Herpetofauna of protected areas in the Caatinga VIII: An updated checklist for the Serra das Confusões region with new data from Serra Vermelha, Piauí, Brazil / Herpetofauna das áreas protegidas da Caatinga VIII: Um inventário atualizado para a região da Serra das Confusões com novos dados da Serra Vermelha, Piauí, Brazil

Abstract It is repeatedly stressed the need to characterize the extant biodiversity in tropical ecosystems. However, inventory studies are still progressing slowly in dry ecosystems, leading to the underestimation of their true biodiversity and hindering conservation efforts. In this study, we present primary and secondary data, along with an updated list of amphibians and reptiles from two localities in the São Francisco-Gurguéia region in Piauí. Additionally, we compare the species composition between nine areas within the Caatinga, which were sampled using standardized methods over the past ten years, to examine broader spatial patterns of community composition. To survey reptiles and amphibians, we employed similar methods and sampling efforts in two areas within the Serra das Confusões National Park (SCNP) region. Our surveys recorded a total of 73 species of amphibians and reptiles, of which 24 are new distribution records for the SCNP region. Consequently, our findings increase the known herpetofauna in the region to 94 species. Despite their proximity, the two sites in the SCNP region exhibited only 42% similarity in species composition, and they differed significantly from other areas within the Caatinga. Furthermore, even the closer Caatinga areas presented differences in species composition, highlighting the necessity to evaluate biodiversity across the landscape and contribute to understanding biogeographic patterns.

Resumo É repetidamente enfatizada a necessidade de caracterizar a biodiversidade vivente em ecossistemas tropicais. No entanto, os estudos de inventário ainda estão progredindo lentamente em ecossistemas secos, levando à subestimação de sua verdadeira biodiversidade e dificultando os esforços de conservação. Neste estudo, apresentamos dados primários e secundários, juntamente com uma lista atualizada de anfíbios e répteis de duas localidades na região de São Francisco-Gurguéia, do Piauí. Além disso, comparamos a composição de espécies entre nove áreas dentro da Caatinga, que foram amostradas usando métodos padronizados nos últimos dez anos, para examinar padrões espaciais mais amplos de composição da comunidade. Para estudar répteis e anfíbios, utilizamos métodos e esforços de amostragem semelhantes em duas áreas na região do Parque Nacional da Serra das Confusões (PNSC). Nossos levantamentos registraram um total de 73 espécies de anfíbios e répteis, das quais 24 são novos registros de distribuição para a região do PNSC. Consequentemente, nossos resultados aumentam a herpetofauna conhecida na região para 94 espécies. Apesar da proximidade, os dois locais na região do PNSC exibiram apenas 42% de similaridade na composição de espécies e diferiram significativamente de outras áreas dentro da Caatinga. Mesmo áreas mais próximas da Caatinga apresentaram diferenças na composição de espécies, destacando a necessidade de avaliar a biodiversidade em toda a paisagem e contribuir para a compreensão de padrões biogeográficos.

A new species of Proceratophrys Miranda-Ribeiro, 1920 (Anura, Odontophrynidae) from Southern Amazonia, Brazil.

Based on concordant differences in morphology, male advertisement call, and 16S mtDNA barcode distance, we describe a new species of Proceratophrys from southern Amazonia, in the states of Mato Grosso and Pará, Brazil. The new species is most similar to P. concavitympanum and P. ararype but differs from these species by its proportionally larger eyes and features of the advertisement call. Additionally, genetic distance between the new species and its congeners is 3.0-10.4% based on a fragment of the 16S rRNA gene, which is greater than the threshold typically characterizing distinct species of anurans. Using an integrative approach (molecular, bioacoustics, and adult morphology), we were able to distinguish the new species from other congeneric species. The new species is known only from the type locality where it is threatened by illegal logging and gold mining as well as hydroelectric dams.

Developmental life history is associated with variation in rates of climatic niche evolution in a salamander adaptive radiation.

