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Aim The widespread megadiverse Neotropical snake family Dipsadidae occurs in a large range of diverse habitats. Therefore, it represents an excellent model to study the diversification of Neotropical biota. Herein, by generating a time-calibrated species-level phylogeny, we investigate the origin and historical biogeography of Dipsadidae and test if its two main Neotropical subfamilies, Xenodontinae and Dipsadinae, have different geographical origins. Location Neotropical region. Taxon Dipsadidae (Serpentes). Methods We generated a new Bayesian time-calibrated phylogeny based on published sequences from six genes for 344 species, including 287 species of Dipsadidae. We subsequently estimated ancestral areas of distribution by comparing models in BioGeoBEARS: DEC (subset sympatry, narrow vicariance), DIVALIKE (narrow and wide vicariance), BAYAREALIKE (no vicariance and widespread sympatry), also testing jump dispersal. We also estimated shifts in the diversification of this group using BAMM, exploring possible relationships with its historical biogeography. Results The best models show that Dipsadidae likely originated approximately 50 million years ago (mya) in Asia. Dispersal was a fundamental process in its historical biogeography. The DEC model with jump dispersal indicated that this family underwent a range extension from Asia and posterior vicariance of North and Central America ancestors. Both Xenodontinae and Dipsadinae originated in Central America and dispersed to South America during Middle Eocene, but did so to different regions (cis and trans-Andean South America, respectively). Xenodontinae entered cis-Andean South America around 39 mya and jump dispersed to the West Indies around 33 mya, while Dipsadinae entered trans-Andean South America multiple times 20–38 mya. The diversification rate decreased through time, except for a clade within Dipsadinae composed of the Dipsadini tribe and the Atractus and Geophis genera. Main Conclusions Our results show that Dipsadidae has an Asian origin and that the two main Neotropical subfamilies originated in Central America, later dispersing to South America in different time periods. This difference is also reflected in the higher diversification rate for the ‘goo-eaters’ in the Dipsadinae subfamily. The current biogeographical patterns of the family Dipsadidae, the most species-rich snake family in the world, have likely been shaped by complex evolutionary and geological processes such as Eocene land bridges, Andean uplift and the formation of the Panama isthmus.

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The emergence of the diagonal of open/dry vegetations, including Chaco, Cerrado and Caatinga, is suggested to have acted as a dispersal barrier for terrestrial organisms by fragmenting a single large forest that existed in South America into the present Atlantic and Amazon forests. Here we tested the hypothesis that the expansion of the South American diagonal of open/dry landscapes acted as a vicariant process for forest lanceheads of the genus Bothrops, by analyzing the temporal range dynamics of those snakes. We estimated ancestral geographic ranges of the focal lancehead clade and its sister clade using a Bayesian dated phylogeny and the BioGeoBEARS package. We compared nine Maximum Likelihood models to infer ancestral range probabilities and their related biogeographic processes. The best fitting models (DECTS and DIVALIKETS) recovered the ancestor of our focal clade in the Amazon biogeographic region of northwestern South America. Vicariant processes in two different subclades resulted in disjunct geographic distributions in the Amazon and the Atlantic Forest. Dispersal processes must have occurred mostly within the Amazon and the Atlantic Forest and not between them. Our results suggest the fragmentation of a single ancient large forest into the Atlantic and Amazon forests acting as a driver of vicariant processes for the snake lineage studied, highlighting the importance of the diagonal of open/dry landscapes in shaping distribution patterns of terrestrial biota in South America.

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To understand the underlying mechanisms generating population genetic divergence and structure is a critical step towards understanding how biodiversity evolves at both micro- and macroevolutionary scales. At the population-level, geographic isolation as well as adaptation to local environmental conditions can generate different patterns of spatial genetic variation among populations. Specific organismal traits as well as the characteristics of the environment might influence the process under which populations become spatially structured. In a From the Cover article in this issue of Molecular Ecology, Myers et al. (2019) present an integrative approach to investigate if the Cochise filter barrier (CFB), lying between the Sonoran and Chihuahuan Deserts, and the surrounding river networks were relevant in driving the population structure of 13 snake species. While local environmental conditions seem to predominantly contribute to lineage divergence, traditionally studied vicariant barriers seem to have played a minor role in shaping population structure across the studied species. This study brings insights into how population-level processes could contribute to the formation of incipient species, which ultimately might affect the speciation rates measured at macroevolutionary scales. Hence, Myers et al. (2019) not only represents an integrative study aiming to understand the drivers of population genetic divergence, but also a potentially important contribution to our ongoing challenge in linking micro- and macroevolution.

