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.
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.
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.
We aim to propose validated, spatially explicit hypotheses for the late Quaternary distribution of the Brazilian Atlantic forest, and thereby provide a framework for integrating analyses of species ...and genetic diversity in the region. The Atlantic forest, stretching along the Brazilian coast. We model the spatial range of the forest under three climatic scenarios (current climate, 6000 and 21,000 years ago) with BIOCLIM and MAXENT. Historically stable areas or refugia are identified as the set of grid cells for which forest presence is inferred in all models and time projections. To validate inferred refugia, we test whether our models are matched by the current distribution of the forest and by fossil pollen data. We then investigate whether the location of inferred forest refugia is consistent with current patterns of species endemism and existing phylogeographical data. Forest models agree with pollen records and predict a large area of historical forest stability in the central corridor (Bahia), as well as a smaller refuge (Pernambuco) along the Brazilian coast, matching current centres of endemism in multiple taxa and mtDNA diversity patterns in a subset of the species examined. Less historical stability is predicted in coastal areas south of the Doce river, which agrees with most phylogeographical studies in that region. Yet some widely distributed taxa show high endemism in the southern Atlantic forest. This may be due to limitations of the modelling approach, differences in ecology and dispersal capability, historical processes not contemplated by the current study or inadequacy of the available test data sets. Palaeoclimatic models predict the presence of historical forest refugia in the Atlantic rain forest and suggest spatial variation in persistence of forests through the Pleistocene, predicting patterns of biodiversity in several local taxa. The results point to the need for further studies to document genetic and species endemism in the relatively poorly known and highly impacted areas of Atlantic rain forests of north-eastern Brazil.
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.
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.
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.
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.
Amphibian Declines in Brazil: An Overview Eterovick, Paula Cabral; De Queiroz Carnaval, Ana Carolina Oliveira; Borges-Nojosa, Diva Maria ...
Biotropica,
06/2005, Volume:
37, Issue:
2
Journal Article
Peer reviewed
Population declines have previously been reported for at least 31 amphibian species in Brazil, in the families Leptodactylidae (19), Hylidae (7), Centrolenidae (2), Dendrobatidae (2), and Bufonidae ...(1). In five Brazilian museum collections, we found no entries of new records dating back to at least 15 yr ago for 13 of these species. We suggest that these taxa be studied in more detail to verify their status and to generate basic ecological data. Museum data indicate that the remaining species have been recently found in areas of reported crashes, or elsewhere. Several apparent declines in Brazil can be associated with habitat loss, interspecific interactions, natural fluctuations, or lack of intensive sampling. Personal observations and field data also indicate possible declines in the states of Parana and Ceará as well as in highlands within the Cerrado biome, in the state of Minas Gerais. Records suggest declines of montane and stream-associated populations of Brazilian amphibians in apparently pristine habitats. Field work is necessary to confirm these cases and to examine whether factors associated with similar extinctions in other parts of the globe-such as pathogens and climate change-are also related to local disappearances. To clarify pending questions and perhaps circumvent new cases, it is important to invest in short- and long-term field studies, and in the maintenance and expansion of museum collections. /// Uma revisão bibliográfica indica a existência de 31 registros de declínios de populações de anfíbios no Brasil, abrangendo as famílias Leptodactylidae (19), Hylidae (7), Centrolenidae (2), Dendrobatidae (2) e Bufonidae (1). Em cinco coleções brasileiras, nenhum registro foi encontrado nos últimos 15 anos para 13 destas espécies. Sugerimos que as mesmas sejam estudadas em maior detalhe, de modo a verificar seu status e gerar dados ecológicos necessários para conservação. Levantamentos em coleções indicam que as demais espécies têm sido recentemente encontradas nas localidades do proposto declínio, ou em outras regiões. Vários registros de declínios no país estão associados a perda de habitat, interações entre espécies, flutuações populacionais, ou amostragem insuficiente. Com base em observações pessoais e dados de campo, levantamos a possibilidade de novos casos de declínios nos estados do Paraná e Ceará, e em áreas de altitude no bioma do Cerrado, em Minas Gerais. Vários casos de declínios populacionais sugeridos para anfíbios brasileiros referem-se a espécies de altitude que se reproduzem em riachos, em áreas aparentemente bem conservadas. Será interessante confirmar tais casos e avaliar se fatores associados a padrões semelhantes de extinções em outras partes do mundo-tais como patógenos ou mudanças climáticasestão também relacionados a desaparecimentos ou declínios no país. Para esclarecer questões pendentes, é importante investir em estudos de campo a curto e longo prazo, bem como na manutenção e expansão das coleções herpetológicas do país.
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