An exhaustive evaluation of modeling ecological niches above species level to predict marine biological invasions.

Identifying the areas of the world with suitable environmental conditions for the establishment of invasive species represents a fundamental basis for preventing their impacts. One of the most widely used tools for this is ecological niche modeling. Nonetheless, this approach may underestimate the specie's physiological tolerances (it's potential niche) since wildlife populations of species usually do not occupy their entire environmental tolerance. Recently, it has been suggested that incorporating occurrences of phylogenetically related species improves the prediction of biological invasions. However, the reproducibility of this technique remains unclear. Here, we evaluated the generality of this protocol by assessing whether the construction of modeling units above species level improves the capacity of niche models to predict the distribution of 26 target marine invasive species. For each, we constructed supraspecific modeling units based on published phylogenies by grouping the native occurrence records of each invasive species with the records of its phylogenetically closest relative. We also considered units at species level, including only the presence of records in the native areas of the target species. We generated ecological niche models for each unit with three modeling methods (minimum volume ellipsoids - MVE, machine learning algorithms - Maxent and a presence-absence method - GLM). In addition, we grouped the 26 target species based on whether or not the species are in environmental pseudo-equilibrium (i.e., it occupies all habitats where it can disperse) and have any geographical or biological constraints. Our results suggest that the construction of supraspecific units improves the predictive capacity of correlative models to estimate the invasion area of our target species. This modeling approach consistently generated models with a higher predictive ability for species in non-environmental pseudo-equilibrium and with geographical constraints.

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.

Seasonal Distribution of the Broad-Tailed Hummingbird (Selasphorus platycercus): A Climatic Approach.

The seasonal movements of birds are a phenomenon that has historically been of interest in ecology and biogeography. Despite this, information on how environmental conditions influence migratory behavior and its regulation is still scarce. In this work, we study the Broad-Tailed hummingbird Selasphorus platycercus from an analysis of its populations through longitudinal and latitudinal gradients. We use the frequencies of monthly presence records throughout the annual cycle to identify the breeding areas (corresponding to the summer months), of winter presence (corresponding to the winter months), and annual residence (presence records throughout the year). Subsequently, we use ecological niche models to reconstruct the potential distribution of the summer and winter niches by correlating the climates of each season with the corresponding records. We evaluate the species' climatic preferences between the breeding and winter seasons by transferring the niches from each season to the opposite and by their capacity to inter-predict records between seasons. In addition, we quantify the overlap between the summer and winter niches using a niche similarity analysis. Geographically, we see a clear seasonal turnover pattern along a north-south gradient and records throughout the year (resident populations) in the south-central region of its distribution. We observed a low inter-prediction of records between seasons. Together with the similarity analysis, we suggest that the species is niche-switching (i.e., has different seasonal niches). We identified three seasonal migration patterns among the species' populations: long-distance migratory, short-distance summer migrant, and resident. Our findings suggest that the different migration patterns in this species' populations all over its distribution can be explained through seasonal climatic variations throughout the year.

Climate predictors and climate change projections for avian haemosporidian prevalence in Mexico.

Long-term, inter-annual and seasonal variation in temperature and precipitation influence the distribution and prevalence of intraerythrocytic haemosporidian parasites. We characterized the climatic niche behind the prevalence of the three main haemosporidian genera (Haemoproteus, Plasmodium and Leucocytozoon) in central-eastern Mexico, to understand their main climate drivers. Then, we projected the influence of climate change over prevalence distribution in the region. Using the MaxEnt modelling algorithm, we assessed the relative contribution of bioclimatic predictor variables to identify those most influential to haemosporidian prevalence in different avian communities within the region. Two contrasting climate change scenarios for 2070 were used to create distribution models to explain spatial turnover in prevalence caused by climate change. We assigned our study sites into polygonal operational climatic units (OCUs) and used the general haemosporidian prevalence for each OCU to indirectly measure environmental suitability for these parasites. A high statistical association between global prevalence and the bioclimatic variables 'mean diurnal temperature range' and 'annual temperature range' was found. Climate change projections for 2070 showed a significant modification of the current distribution of suitable climate areas for haemosporidians in the study region.

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.

Museum genomics reveals the speciation history of Dendrortyx wood-partridges in the Mesoamerican highlands.

