Predicting daily activity time through ecological niche modelling and microclimatic data.

Climate temporality is a phenomenon that affects species activity and distribution patterns across spatial and temporal scales. Despite the global availability of microclimatic data, their use to predict activity patterns and distributions remains scarce, particularly at fine temporal scales (e.g. < month). Predicting activity patterns based on climatic data may allow us to foresee some of the consequences of climate change, particularly for ectothermic vertebrates. The Gila monster exhibits marked daily and seasonal activity patterns linked to physiology and reproduction. Here we evaluate whether ecological niche models fitted using microclimate data can predict temporal activity patterns using the Gila monster Heloderma suspectum as a study system. Furthermore, we identified whether the activity patterns are related to physiological constraints. We used dated occurrences from museum specimens and human observations to generate and test ecological niche models using minimum volume ellipsoids. We generated hourly microclimatic data for each occurrence site for 10 years using the NicheMapR package. For ecological niche modelling, we compared the traditional seasonal approach versus a daily activity pattern strategy for model construction. We tested both using the omission rate of independent observations (citizen science data). Finally, we tested whether unimodal and bimodal activity patterns for each season could be recreated through ecological niche modelling and whether these patterns followed known physiological constraints. The unimodal and bimodal activity patterns previously reported directly from tracking individuals across the year were recovered using niche modelling and microclimate across the species' geographical range. We found that upper thermal tolerances can explain the daily activity patterns of this species. We conclude that ecological niche models trained with microclimatic data can be used to predict activity patterns at high temporal resolutions, particularly on ectotherm species of arid zones coping with rapid climate modifications. Furthermore, the use of high temporal resolution variables can lead to a better niche delimitation, enhancing the results of any research objective that uses correlative models.

La estacionalidad climática es un fenómeno que afecta la actividad de las especies y los patrones de distribución a diferentes escalas espaciales y temporales. A pesar de la disponibilidad global de datos microclimáticos para estudiar dichos patrones, su uso sigue siendo escaso, particularmente en escalas temporales finas (e.g., < mes). La predicción de patrones de actividad basados en datos climáticos puede permitirnos prever algunas de las potenciales consecuencias del cambio climático, particularmente para los vertebrados ectotérmicos. El monstruo de Gila (Heloderma suspectum) exhibe marcados patrones de actividad diarios y estacionales vinculados a la fisiología y la reproducción. En este trabajo evaluamos cómo los modelos de nichos ecológicos ajustados con datos de microclima, pueden predecir patrones de actividad temporal, utilizando al monstruo de Gila como sistema de estudio. Además, identificamos si los patrones de actividad están relacionados con restricciones fisiológicas. Usamos registros de presencia provenientes de colecciones científicas y de ciencia ciudadana para generar y probar modelos de nichos ecológicos usando elipsoides de volumen mínimo. Generamos datos microclimáticos para cada hora en cada sitio de presencia durante diez años utilizando el paquete NicheMapR. Para el modelado de nichos ecológicos, comparamos el enfoque estacional tradicional con una estrategia de patrón de actividad diaria para la construcción del nicho. Ambos enfoques fueron probados utilizando la tasa de omisión de observaciones independientes (provenientes de datos de ciencia ciudadana). Finalmente, probamos si los patrones de actividad unimodales y bimodales para cada estación podían recrearse a través de modelos de nichos ecológicos y si estos patrones seguían restricciones fisiológicas conocidas. Los patrones de actividad unimodal y bimodal previamente informados directamente del seguimiento de individuos a lo largo del año, sí se recuperaron mediante el uso de modelos de nicho y microclimas en todo el rango geográfico de la especie. Encontramos también que las tolerancias térmicas superiores pueden explicar los patrones de actividad diaria de esta especie. Concluimos que los modelos de nichos ecológicos entrenados con datos microclimáticos pueden usarse para predecir patrones de actividad en altas resoluciones temporales, particularmente en especies ectotermas de zonas áridas que se enfrentan a modificaciones climáticas rápidas. Además, consideramos que el uso de variables con alta resolución temporal puede conducir a una mejor delimitación de nichos, mejorando los resultados de cualquier objetivo de investigación que utilice estos modelos correlativos.

Red List assessment of amphibian species of Ecuador: A multidimensional approach for their conservation.