Rates of climatic niche evolution vary widely across the tree of life and are strongly associated with rates of diversification among clades. However, why the climatic niche evolves more rapidly in some clades than others remains unclear. Variation in life history traits often plays a key role in determining the environmental conditions under which species can survive, and therefore, could impact the rate at which lineages can expand in available climatic niche space. Here, we explore the relationships among life-history variation, climatic niche breadth, and rates of climatic niche evolution. We reconstruct a phylogeny for the genus Desmognathus, an adaptive radiation of salamanders distributed across eastern North America, based on nuclear and mitochondrial genes. Using this phylogeny, we estimate rates of climatic niche evolution for species with long, short, and no aquatic larval stage. Rates of climatic niche evolution are unrelated to the mean climatic niche breadth of species with different life histories. Instead, we find that the evolution of a short larval period promotes greater exploration of climatic space, leading to increased rates of climatic niche evolution across species having this trait. We propose that morphological and physiological differences associated with variation in larval stage length underlie the heterogeneous ability of lineages to explore climatic niche space. Rapid rates of climatic niche evolution among species with short larval periods were an important dimension of the clade's adaptive radiation and likely contributed to the rapid rate of lineage accumulation following the evolution of an aquatic life history in this clade. Our results show how variation in a key life-history trait can constrain or promote divergence of the climatic niche, leading to variation in rates of climatic niche evolution among species.

Life-History Patterns of Lizards of the World.

Identification of mechanisms that promote variation in life-history traits is critical to understand the evolution of divergent reproductive strategies. Here we compiled a large life-history data set (674 lizard populations, representing 297 species from 263 sites globally) to test a number of hypotheses regarding the evolution of life-history traits in lizards. We found significant phylogenetic signal in most life-history traits, although phylogenetic signal was not particularly high. Climatic variables influenced the evolution of many traits, with clutch frequency being positively related to precipitation and clutches of tropical lizards being smaller than those of temperate species. This result supports the hypothesis that in tropical and less seasonal climates, many lizards tend to reproduce repeatedly throughout the season, producing smaller clutches during each reproductive episode. Our analysis also supported the hypothesis that viviparity has evolved in lizards as a response to cooler climates. Finally, we also found that variation in trait values explained by clade membership is unevenly distributed among lizard clades, with basal clades and a few younger clades showing the most variation. Our global analyses are largely consistent with life-history theory and previous results based on smaller and scattered data sets, suggesting that these patterns are remarkably consistent across geographic and taxonomic scales.

Molecular systematics and historical biogeography of tree boas (Corallus spp.).

Inferring the evolutionary and biogeographic history of taxa occurring in a particular region is one way to determine the processes by which the biodiversity of that region originated. Tree boas of the genus Corallus are an ancient clade and occur throughout Central and South America and the Lesser Antilles, making it an excellent group for investigating Neotropical biogeography. Using sequenced portions of two mitochondrial and three nuclear loci for individuals of all recognized species of Corallus, we infer phylogenetic relationships, present the first molecular analysis of the phylogenetic placement of the enigmatic C. cropanii, develop a time-calibrated phylogeny, and explore the biogeographic history of the genus. We found that Corallus diversified within mainland South America, via over-water dispersals to the Lesser Antilles and Central America, and via the traditionally recognized Panamanian land bridge. Divergence time estimates reject the South American Caribbean-Track as a general biogeographic model for Corallus and implicate a role for events during the Oligocene and Miocene in diversification such as marine incursions and the uplift of the Andes. Our findings also suggest that recognition of the island endemic species, C. grenadensis and C. cookii, is questionable as they are nested within the widely distributed species, C. hortulanus. Our results highlight the importance of using widespread taxa when forming and testing biogeographic hypotheses in complex regions and further illustrate the difficulty of forming broadly applicable hypotheses regarding patterns of diversification in the Neotropical region.

LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders.

Among vertebrates, most of the largest genomes are found within the salamanders, a clade of amphibians that includes 613 species. Salamander genome sizes range from ~14 to ~120 Gb. Because genome size is correlated with nucleus and cell sizes, as well as other traits, morphological evolution in salamanders has been profoundly affected by genomic gigantism. However, the molecular mechanisms driving genomic expansion in this clade remain largely unknown. Here, we present the first comparative analysis of transposable element (TE) content in salamanders. Using high-throughput sequencing, we generated genomic shotgun data for six species from the Plethodontidae, the largest family of salamanders. We then developed a pipeline to mine TE sequences from shotgun data in taxa with limited genomic resources, such as salamanders. Our summaries of overall TE abundance and diversity for each species demonstrate that TEs make up a substantial portion of salamander genomes, and that all of the major known types of TEs are represented in salamanders. The most abundant TE superfamilies found in the genomes of our six focal species are similar, despite substantial variation in genome size. However, our results demonstrate a major difference between salamanders and other vertebrates: salamander genomes contain much larger amounts of long terminal repeat (LTR) retrotransposons, primarily Ty3/gypsy elements. Thus, the extreme increase in genome size that occurred in salamanders was likely accompanied by a shift in TE landscape. These results suggest that increased proliferation of LTR retrotransposons was a major molecular mechanism contributing to genomic expansion in salamanders.

