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Evolutionary processes are known to influence contemporary patterns of biological diversity, yet disentangling the effects of current and historical drivers of biodiversity patterns remain challenging. We use spatial analyses of community dissimilarity to generate hypotheses about the current and historical processes underlying patterns of beta diversity in anuran species in the Brazilian Cerrado. Specifically, we use a generalized dissimilarity modeling (GDM) approach to model compositional dissimilarity of anuran species and endemics as a function of geographic separation and local (within-Cerrado) environmental conditions. To gain insight about potential historical processes, we incorporate information from biomes adjacent to the Cerrado to investigate whether environmental conditions in neighboring areas can help explain patterns of beta diversity within the Cerrado. Patterns of anuran beta diversity of both endemics and all species in the Cerrado appear to be strongly influenced by local environmental gradients, with elevation as one of the most important variables in all models. However, in models using endemic species only, environmental conditions of adjacent biomes were related to beta-diversity patterns, and more strongly so, than to total species models.These results suggest that phylogenetic niche conservatism within species groups that invaded the Cerrado from adjacent biomes may cause these species to be restricted to environmental conditions within the Cerrado that are most similar to the conditions in the adjacent biome where they originated. Time-calibrated phylogenies of Cerrado endemics and studies of ancestral and current ranges of Cerrado species are needed to test this hypothesis.

Many studies suggest that aside from environmental variables, such as topography and climate, species‐specific ecological traits are relevant to explain the geographic distribution of intraspecific genetic lineages. Here, we investigated whether and to what extent incorporating such traits systematically improves the accuracy of random forest models in predicting genetic differentiation among pairs of localities. We leveraged available ecological datasets for birds and tested the inclusion of two categories of ecological traits: dispersal‐related traits (i.e. morphology and foraging ecology) and demographic traits (such as species survival rate and generation length). We estimated genetic differentiation from published mitochondrial DNA sequences for 28 species of birds (1578 total genetic samples, 391 localities) in the Atlantic Forest of South America. Aside from the aforementioned ecological traits, we included geographic, topographic and climatic distances between localities as environmental predictors. We then created models using all available data to evaluate model uncertainty both across space and across the different categories of predictors. Finally, we investigated model uncertainty in predicting genetic differentiation individually for each species (a common challenge in conservation biology). Our results show that while environmental conditions are the most important predictors of genetic differentiation, model accuracy largely increases with the addition of ecological traits. Additionally, the inclusion of dispersal traits improves model accuracy to a larger extent than the inclusion of demographic traits. Similar results are observed in models for individual species, although model accuracy is highly variable. We conclude that ecological traits improve predictive models of genetic differentiation, refining our ability to predict phylogeographic patterns from existing data. Additionally, demographic traits may not be as informative as previously hypothesized. Finally, prediction of genetic differentiation for species with conservation concerns may require further careful assessment of the environmental and ecological variation within the species range.

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.

Howler monkeys (Alouatta), comprising between nine and 14 species and ranging from southern Mexico to northern Argentina, are the most widely distributed platyrrhines. Previous phylogenetic studies of howlers have used chromosomal and morphological characters and a limited number of molecular markers; however, branching patterns conflict between studies or remain unresolved. We performed a new phylogenetic analysis of Alouatta using both concatenated and coalescent-based species tree approaches based on 14 unlinked non-coding intergenic nuclear regions. Our taxon sampling included five of the seven South American species (Alouatta caraya, Alouatta belzebul, Alouatta guariba, Alouatta seniculus, Alouatta sara) and the two recognized species from Mesoamerica (Alouatta pigra, Alouatta palliata). Similarly to previous studies, our phylogenies supported a Mesoamerican clade and a South American clade. For the South American howlers, both methods recovered the Atlantic Forest endemic A. guariba as sister to all remaining South American species, albeit with moderate support. Moreover, we found no support for the previously proposed sister relationship between A. guariba and A. belzebul. For the first time, a clade composed of A. sara and A. caraya was identified. The relationships among the other South American howlers, however, were not fully supported. Our estimates for divergence times within Alouatta are generally older compared to estimates in earlier studies. However, they conform to recent studies proposing a Miocene age for the Isthmus of Panama and for the uplift of the northern Andes. Our results also point to an early genetic isolation of A. guariba in the Atlantic Forest, in agreement with the hypothesis of biotic exchange across South American rain forests in the Miocene. Collectively, these findings contribute to a better understanding of the diversification processes among howler monkey species; however, they also suggest that further comprehension of the evolutionary history of the Alouatta radiation will rely on broadened taxonomic, geographic, and genomic sampling.