Ecuador is one of the most biodiverse countries in the world, but faces severe pressures and threats to its natural ecosystems. Numerous species have declined and require to be objectively evaluated and quantified, as a step towards the development of conservation strategies. Herein, we present an updated National Red List Assessment for amphibian species of Ecuador, with one of the most detailed and complete coverages for any Ecuadorian taxonomic group to date. Based on standardized methodologies that integrate taxonomic work, spatial analyses, and ecological niche modeling, we assessed the extinction risk and identified the main threats for all Ecuadorian native amphibians (635 species), using the IUCN Red List Categories and Criteria. Our evaluation reveals that 57% (363 species) are categorized as Threatened, 12% (78 species) as Near Threatened, 4% (26 species) as Data Deficient, and 27% (168 species) as Least Concern. Our assessment almost doubles the number of threatened species in comparison with previous evaluations. In addition to habitat loss, the expansion of the agricultural/cattle raising frontier and other anthropogenic threats (roads, human settlements, and mining/oil activities) amplify the incidence of other pressures as relevant predictors of ecological integrity. Potential synergic effects with climate change and emergent diseases (apparently responsible for the sudden declines), had particular importance amongst the threats sustained by Ecuadorian amphibians. Most threatened species are distributed in montane forests and paramo habitats of the Andes, with nearly 10% of them occurring outside the National System of Protected Areas of the Ecuadorian government. Based on our results, we recommend the following actions: (i) An increase of the National System of Protected Areas to include threatened species. (ii) Supporting the ex/in-situ conservation programs to protect species considered like Critically Endangered and Endangered. (iii) Focalizing research efforts towards the description of new species, as well as species currently categorized as Data Deficient (DD) that may turn out to be threatened. The implementation of the described actions is challenging, but urgent, given the current conservation crisis faced by amphibians.

Distributional patterns of Neotropical seasonally dry forest birds: a biogeographical regionalization.

Neotropical seasonally dry forests (NSDFs) are widely distributed and possess high levels of species richness and endemism; however, their biogeography remains only partially understood. Using species distribution modelling and parsimony analysis of endemicity, we analysed the distributional patterns of the NSDF avifauna in order to identify their areas of endemism and provide a better understanding of the historical relationships among those areas. The strict consensus trees revealed 17 areas of endemism for NSDFs, which involve four large regions: Baja California, Caribbean-Antilles islands, Mesoamerica and South America. These well-resolved clades are circumscribed by geographical and ecological barriers associated with the Gulf of California, the leading edge of the Caribbean plate, the Tehuantepec Isthmus, the Polochic-Motagua fault, the Nicaragua Depression, the Chocó forest, the Amazon basin and the Andean Cordillera. Relationships among groups of NSDFs found here suggest that evolution of their avifauna involved a mixture of vicariance and dispersal events. Our results support the idea of independent diversification patterns and biogeographical processes in each region, including those previously associated with the Pleistocene Arc Hypothesis for NSDFs of south-eastern South America. This study provides a biogeographical framework to open new lines of research related to the biotic diversification of NSDFs.

Crumble analysis of the historic sympatric distribution between Dendrortyx macroura and D. barbatus (Aves: Galliformes).

In Mexico, the Long-tailed Wood-Partridge (Dendrortyx macroura) is distributed in the mountains of the Trans-Mexican Volcanic Belt, Sierra Madre del Sur and Sierra Norte de Oaxaca; while the Bearded Wood-Partridge (D. barbatus) is distributed in the Sierra Madre Oriental (SMO). There is a controversial overlap in distribution (sympatry) between these two species (on the Cofre de Perote and Pico de Orizaba volcanoes, SMO and Sierra Norte de Oaxaca), based on the ambiguity and current lack of information regarding the distribution of these two species. In order to disentangle the possible presence of both species in the area of sympatry, we conducted a crumble analysis of the historic knowledge regarding the geographic distribution of both species, based on a review of scientific literature, database records, the specimen examination (in ornithological collections), field work and a reconstruction of the distribution range based on Ecological Niche Modeling. Our results support the presence of only one of these two species in the overlapping area, rejecting the existence of such an area of sympatry between the two species. We discuss alternative hypotheses that could explain the historically reported distribution pattern: 1) an error in the single existing historical record; 2) a possible local extinction of the species and 3) the past existence of interspecific competition that has since been resolved under the principle of competitive exclusion. We propose that the Santo Domingo River in northern Oaxaca and western slope of the Sierra Madre Oriental, mark the distribution limits between these species.

Nuclear locus divergence at the early stages of speciation in the Orchard Oriole complex.