Local-scale environmental variation generates highly divergent lineages associated with stream drainages in a terrestrial salamander, Plethodon caddoensis.

Spatial and temporal heterogeneity in environmental factors can have profound effects on diversification in species that are tightly linked to their environments. The Caddo Mountain Salamander (Plethodon caddoensis) inhabits a unique physiographic section of the Ouachita Mountains in central North America, a region in which Pleistocene climatic fluctuations have been implicated in driving lineage diversification in two other closely related salamanders. We examined P. caddoensis to determine whether it was similarly impacted by historic climatic changes and test whether physiographic features unique to the area also contributed to its diversification. We found that P. caddoensis is composed of four highly divergent, geographically distinct lineages that abut one another along an east-west axis. Phylogeographic structure was significantly related to both geographic distance and stream drainages, indicating that connectivity of streams and stream-associated habitats (e.g., talus) influence patterns of interpopulation gene flow. Lineages originated during the Middle Miocene and population size decreased in all lineages during the Pleistocene. Surface Geology and precipitation were the most important variables predicting the species distribution. Our results show that the unique physiographic features of the area coupled with species response to climatic factors have driven lineage diversification and phylogeographic structure in P. caddoensis. Variation in responses to historic climatic fluctuations among salamander species in this region underscore the importance of integrating species ecology with other factors such as geology and hydrology in order to better understand the effects of climate change on species with close associations to their environments.

Phylogeographic and demographic effects of Pleistocene climatic fluctuations in a montane salamander, Plethodon fourchensis.

Climatic changes associated with Pleistocene glacial cycles profoundly affected species distributions, patterns of interpopulation gene flow, and demography. In species restricted to montane habitats, ranges may expand and contract along an elevational gradients in response to environmental fluctuations and create high levels of genetic variation among populations on different mountains. The salamander Plethodon fourchensis is restricted to high-elevation, mesic forest on five montane isolates in the Ouachita Mountains. We used DNA sequence data along with ecological niche modelling and coalescent simulations to test several hypotheses related to the effects of Pleistocene climatic fluctuations on species in montane habitats. Our results revealed that P. fourchensis is composed of four well-supported, geographically structured lineages. Geographic breaks between lineages occurred in the vicinity of major valleys and a narrow high-elevation pass. Ecological niche modelling predicted that environmental conditions in valleys separating most mountains are suitable; however, interglacial periods like the present are predicted to be times of range expansion in P. fourchensis. Divergence dating and coalescent simulations indicated that lineage diversification occurred during the Middle Pleistocene via the fragmentation of a wide-ranging ancestor. Bayesian skyline plots showed gradual decreases in population size in three of four lineages over the most recent glacial period and a slight to moderate amount of population growth during the Holocene. Our results not only demonstrate that climatic changes during the Pleistocene had profound effects on species restricted to montane habitats, but comparison of our results for P. fourchensis with its parapatric, sister taxon, P. ouachitae, also emphasizes how responses can vary substantially even among closely related, similarly distributed taxa.

Lineage diversification and historical demography of a sky island salamander, Plethodon ouachitae, from the Interior Highlands.

Sky islands provide ideal opportunities for understanding how climatic changes associated with Pleistocene glacial cycles influenced species distributions, genetic diversification, and demography. The salamander Plethodon ouachitae is largely restricted to high-elevation, mesic forest on six major mountains in the Ouachita Mountains. Because these mountains are separated by more xeric, low-elevation valleys, the salamanders appear to be isolated on sky islands where gene flow among populations on different mountains may be restricted. We used DNA sequence data along with ecological niche modelling and coalescent simulations to test several hypotheses related to diversifications in sky island habitats. Our results revealed that P. ouachitae is composed of seven well-supported lineages structured across six major mountains. The species originated during the Late Pliocene, and lineage diversification occurred during the Middle Pleistocene in a stepping stone fashion with a cyclical pattern of dispersal to a new mountain followed by isolation and divergence. Diversification occurred primarily on an east-west axis, which is likely related to the east-west orientation of the Ouachita Mountains and the more favourable cooler and wetter environmental conditions on north slopes compared to south-facing slopes and valleys. All non-genealogical coalescent methods failed to detect significant population expansion in any lineages. Bayesian skyline plots showed relatively stable population sizes over time, but indicated a slight to moderate amount of population growth in all lineages starting approximately 10 000-12 000 years ago. Our results provide new insight into sky island diversifications from a previously unstudied region, and further demonstrate that climatic changes during the Pleistocene had profound effects on lineage diversification and demography, especially in species from environmentally sensitive habitats in montane regions.