To investigate the occurrence of the chytrid fungus Batrachochytrium dendrobatidis in Brazil, we conducted histological screenings of 96 preserved specimens of anurans collected at 10 sites in the Atlantic rain forest. Data show this fungus to be widely distributed. Infected specimens included Colostethus olfersioides (Dendrobatidae), Bokermannohyla gouveai and Hypsiboas freicanecae (Hylidae), as well as Thoropa miliaris and Crossodactylus caramaschii (Leptodactylidae), extending the area of B. dendrobatidis occurrence in Brazil approximately 1,600 km N, 200 km S, and 270 km E. The altitudinal range of the chytrid is broad, spanning from less than 100 m (Estação Ecológica Juréia-Itatins, Reserva Biológica do Tinguá) to about 2,400 m (Parque Nacional do Itatiaia). An infection record dating to 1981 roughly coincides with the time of the first observations of amphibian declines in the country. Widespread occurrence of B. dendrobatidis in the Atlantic Forest adds to the challenge of conserving an already endangered biome given the potential risk of further local biodiversity loss. Further research is needed to understand how environmental and genetic factors relate to chytridiomycosis in leading to or preventing local die-offs. Protected sites at mid and high elevations may be particularly threatened, while lowland populations may be functioning as reservoirs. Conservation efforts should also involve monitoring studies and habitat protection.[PUBLICATION ABSTRACT]

Quaternary climatic oscillations affected species distributions worldwide, creating cycles of connectivity and isolation that impacted population demography and promoted lineage divergence. These effects have been well studied in temperate regions. Taxa inhabiting mesic montane habitats in tropical ecosystems show high levels of endemism and diversification in the distinct mountain ranges they inhabit; such a pattern has commonly been ascribed to past climatic oscillations, but few phylogeographic studies have tested this hypothesis. Here, we combine ecological niche models of species distributions with molecular data to study phylogeographic patterns in two rodents endemic to the highlands of Costa Rica and western Panama (Reithrodontomys creper and Nephelomys devius). In so doing, we apply a novel approach that incorporates a basic ecological principle: the expected positive relationship between environmental suitability and population abundance. Specifically, we use niche models to predict potential patterns of population connectivity and stability of different suitability levels during climatic extremes of the last glacial–interglacial cycle; we then test these predictions with population genetic analyses of a mitochondrial and a nuclear marker. The detailed predictions arising from the different levels of suitability were moderately to highly congruent with the molecular data depending on the species. Overall, results suggest that in these tropical montane ecosystems, cycles of population connectivity and isolation followed a pattern opposite to that typically described for temperate or lowland tropical ecosystems: namely, higher connectivity during the colder glacials, with isolation in montane refugia during the interglacials, including today. Nevertheless, the individualistic patterns for each species indicate a potentially wide gamut of phylogeographic histories reflecting particularities of their niches. Taken together, this study illustrates how phylogeographic inferences may benefit from niche model outputs that provide more detailed predictions of connectivity and finer characterizations of potential refugia through time.

Critical thermal limits are thought to be correlated with the elevational distribution of species living in tropical montane regions, but with upper limits being relatively invariant compared to lower limits. To test this hypothesis, we examined the variation of thermal physiological traits in a group of terrestrial breeding frogs (Craugastoridae) distributed along a tropical elevational gradient. We measured the critical thermal maximum (CTmax; n = 22 species) and critical thermal minimum (CTmin; n = 14 species) of frogs captured between the Amazon floodplain (250 m asl) and the high Andes (3,800 m asl). After inferring a multilocus species tree, we conducted a phylogenetically informed test of whether body size, body mass, and elevation contributed to the observed variation in CTmax and CTmin along the gradient. We also tested whether CTmax and CTmin exhibit different rates of change given that critical thermal limits (and their plasticity) may have evolved differently in response to different temperature constraints along the gradient. Variation of critical thermal traits was significantly correlated with species’ elevational midpoint, their maximum and minimum elevations, as well as the maximum air temperature and the maximum operative temperature as measured across this gradient. Both thermal limits showed substantial variation, but CTmin exhibited relatively faster rates of change than CTmax, as observed in other taxa. Nonetheless, our findings call for caution in assuming inflexibility of upper thermal limits and underscore the value of collecting additional empirical data on species’ thermal physiology across elevational gradients. A widely held assumption is that climatic niches have not changed along the history of species, both within and among closely related species. Using a phylogenetic framework, this study documents high variability in both elevational distribution and tolerance to heat among closely related species. Our findings suggest that thermal traits in ectotherms can adjust rapidly and so cannot be simply extrapolated from relatives.

The glacial refugia paradigm has been broadly applied to patterns of species dynamics and population diversification. However, recent geological studies have demonstrated striking Pleistocene climate changes in currently semiarid northeastern Brazil at time intervals much more frequent than the climatic oscillations associated with glacial and interglacial periods. These geomorphic data documented recurrent pulses of wet regimes in the past 210,000 years that correlate with climate anomalies affecting multiple continents. While analyzing DNA sequences of two mitochondrial genes (cytochrome b and NADH-dehydrogenase subunit 2) and one nuclear marker (cellular-myelocytomatosis proto-oncogene) in the forest-associated frogs Proceratophrys boiei and Ischnocnema gr. ramagii, we found evidence of biological responses consistent with these pluvial maxima events. Sampled areas included old, naturally isolated forest enclaves within the semiarid Caatinga, as well as recent man-made fragments of humid coastal Atlantic forest. Results show that mtDNA lineages in enclave populations are monophyletic or nearly so, whereas nonenclave populations are polyphyletic and more diverse. The studied taxa show evidence of demographic expansions at times that match phases of pluvial maxima inferred from geological data. Divergence times between several populations fall within comparatively drier intervals suggested by geomorphology. Mitochondrial and nuclear data show local populations to be genetically structured, with some high levels of differentiation that suggest the need of further taxonomic work.

