observed in the larval shape may not necessarily correspond to those found in the adult shape for the same species, a premise that can be tested through the Adaptive Decoupling Hypothesis (ADH). Herein, we investigate the ADH for larval and adult shape differentiation in Neoaustrarana frogs. Neoaustrarana frogs, particularly within the Cycloramphidae family, exhibit remarkable diversity in tadpole morphology, making them an ideal model for studying adaptive decoupling. By analyzing 83 representative species across four families (Alsodidae, Batrachylidae, Cycloramphidae, and Hylodidae), we generate a morphological dataset for both larval and adult forms. We found a low correlation between larval and adult shapes, species with a highly distinct larval shape having relatively similar shape when adults. Larval morphological disparity is not a good predictor for adult morphological disparity within the group, with distinct patterns observed among families. Differences between families are notable in other aspects as well, such as the role of allometric components influencing shape and morphospace occupancy. The larval shape has higher phylogenetic structure than the adult. Evolutionary convergence emerges as a mechanism of diversification for both larval and adult shapes in the early evolution of neoaustraranans, with shape disparity of tadpoles reaching stable levels since the Oligocene. The widest occupation in morphospace involves families associated with dynamically changing environments over geological time. Our findings support the ADH driving phenotypic diversity in Neoaustrarana, underscoring the importance of considering ontogenetic stages in evolutionary studies.

Species limits and diversification of the Dendropsophus rubicundulus subgroup (Anura, Hylidae) in Neotropical savannas

Understanding the processes that generate and maintain biodiversity at and below the species level is a central goal of evolutionary biology. Here we explore the spatial and temporal drivers of diversification of the treefrog subgroup Dendropsophus rubicundulus, a subgroup of the D. microcephalus species group, over periods of pronounced geological and climatic changes in the Neotropical savannas that they inhabit. This subgroup currently comprises 11 recognized species distributed across the Brazilian and Bolivian savannas, but the taxonomy has been in a state of flux, necessitating reexamination. Using newly generated single nucleotide polymorphism (SNP) data from restriction-site associated DNA sequencing (RADseq) and mitochondrial 16S sequence data for ∼150 specimens, we inferred phylogenetic relationships, tested species limits using a model-based approach, and estimated divergence times to gain insights into the geographic and climatic events that affected the diversification of this subgroup. Our results recognized at least nine species: D. anataliasiasi, D. araguaya, D. cerradensis, D. elianeae, D. jimi, D. rubicundulus, D. tritaeniatus, D. rozenmani, and D. sanborni. Although we did not collect SNP data for the latter two species, they are likely distinct based on mitochondrial data. In addition, we found genetic structure within the widespread species D. rubicundulus, which comprises three allopatric lineages connected by gene flow upon secondary contact. We also found evidence of population structure and perhaps undescribed diversity in D. elianeae, which warrants further study. The D. rubicundulus subgroup is estimated to have originated in the Late Miocene (∼5.45 million years ago), with diversification continuing through the Pliocene and Early Pleistocene, followed by the most recent divergence of D. rubicundulus lineages in the Middle Pleistocene. The epeirogenic uplift followed by erosion and denudation of the central Brazilian plateau throughout the Pliocene and Pleistocene, in combination with the increasing frequency and amplitude of climatic fluctuations during the Pleistocene, was important for generating and structuring diversity at or below the species level in the D. rubicundulus subgroup.

Deep Genomic Divergence and Phenotypic Admixture of the Treefrog Dendropsophus elegans (Hylidae: Amphibia) Coincide With Riverine Boundaries at the Brazilian Atlantic Forest