Natural history collections are increasingly valued as genomic resources. Their specimens reflect the combined efforts of collectors and curators over hundreds of years. For many rare or endangered species, specimens are the only readily available source of DNA. We leveraged specimens from a historical collection to study the evolutionary history of wood-partridges in the genus Dendrortyx. The three Dendrortyx species are found in the highlands of central Mexico and Central America south to Costa Rica. One of these species is endangered, and in general, Dendrortyx are secretive and poorly represented in tissue collections. We extracted DNA from historical museum specimens and sequenced ultraconserved elements (UCEs) and mitochondrial DNA (mtDNA) to assess their phylogeny and divergence times. Phylogenies built from hundreds to thousands of nuclear markers were well resolved and largely congruent with an mtDNA phylogeny. The divergence times revealed an unusually old avian divergence across the Isthmus of Tehuantepec in the Pliocene around 3.6 million years ago. Combined with other recent studies, our results challenge the general pattern that highland bird divergences in Mesoamerica are relatively young and influenced by the Pleistocene glacial cycles compared to the older divergences of reptiles and plants, which are thought to overlap more with periods of mountain formation. We also found evidence for monophyletic genetic lineages in mountain ranges within the widespread D. macroura, which should be investigated further with integrative taxonomic methods. Our study demonstrates the power of museum genomics to provide insight into the evolutionary histories of groups where modern samples are lacking.

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.

Climate complexity in the migratory cycle of Ammodramus bairdii.

One way to understand the ecology of bird migration is to analyze how birds use their ecological niche during their annual cycle. Ammodramus bairdii is a grassland specialist sparrow that breeds in southern Canada and the northern U.S.A. and winters in the Chihuahuan Desert. A continuous and alarming decrease of its populations has been observed over the last 50 years, and studying its seasonal distribution and associated climatic niches could help improve strategies for its conservation. We analyzed the temporal use of its Grinnellian niche (GN) -set of environmental conditions under which a species can establish and persist; in this case the climatic attributes-. We modeled the GN for the reproductive and winter seasons and projected them onto each other (inter-prediction), and also onto transient migratory periods. To measure niche breadth and their overlap, minimum convex polygons (MCP) were calculated for the climatic space. The niches of each of the two seasons were tested for similarity using the PCA axes of climatic variables. The geographic areas with optimal, suboptimal and marginal conditions were identified, based on the distance to the centroid of the GN. The models for each season revealed no geographic inter-prediction among them, with the exception of winter to migratory seasons. The niche breadth of the winter was greater than that of the reproductive season, with an overlap of 22.47% and 45.18%, respectively. The similarity analyses showed a value of zero between seasons. The climate conditions for the records during the migratory months corresponded with suboptimal and marginal conditions of the sparrow's winter niche. These results suggest that A. bairdii uses different climate conditions within ecological niches of each season during its migratory cycle.

Diversity and distribution of Phanaeini (Coleoptera: Scarabaeidae: Scarabaeinae) in Mexico.

In this study, we systematized available distribution data, obtained from biological databases and relevant literature, for Mexican species belonging to the tribe Phanaeini. The main objectives were to provide an overall description of the distribution records in biological collections, to detect potential sampling biases, to describe the seasonality of collections and to obtain species distribution models using the Desktop GARP algorithm. A total of 5,562 records, corresponding to 32 species in Mexico, were compiled, including the recently described Phanaeus zoque Moctezuma & Halffter, 2017. This compilation includes 784 unique collection records at 325 localities. These records were mainly distributed along the Trans-Mexican Volcanic Belt, the Sierra Madre Oriental and Sierra Madre Occidental mountain ranges and throughout the states of Chiapas and Veracruz. The Mexican High Plateau, the state of Tlaxcala and the Yucatan Peninsula are lacking in records. Distribution maps were created for species of three genera (Phanaeus MacLeay, 1819, Coprophanaeus Olsoufieff, 1924, and Sulcophanaeus Olsoufieff, 1924) and for 29 species present in Mexico. These species distributions are largely delimited by geomorphological features and vegetation types and coincide with expert descriptions of this tribe; some species show expanded distribution ranges. These maps provide a starting point for further analyses, the planning of future field studies, and the verification of possible new species in the Mexican territory.

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.

Variación temporal en la distribución geográfica y ecológica de Amazona finschi (Psittaciformes: Psittacidae) / Temporal variation in ecological and geographical distribution of Amazona finschi (Psittaciformes: Psittacidae)