As two lineages diverge from one another, mitochondrial DNA should evolve fixed differences more rapidly than nuclear DNA due to its smaller effective population size and faster mutation rate. As a consequence, molecular systematists have focused on the criteria of reciprocal monophyly in mitochondrial DNA for delimiting species boundaries. However, mitochondrial gene trees do not necessarily reflect the evolutionary history of the taxa in question, and even mitochondrial loci are not expected to be reciprocally monophyletic when the speciation event happened very recently. The goal of this study was to examine mitochondrial paraphyly within the Orchard Oriole complex, which is composed of Icterus spurius (Orchard Oriole) and Icterus fuertesi (Fuertes' Oriole). We increased the geographic sampling, added four nuclear loci, and used a range of population genetic and coalescent methods to examine the divergence between the taxa. With increased taxon sampling, we found evidence of clear structure between the taxa for mitochondrial DNA. However, nuclear loci showed little evidence of population structure, indicating a very recent divergence between I. spurius and I. fuertesi. Another goal was to examine the genetic variation within each taxon to look for evidence of a past founder event within the I. fuertesi lineage. Based on the high amounts of genetic variation for all nuclear loci, we found no evidence of such an event - thus, we found no support for the possible founding of I. fuertesi through a change in migratory behavior, followed by peripheral isolates speciation. Our results demonstrate that these two taxa are in the earliest stages of speciation, at a point when they have fixed differences in plumage color that are not reflected in monophyly of the mitochondrial or nuclear DNA markers in this study. This very recent divergence makes them ideal for continued studies of species boundaries and the earliest stages of speciation.

Reconstructing the Mexican Tropical Dry Forests via an Autoecological Niche Approach: Reconsidering the Ecosystem Boundaries.

We used Ecological Niche Modeling (ENM) of individual species of two taxonomic groups (plants and birds) in order to reconstruct the climatic distribution of Tropical Dry Forests (TDFs) in Mexico and to analyze their boundaries with other terrestrial ecosystems. The reconstruction for TDFs' distribution was analyzed considering the prediction and omission errors based upon the combination of species, obtained from the overlap of individual models (only plants, only birds, and all species combined). Two verifications were used: a primary vegetation map and 100 independent TDFs localities. We performed a Principal Component (PCA) and Discriminant Analysis (DA) to evaluate the variation in the environmental variables and ecological overlap among ecosystems. The modeling strategies showed differences in the ecological patterns and prediction areas, where the "all species combined" model (with a threshold of ≥10 species) was the best strategy to use in the TDFs reconstruction. We observed a concordance of 78% with the primary vegetation map and a prediction of 98% of independent locality records. Although PCA and DA tests explained 75.78% and 97.9% of variance observed, respectively, we observed an important overlap among the TDFs with other adjacent ecosystems, confirming the existence of transition zones among them. We successfully modeled the distribution of Mexican TDFs using a number of bioclimatic variables and co-distributed species. This autoecological niche approach suggests the necessity of rethinking the delimitations of ecosystems based on the recognition of transition zones among them in order to understand the real nature of communities and association patterns of species.

Response of the endangered tropical dry forests to climate change and the role of Mexican Protected Areas for their conservation.

Assuming that co-distributed species are exposed to similar environmental conditions, ecological niche models (ENMs) of bird and plant species inhabiting tropical dry forests (TDFs) in Mexico were developed to evaluate future projections of their distribution for the years 2050 and 2070. We used ENM-based predictions and climatic data for two Global Climate Models, considering two Representative Concentration Pathway scenarios (RCP4.5/RCP8.5). We also evaluated the effects of habitat loss and the importance of the Mexican system of protected areas (PAs) on the projected models for a more detailed prediction of TDFs and to identify hot spots that require conservation actions. We identified four major distributional areas: the main one located along the Pacific Coast (from Sonora to Chiapas, including the Cape and Bajío regions, and the Balsas river basin), and three isolated areas: the Yucatán peninsula, central Veracruz, and southern Tamaulipas. When considering the effect of habitat loss, a significant reduction (~61%) of the TDFs predicted area occurred, whereas climate-change models suggested (in comparison with the present distribution model) an increase in area of 3.0-10.0% and 3.0-9.0% for 2050 and 2070, respectively. In future scenarios, TDFs will occupy areas above its current average elevational distribution that are outside of its present geographical range. Our findings show that TDFs may persist in Mexican territory until the middle of the XXI century; however, the challenges about long-term conservation are partially addressed (only 7% unaffected within the Mexican network of PAs) with the current Mexican PAs network. Based on our ENM approach, we suggest that a combination of models of species inhabiting present TDFs and taking into account change scenarios represent an invaluable tool to create new PAs and ecological corridors, as a response to the increasing levels of habitat destruction and the effects of climate change on this ecosystem.