The Atlantic Forest (AF) domain is one of the Earth’s biodiversity hotspots, known for its high levels of species diversity and endemism. Factors related to palaeoenvironmental dynamics, such as the establishment of vegetational refugia and river basins, have different impacts on biological communities and biodiversity patterns in this domain. Here, we sample genome-wide RADseq data from a widespread treefrog (Dendropsophus elegans), inhabiting natural and human-impacted ecosystems at the Brazilian AF to test the impact of riverine boundaries and climatic refugia on population structure and diversification. We estimate divergence times and migration rate across identified genetic breaks related to the rivers Doce, Paraíba do Sul, Ribeira de Iguape, and Paraguaçu, known to represent barriers to gene flow for other AF endemic species, and test the role of climatic refugia. Finally, we investigate the impact of spatio-temporal population history on morphological variation in this species. We recovered a phylogeographic history supporting three distinct clades separated into two geographically structured populations, corresponding to the north and south of AF. In addition, we identified an admixture zone between north and south populations in the latitude close to the Doce River. Our findings support a pattern of isolation-by-distance and the existence of a secondary contact zone between populations, which might have been promoted by gene flow during population expansion. Further, we found support for models considering migration parameters for all the tested rivers with different population divergence times. Based on the species history and the AF palaeoenvironmental dynamics, we corroborate the role of forest refugia impacting population structure for this species through recent range expansion after the Last Glacial Maximum (LGM). The Doce and Paraíba do Sul Rivers coincide with the main genetic breaks, suggesting they might also have played a role in the diversification processes. Finally, despite finding subtle correlations for phenotypic data among different populations, variation is not strongly detectable and does not seem associated with speciation-level processes that could warrant taxonomic changes. Such results can be explained by phenotypic plasticity of the evaluated traits and by recent divergence times, where there has been insufficient time and weak selective pressures to accumulate enough phenotypic differences.

Ecological divergence and synchronous Pleistocene diversification in the widespread South American butter frog complex

Phylogeographic studies primarily focus on the major role of landscape topography in driving lineage diversification. However, populational phylogeographic breaks may also occur as a result of either niche conservatism or divergence, in the absence of geographic barriers to gene flow. Furthermore, these two factors are not mutually exclusive and can act in concert, making it challenging to evaluate their relative importance on explaining genetic variation in nature. Herein, we use sequences of two mitochondrial and four nuclear genes to investigate the timing and diversification patterns of species pertaining to the Leptodactylus latrans complex, which harbors four morphologically cryptic species with broad distributions across environmental gradients in eastern South America. The origin of this species complex dates back to the late Miocene (ca. 5.5 Mya), but most diversification events occurred synchronically during the late Pleistocene likely as the result of ecological divergence driven by Quaternary climatic oscillations. Further, significant patterns of environmental niche divergences among species in the L. latrans complex imply that ecological isolation is the primary mode of genetic diversification, mostly because phylogenetic breaks are associated with environmental transitions rather than topographic barriers at both species and populational scale. We provided new insights about diversification patterns and processes within a species complex of broadly and continuously distributed group of frogs along South America.

From genes to ecosystems: a synthesis of amphibian biodiversity research in Brazil

Abstract Here, we summarize examples of significant advances in amphibian research supported by the São Paulo Research Foundation (FAPESP), focusing on recent discoveries in the fields of community ecology, habitat change, infection diseases, and multipurpose DNA sequencing. We demonstrated that FAPESP has been fundamental not only by directly funding research projects and scholarships, but also through its science training policy, fostering international collaborations with world-class research institutions, improving and consolidating new lines of research that often depended on a synergetic combination of different knowledge and complex tools. We emphasized that future studies will continue to focus on basic questions, such as description of new species, as well as taxonomic and systematic corrections. Furthermore, we also expect that there will be a strong integration among different disciplines using novel bioinformatics tools and modeling approaches, such as machine learning. These new approaches will be critical to further develop our understanding of foundational questions of amphibian life-history trait variation, disease transmission, community assembly, biogeography, and population forecasts under different global change scenarios such as agricultural expansion, agrochemical use, habitat loss, and climate change.

Phenotypic and genomic differences between biomes of the South America marsh rat, Holochilus brasiliensis

Abiotic factors can influence genetic and phenotypic divergence in several ways, and identifying the mechanisms responsible for generating this variation is challenging. However, when evaluated in combination, ecological characteristics and genetic and phenotypic information can help us to understand how habitat preferences can influence morphological and genetic patterns exhibited by taxa distributed between distinct biomes, such as the Atlantic Forest and Pampas biomes in South America. By combining distributional, environmental, phenotypic and genomic information from a habitat-specialist semi-aquatic rodent (Holochilus brasiliensis), we quantified the relationship between ecological niche differences and the phenotypic and genetic variation. The results demonstrate notable segregation among the ecological niches of H. brasiliensis within each biome, although we could not refute the hypothesis of niche similarity or equivalency. Such differences are consistent with a solid morphometric variation associated with the size of these rodents. However, the ecological and morphometric differentiation is not accompanied by the same pattern of genetic variation. Despite differences in the connectivity patterns in both biomes, the genetic differences corroborate a consistent level of migration history between biomes. Additionally, the association tests show that the environment explains a small and non- significant part of the genetic variation but a significant portion of the morphometric variation.