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The fossil record shows that the vast majority of all species that ever existed are extinct and that most lineages go through an expansion and decline in diversity. However, macroevolutionary analyses based upon molecular phylogenies have difficulty inferring extinction dynamics, raising questions about whether the neontological record can contribute to an understanding of the decline phenomenon. Two recently developed diversification methods for molecular phylogenies (RPANDA and BAMM) incorporate models that theoretically have the capacity to capture decline dynamics by allowing extinction to be higher than speciation. However, the performance of these frameworks over a wide range of decline scenarios has not been studied. Here, we investigate the behavior of these methods under decline scenarios caused by decreasing speciation and increasing extinction through time on simulated trees at fixed intervals over diversity trajectories with expansion and decline phases. We also compared method performance over a comprehensive data set of 214 empirical trees. Our results show that both methods perform equally well when varying speciation rates control decline. When decline was only caused by an increase in extinction rates both methods wrongly assign the variation in net diversification to a drop in speciation, even though the positive gamma values of those trees would suggest otherwise. We also found a tendency for RPANDA to favor increasing extinction and BAMM to favor decreasing speciation as the most common cause of decline in empirical trees. Overall our results shed light on the limitations of both methods, encouraging researchers to carefully interpret the results from diversification studies.

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Enigmatic amphibian declines were first reported in southern and southeastern Brazil in the late 1980s and included several species of stream-dwelling anurans (families Hylodidae and Cycloramphidae). At that time, we were unaware of the amphibian-killing fungus Batrachochytrium dendrobatidis (Bd); therefore, pollution, habitat loss, fragmentation and unusual climatic events were hypothesized as primary causes of these declines. We now know that multiple lineages of Bd have infected amphibians of the Brazilian Atlantic forest for over a century, yet declines have not been associated specifically with Bd outbreaks. Because stream-dwelling anurans occupy an environmental hotspot ideal for disease transmission, we investigated temporal variation in population and infection dynamics of three stream-adapted species (Hylodes asper, H. phyllodes, and Cycloramphus boraceiensis) on the northern coast of São Paulo state, Brazil. We surveyed standardized transects along streams for four years, and show that fluctuations in the number of frogs correlate with specific climatic variables that also increase the likelihood of Bd infections. In addition, we found that Bd infection probability in C. boraceiensis, a nocturnal species, was significantly higher than in Hylodes spp., which are diurnal, suggesting that the nocturnal activity may either facilitate Bd zoospore transmission or increase susceptibility of hosts. Our findings indicate that, despite long-term persistence of Bd in Brazil, some hosts persist with seasonally variable infections, and thus future persistence in the face of climate change will depend on the relative effect of those changes on frog recruitment and pathogen proliferation.

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Even though natural history information is crucial for answering key ecological, evolutionary, and conservation questions, basic studies are still lacking for Neotropical snakes. This study aims at contributing to the knowledge of the Neotropical tribe Pseudoboini, based on literature data, analysis of museum specimens and unpublished data. The tribe is mainly composed of moderate-sized snakes, although small and large-sized snakes also occur in the clade. Mean fecundity ranged from two (Rodriguesophis iglesiasi) to 29 eggs (Clelia plumbea) and the species are predominantly terrestrial and nocturnal. Most species are diet specialists and lizards are the most commonly consumed prey (found in the diet of 29 species), followed by small mammals (consumed by 20 species) and snakes (consumed by 18 species). Although the tribe Pseudoboini appears to be well studied, for 15 species (32%) only a small amount of information or none was available. We hope that our study can motivate research on the least known species.(AU)

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Even though natural history information is crucial for answering key ecological, evolutionary, and conservation questions, basic studies are still lacking for Neotropical snakes. This study aims at contributing to the knowledge of the Neotropical tribe Pseudoboini, based on literature data, analysis of museum specimens and unpublished data. The tribe is mainly composed of moderate-sized snakes, although small and large-sized snakes also occur in the clade. Mean fecundity ranged from two (Rodriguesophis iglesiasi) to 29 eggs (Clelia plumbea) and the species are predominantly terrestrial and nocturnal. Most species are diet specialists and lizards are the most commonly consumed prey (found in the diet of 29 species), followed by small mammals (consumed by 20 species) and snakes (consumed by 18 species). Although the tribe Pseudoboini appears to be well studied, for 15 species (32%) only a small amount of information or none was available. We hope that our study can motivate research on the least known species.

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