Insights from Integrative Systematics Reveal Cryptic Diversity in Pristimantis Frogs (Anura: Craugastoridae) from the Upper Amazon Basin.

Pluralistic approaches to taxonomy facilitate a more complete appraisal of biodiversity, especially the diversification of cryptic species. Although species delimitation has traditionally been based primarily on morphological differences, the integration of new methods allows diverse lines of evidence to solve the problem. Robber frogs (Pristimantis) are exemplary, as many of the species show high morphological variation within populations, but few traits that are diagnostic of species. We used a combination of DNA sequences from three mitochondrial genes, morphometric data, and comparisons of ecological niche models (ENMs) to infer a phylogenetic hypothesis for the Pristimantis acuminatus complex. Molecular phylogenetic analyses revealed a close relationship between three new species-Pristimantis enigmaticus sp. nov., P. limoncochensis sp. nov. and P. omeviridis sp. nov.-originally confused with Pristimantis acuminatus. In combination with morphometric data and geographic distributions, several morphological characters such as degree of tympanum exposure, skin texture, ulnar/tarsal tubercles and sexual secondary characters (vocal slits and nuptial pads in males) were found to be useful for diagnosing species in the complex. Multivariate discriminant analyses provided a successful classification rate for 83-100% of specimens. Discriminant analysis of localities in environmental niche space showed a successful classification rate of 75-98%. Identity tests of ENMs rejected hypotheses of niche equivalency, although not strongly because the high values on niche overlap. Pristimantis acuminatus and P. enigmaticus sp. nov. are distributed along the lowlands of central-southern Ecuador and northern Peru, in contrast with P. limoncochensis sp. nov. and P. omeviridis sp. nov., which are found in northern Ecuador and southern Colombia, up to 1200 m in the upper Amazon Basin. The methods used herein provide an integrated framework for inventorying the greatly underestimated biodiversity in Amazonia.

Activity response to climate seasonality in species with fossorial habits: a niche modeling approach using the lowland burrowing treefrog (Smilisca fodiens).

The importance of climatic conditions in shaping the geographic distribution of amphibian species is mainly associated to their high sensitivity to environmental conditions. How they cope with climate gradients through behavioral adaptations throughout their distribution is an important issue due to the ecological and evolutionary implications for population viability. Given their low dispersal abilities, the response to seasonal climate changes may not be migration, but behavioral and physiological adaptations. Here we tested whether shifts in climatic seasonality can predict the temporal variation of surface activity of the fossorial Lowland Burrowing Treefrog (Smilisca fodiens) across its geographical distribution. We employed Ecological Niche Modeling (ENM) to perform a monthly analysis of spatial variation of suitable climatic conditions (defined by the July conditions, the month of greatest activity), and then evaluated the geographical correspondence of monthly projections with the occurrence data per month. We found that the species activity, based on the species' occurrence data, corresponds with the latitudinal variation of suitable climatic conditions. Due to the behavioral response of this fossorial frog to seasonal climate variation, we suggest that precipitation and temperature have played a major role in the definition of geographical and temporal distribution patterns, as well as in shaping behavioral adaptations to local climatic conditions. This highlights the influence of macroclimate on shaping activity patterns and the important role of fossorials habits to meet the environmental requirements necessary for survival.

Ecological niche modeling of coastal dune plants and future potential distribution in response to climate change and sea level rise.

Climate change (CC) and sea level rise (SLR) are phenomena that could have severe impacts on the distribution of coastal dune vegetation. To explore this we modeled the climatic niches of six coastal dunes plant species that grow along the shoreline of the Gulf of Mexico and the Yucatan Peninsula, and projected climatic niches to future potential distributions based on two CC scenarios and SLR projections. Our analyses suggest that distribution of coastal plants will be severely limited, and more so in the case of local endemics (Chamaecrista chamaecristoides, Palafoxia lindenii, Cakile edentula). The possibilities of inland migration to the potential 'new shoreline' will be limited by human infrastructure and ecosystem alteration that will lead to a 'coastal squeeze' of the coastal habitats. Finally, we identified areas as future potential refuges for the six species in central Gulf of Mexico, and northern Yucatán Peninsula especially under CC and SLR scenarios.