A holocenic and dynamic hybrid zone between two cactophilic Drosophila species in a coastal lowland plain of the Brazilian Atlantic Forest

Hybridization and introgression are processes that contribute to shaping biological diversity. The factors promoting the formation of these processes are multiples but poorly explored in a biogeographical and ecological context. In the southeast coastal plain of the Brazilian Atlantic Forest, a hybrid zone was described between two closely related cactophilic species, Drosophila antonietae and D. serido. Here, we revisited and analysed specimens from this hybrid zone to evaluate its temporal and spatial dynamic. We examined allopatric and sympatric populations of the flies using independent sources of data such as mitochondrial and nuclear sequences, microsatellite loci, morphometrics of wings and male genitalia, and climatic niche models. We also verified the emergence of the flies from necrotic tissues of collected cacti to verify the role of host association for the population dynamics. Our results support the existence of a hybrid zone due to secondary contact and limited to the localities where the two species are currently in contact. Furthermore, we detected asymmetric bidirectional introgression and the maintenance of the species integrity, ecological association and morphological characters, suggesting selection and limited introgression. Considering our paleomodels, probably this hybrid zone is recent and the contact occurred during the Holocene to the present day, favoured by range expansion of their populations due to expansion of open and dry areas in eastern South America during palaeoclimatic and geomorphological events.

Sympatric and independently evolving lineages in the Thoropa miliaris - T. taophora species complex (Anura: Cycloramphidae)

Species delimitation can be challenging and affected by subjectivity. Sibling lineages that occur in sympatry constitute good candidates for species delimitation regardless of the adopted species concept. The Thoropa miliaris + T. taophora species complex exhibits high genetic diversity distributed in several lineages that occur sympatrically in the southeastern Atlantic Forest of Brazil. We used 414 loci obtained by anchored hybrid enrichment to characterize genetic variation in the Thoropa miliaris species group (T. saxatilis, T megatympanum, T. miliaris, and T. taophora), combining assignment analyses with traditional and coalescent phylogeny reconstruction. We also investigated evolutionary independence in co-occurring lineages by estimating gene flow, and validated lineages under the multispecies coalescent. We recovered most previously described lineages as unique populations in assignment analyses; exceptions include two lineages within T. miliaris that are further substructured, and the merging of all T. taophora lineages. We found very low probabilities of gene flow between sympatric lineages, suggesting independent evolution. Species tree inferences and species delimitation yielded resolved relationships and indicate that all lineages constitute putative species that diverged during the Pliocene and Pleistocene, later than previously estimated.

Amphibians of the Sinos River Basin, southern Brazil

The Sinos River encompasses a wide area of natural habitats and, at the same time, supports one of the highest population densities of southern Brazil. Consequently, natural habitats along the Basin present a high degree of habitat disturbance. Despite of the existence of threatened species, information about diversity of amphibians in that area is scarce. Thus, we aimed to catalogue the amphibian species of the Sinos River Basin from records in scientific collections and compilation of published articles. We recorded 52 species, all with geographic coordinates validated at the collection point, indicating that the Sinos River Basin harbours about 50% of the amphibian species of the State of Rio Grande do Sul. Three anuran species were classified as having some degree of threat: Melanophryniscus cambaraensis, Melanophryniscus dorsalis and Thoropa saxatilis. We also expected other 18 species with a high probability of occurrence in the Basin. This work shows that, despite the intense human impact, the Sinos River Basin has a relevant role for the maintenance of a considerable fraction of the amphibian biodiversity in southern Brazil.

Amphibians and reptiles from the Parque Nacional da Tijuca, Brazil, one of the world’s largest urban forests

Abstract: The Parque Nacional da Tijuca in Rio de Janeiro, Brazil, is considered to be one of the world’s largest urban forests, however no systematic inventory of its herpetofauna is available. In the present study, we surveyed the amphibians and reptiles of this park to assess its species composition (including secondary data) and obtain estimates of species richness and abundance. We conducted active searches (460 hours) between January 2013 and December 2015. We identified the taxa endemic to either the Atlantic Forest or Rio de Janeiro state, and verified the conservation status of each species in the international, Brazilian, and state red lists. We also estimated the species richness and sampling sufficiency by rarefaction curves and Bootstrap richness estimator, and analyzed the distribution of the species abundance in Whittaker plots. We recorded 3,288 individuals over 36 months, representing 24 species of amphibians and 25 reptiles. The cumulative species curves, rarefaction, and the richness estimated indicated that sampling effort was adequate. Species abundance adjusted to the log-series model in both amphibians and reptiles. The four most abundant amphibians represented 70% of the individuals recorded in this group, while the two most abundant reptiles represented 60% of the total individuals. The inclusion of the secondary data raised the number of amphibian species to 38, and the number of reptiles to 36. Approximately 80% of the amphibian species and 28% of the reptile species recorded are endemic to the Atlantic Forest, and six of the amphibian species are endemic to Rio de Janeiro state. Six amphibian species and one reptile species are classified under some threat of extinction, and two reptile species were exotic. The considerable diversity of the herpetofauna of the Parque Nacional da Tijuca, which includes endemic and threatened species, reflects the effectiveness of the reforestation of this protected area and emphasizes the importance of its conservation.