We combined mitochondrial DNA sequence data and paleoclimatic distribution models to document phylogeographic patterns and investigate the historical demography of two manakins, Ceratopipra rubrocapilla and Pseudopipra pipra, as well as to explore connections between Amazonia and the Atlantic Forest. ND2 sequences of C. rubrocapilla (75 individuals, 24 sites) and P. pipra (196, 77) were used in Bayesian inference and maximum likelihood analyses. We estimated mitochondrial nucleotide diversity, employed statistical tests to detect deviations from neutral evolution and constant population sizes, and used species distribution modeling to infer the location of suitable climate for both species under present‐day conditions, the Last Glacial Maximum (LGM), and the Last Interglacial Maximum (LIG). Mitochondrial sequence data from C. rubrocapilla indicate one Amazonian and one Atlantic Forest haplogroup. In P. pipra, we recovered a highly supported and differentiated Atlantic Forest haplogroup embedded within a large Southern Amazonian clade. Genetic and taxonomic structure in Amazonia differs widely between these two species; older P. pipra has a more marked genetic structure and taxonomic differentiation relative to the younger C. rubrocapilla. Both species have similar genetic patterns in the Atlantic Forest. Paleoclimatic distribution models suggest connections between southwestern Amazonia and the southern Atlantic Forest during the LIG, but not between eastern Amazonia and the northeastern Atlantic Forest, as suggested by previous studies. This indicates that multiple corridors, and at different locations, may have been available over the Pliocene and Pleistocene between these two regions. We combined mitochondrial DNA sequence data and paleoclimatic distribution models to document phylogeographic patterns and investigate the historical demography of two manakins, Ceratopipra rubrocapilla and Pseudopipra pipra, as well as to explore connections between Amazonia and the Atlantic Forest. Genetic and taxonomic structure in Amazonia differs widely between these taxa; P. pipra has a more marked genetic structure, agreeing with existing subspecies delimitation. Both species have similar genetic patterns in the Atlantic Forest. Paleoclimatic distribution models indicate connections between southwestern Amazonia and the southern Atlantic Forest during the LIG, but not between eastern Amazonia and the northeastern Atlantic Forest.

Vegetation and fire activity have dynamically changed in response to past variations in global and regional climate. Here we investigate these responses across the Neotropics based on the analysis of modern vegetation distribution and fire activity in relation to modern climate patterns, and a compilation of 255 vegetation records and 131 charcoal records encompassing the last 21 000 years before present (ka) in relation to past climate changes. Our analyses on the dynamics of past tree cover and fire activity focus on seven subregions: (1) northern Neotropics (NNeo); (2) tropical Andes (TrAn); (3) Amazonia; (4) northeastern Brazil (NEB); (5) central-eastern Brazil (CEB); (6) southeastern South America (SESA); and (7) extratropical Andes (ExTrAn). The regionalized assessment unveils spatial heterogeneity in the timing and controls of vegetation and fire dynamics. Temperature, atmospheric CO2 concentrations, and precipitation exhibit distinct and alternating roles as primary drivers of tree cover and fire regime changes with additional impacts from human activity. During the Last Glacial Maximum (LGM, here covering 21–19 ka), arboreal growth in high elevation sites (TrAn) and in sub- and extra-tropical latitudes (SESA and ExTrAn) was mainly limited by low temperatures and atmospheric CO2 concentrations, while fuel-limited conditions restrained fire activity. In warmer tropical regions (NNeo, Amazonia, CEB), moisture availability was likely the main controlling factor of both vegetation and fire, with the effects of low CO2 amplifying these constraints. Throughout the deglacial phase (19–11.7 ka), progressive warming and increasing atmospheric CO2 concentrations fostered a gradual biomass expansion, and together these changes led to intensified fire activity in the sub- and extra-tropical temperature-limited regions. Meanwhile, increased (decreased) precipitation associated with millennial-scale events favored increases (decreases) in tree cover in regions such as CEB and NEB (NNeo). Between 14–13 ka, most southern latitude subregions (Amazonia, CEB, SESA, ExTrAn) saw a rise in fire activity coeval with a second rapid warming, contrary to decreased fire activity in NNeo amid relatively wetter conditions. Throughout the Holocene, when temperature and atmospheric CO2 fluctuations were lower, shifts in precipitation became the primary driver of vegetation and fire dynamics across all the Neotropics. Changes in the Intertropical Convergence Zone and gradual intensification of the South American Summer Monsoon throughout the Holocene favored a continuous increase in tree cover over Amazonia, CEB, and SESA, but led to a forest cover decrease in NNeo and NEB. From the early- to the mid-Holocene, the strengthening of the Southern Westerly Winds promoted vegetation expansion and fire regime weakening in ExTrAn. In the late Holocene, human impacts became more pronounced, with a clearer effect on regional tree cover and fire activity, particularly in NNeo and TrAn.