Cytogenetic analysis of the genus Thoropa Cope, 1865 (Anura-Cycloramphidae) with evolutionary inferences based on repetitive sequences

Cytogenetics can be a useful tool to assist in taxonomic problems by adding information to the widely used morphological and molecular approaches. These taxonomic problems are especially common in anurans, once they are very diverse, highly polymorphic, and present many cryptic species. The genus Thoropa Cope, 1865 is composed of six specialist species that reproduce in rocky outcrops and are distributed throughout the Atlantic Forest and Cerrado ecotones. Phylogenetic studies point to possible cryptic species within the T. miliaris group. To assist in the evolutionary and taxonomic understanding of this group, classical cytogenetic techniques were used to find possible molecular markers for the genus through rDNA5S, rDNA18S, and U2snDNA probes and analyze their chromosome distribution in the group of T. miliaris. Despite the well conserved karyotype under conventional staining and classical techniques, such as Ag-NOR, our C-banding results showed differences in the centromeric heterochromatin concentration between two populations of T. miliaris. Furthermore, some differences among the populations and species were found for rDNA5S and U2snDNA. This study contributes to a better understanding of the evolutionary relationships within the genus; however, the use of different probe sequences, such as satDNA, is essential for a more robust cytogenetic analysis.

Multilocus phylogeny of Paratelmatobiinae (Anura: Leptodactylidae) reveals strong spatial structure and previously unknown diversity in the Atlantic Forest hotspot

The Brazilian Atlantic Forest harbors high levels of anuran diversity and endemism, including several taxa restricted to small geographic ranges. Here, we provide a multilocus phylogeny for Paratelmatobiinae, a leptodactylid subfamily composed of small-ranged species distributed in the Brazilian Atlantic Forest and in the campo rupestre ecosystem. We performed Bayesian inference and maximum likelihood analyses using three mitochondrial and five nuclear markers, and a matrix comprising a broad taxonomic sampling. We then delimitated independently evolving lineages within the group. We recovered Paratelmatobiinae and each of its four genera as monophyletic and robustly supported. Five putatively new species included in our analyses were unambiguously supported in the phylogenetic trees and delimitation analyses. We also recovered other deeply divergent and geographically structured lineages within the four genera of Paratelmatobiinae. Our estimation of divergence times indicates that diversification in the subfamily began in the Eocene and continued until the Pleistocene. We discuss possible scenarios of diversification for the four genera of Paratelmatobiinae, and outline the implications of our findings for taxonomy and conservation.

Outstanding diversity and microendemism in a clade of rare Atlantic Forest montane frogs

Distributed across topographically complex landscapes that vary from lowland to high elevation, the Atlantic Forest harbors one of the richest biotas worldwide. Atlantic Forest amphibians are particularly speciose, taxonomic accounts are rising and the group is used as model for biogeographic inference. Past climate-related habitat fragmentation is often invoked to explain diversification, with montane taxa expected to become more widespread during glacial times and restrained at interglacials. In this study we investigate diversification in Ischnocnema lactea and I. holti (Anura: Brachycephalidae), two rare frog species inhabiting Atlantic Forest montane regions in Southeastern Brazil. Previous phylogenetic accounts have suggested uncertain limits between these two sister species. We assembled a multilocus DNA dataset, delimited lineages in this clade, and used ecological niche modeling to explore past and future putative ranges. Assignment analyses and traditional and coalescent phylogenetic methods confirmed the existence of a species complex of Miocene origin comprising nine lineages, most of which show very narrow ranges. Lineages were fully supported as species based in coalescent species delimitation, but the phylogenetic relationships among lineages in higher elevation were unresolved. Models of past ranges suggest extensive suitable areas at the last glacial maximum which, along with phylogenetic uncertainty, are consistent with a hypothesis that climate driven vicariance at higher elevation areas resulted in hard polytomies. Species distribution models under future climates suggest narrower ranges of the lineages relative to now, but no species are currently considered endangered. Overall, our results argue in favor for the reassessment of the taxonomic and conservation status of the I. holti - I. lactea species complex.

Historical biogeography and multi-trait evolution in miniature toadlets of the genus Brachycephalus (Anura: Brachycephalidae)

Evolutionary changes towards a miniaturized body plan may directly affect other important phenotypic traits related to the physiology, behaviour and ecology of organisms. The frog genus Brachycephalus is an outstanding example of a radiation of miniaturized species endemic to the Brazilian Atlantic Forest. We inferred ancestral states and historical changes in body size, body colour and hyperossification to test hypotheses about diversification and selective environmental mechanisms leading to the evolution of these specialized traits. The ancestral distribution was associated with high-elevation regions in the northern Serra do Mar mountain range, and diversification in the genus was coincident with important geological and climatic events during the history of the Atlantic Forest. The dynamic historical changes provided an opportunity for multiple lowland lineages and for speciation via dispersal and vicariance in multiple invasions of the highlands. The ancestral Brachycephalus was reconstructed as miniaturized and dull coloured, without hyperossification in the skin, skull or postcranial skeleton. A parallel evolution of phenotypic traits has occurred in northern and southern Atlantic Forest lineages, beginning in the Miocene. Shifts in body size are not related to elevation range or latitude. However, we found a significant correlation between the evolution of hyperossification and aposematism with increasing body size.

Male-male competition and repeated evolution of terrestrial breeding in Atlantic Coastal Forest frogs

Terrestrial breeding is a derived condition in frogs, with multiple transitions from an aquatic ancestor. Shifts in reproductive mode often involve changes in habitat use, and these are typically associated with diversification in body plans, with repeated transitions imposing similar selective pressures. We examine the diversification of reproductive modes, male and female body sizes, and sexual size dimorphism (SSD) in the Neotropical frog genera Cycloramphus and Zachaenus, both endemic to the Atlantic rainforest of Brazil. Species in this clade either breed in rocky streams (saxicolous) or in terrestrial environments, allowing us to investigate reproductive habitat shifts. We constructed a multilocus molecular phylogeny and inferred evolutionary histories of reproductive habitats, body sizes, and SSD. The common ancestor was small, saxicolous, and had low SSD. Terrestrial breeding evolved independently three times and we found a significant association between reproductive habitat and SSD, with shifts to terrestrial breeding evolving in correlation with decreases in male body size, but not female body size. Terrestrial breeding increases the availability of breeding sites and results in concealment of amplexus, egg-laying, and parental care, therefore reducing male-male competition at all stages of reproduction. We conclude that correlated evolution of terrestrial reproduction and small males is due to release from intense male-male competition that is typical of exposed saxicolous breeding.

Thermal and salinity effects on locomotor performance of Thoropa taophora tadpoles (Anura, Cycloramphidae)

It is well known that environmental temperature influences several biological functions of ectotherms, notably in amphibians. The high permeability of anuran skin, associated with the effect of elevated environmental temperature, potentiates the dehydration process and this combination may restrict locomotor performance. Thoropa taophora is an endemic species from the Atlantic Rainforest whose tadpoles are semiterrestrial and predominantly diurnal, and are found in rocky seashores where they are exposed to sea spray and high temperatures. In this study we investigated how temperature and salinity conditions affect the locomotor performance in Thoropa taophora tadpoles. We also assessed how different osmotic concentrations affect the activity of the metabolic pathways that support muscle function. We measured the sprint speed of tadpoles of various sizes at different temperatures and salinities in the field. We also measured the activity of the enzymes pyruvate kinase (PK), lactate dehydrogenase (LDH) and citrate synthase (CS) in different temperatures and osmotic concentrations, and calculated the thermal sensitivity and the activity constants for each osmolality. Our results showed that, in general, sprint speed decreased with increasing temperature and salinity. However, whereas the effect of increased salinity was similar in smaller and larger tadpoles, increased temperature had a higher negative impact on sprint speed of larger tadpoles, thus indicating low thermal sensitivity of small tadpoles. PK and LDH thermal sensitivities and LDH constant of activity decreased as the osmolality increased. In conclusion, the locomotor capacity of tadpoles was decreased by temperature and salinity, which may be related to a decrease in anaerobic metabolism both in terms of sensitivity and total energy turnover through enzymatic activity. We discuss the ecological consequences, including the potential impacts on predator escape behavior promoted by changes in metabolism and locomotor performance in an early stage of development of this species.