Resumen: El loro corona lila (Amazona finschi), es una especie endémica de las tierras bajas de la costa del Pacífico mexicano y está considerada en peligro. Sin embargo, ha sido documentado que la especie presenta migraciones estacionales y altitudinales a lo largo de su rango geográfico, lo que sugiere que su distribución ecológica y temporal permanece incierta. Se modeló la distribución potencial del loro corona lila considerando sus dos principales periodos de actividad: reproductiva y no reproductiva. Para desarrollar modelos de nicho ecológico, se usaron 428 presencias históricas de bases de datos de libre acceso en internet, que fueron combinados con cinco coberturas ambientales: tres climáticas y dos topográficas para cada periodo, mediante el algoritmo de Maxent. Posteriormente transferimos cada modelo estacional al resto de los meses para analizar si los movimientos estacionales de la especie estaban dirigidos por el clima. Se evaluaron las diferencias en las variables ecológicas entre estaciones mediante el uso de una prueba de "t". Analizamos mediante la superposición de los mapas, la correspondencia geográfica entre la distribución de loro y la de los recursos (plantas), usados por la especie. Se encontró una marcada estacionalidad en la distribución del loro corona lila. La especie presenta una mayor amplitud ecológica en términos de temperatura mínima durante la temporada reproductiva, pero una notable reducción en lo que se refiere a la precipitación. La distribución de los recursos de anidación y alimentación corresponde en gran medida con la distribución del loro corona lila. En el centro del rango de distribución de la especie existe un área donde se presentan las condiciones de las que la especie hace uso en ambas temporadas y en los periodos de transición entre estas. Finalmente, además de las implicaciones en la conservación de la especie, nuestros resultados acerca de la variación estacional en la distribución geográfica y ecológica del loro corona lila, son importantes para la comprensión de la distribución de otras especies, particularmente aquellas que se encuentran asociadas con ambientes altamente estacionales.

Abstract: The lilac-crowned parrot (Amazona finschi) is an endemic species restricted to lowlands of the Mexican Pacific coast and is currently considered as endangered. It has been documented that it shows altitudinal and seasonal migrations along its distributional range, suggesting that its ecological and temporal distribution is still uncertain. We modeled the potential distribution of the A. finschi considering the two main activity seasons for the species: reproductive and non-reproductive. We used 428 historical occurrences (1882-2014), obtained from open access databases, combined with five environmental layers: three climatic and two topographic for each season, to perform ecological niche models using Maxent. We then transferred each model to the rest of the months to analyze the seasonal movements guided by climate. Differences in ecological variables between seasons were evaluated using a t-test. The geographic correspondence among the parrot distribution and the resources (plants) distributions were analyzed by superimposing maps. A marked seasonality in the distribution of A. finschi was observed. Ecologically, the species displays greater amplitude during the breeding seasons in terms of minimum temperature, but a noticeable reduction as far as precipitation is concerned. The distribution of food and nesting resources largely corresponds to the distribution of this parrot. There is a wide area in the center of the geographical distribution in which the species finds conditions that meet both periods of activity, as well as transition conditions between these periods. Finally, our results on the seasonal variation in the geographical and ecological distribution of this species, possess a strong ecological meaning in the understanding of other species distribution, particularly those associated with highly seasonal environments, and definitively will contribute to the conservation of this species. Rev. Biol. Trop. 65 (3): 1194-1207. Epub 2017 September 01.

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.

Climatic patterns in the establishment of wintering areas by North American migratory birds.

Long-distance migration in birds is relatively well studied in nature; however, one aspect of this phenomenon that remains poorly understood is the pattern of distribution presented by species during arrival to and establishment of wintering areas. Some studies suggest that the selection of areas in winter is somehow determined by climate, given its influence on both the distribution of bird species and their resources. We analyzed whether different migrant passerine species of North America present climatic preferences during arrival to and departure from their wintering areas. We used ecological niche modeling to generate monthly potential climatic distributions for 13 migratory bird species during the winter season by combining the locations recorded per month with four environmental layers. We calculated monthly coefficients of climate variation and then compared two GLM (generalized linear models), evaluated with the AIC (Akaike information criterion), to describe how these coefficients varied over the course of the season, as a measure of the patterns of establishment in the wintering areas. For 11 species, the sites show nonlinear patterns of variation in climatic preferences, with low coefficients of variation at the beginning and end of the season and higher values found in the intermediate months. The remaining two species analyzed showed a different climatic pattern of selective establishment of wintering areas, probably due to taxonomic discrepancy, which would affect their modeled winter distribution. Patterns of establishment of wintering areas in the species showed a climatic preference at the macroscale, suggesting that individuals of several species actively select wintering areas that meet specific climatic conditions. This probably gives them an advantage over the winter and during the return to breeding areas. As these areas become full of migrants, alternative suboptimal sites are occupied. Nonrandom winter area selection may also have consequences for the conservation of migratory bird species, particularly under a scenario of climate change.

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.

Using Range-Wide Abundance Modeling to Identify Key Conservation Areas for the Micro-Endemic Bolson Tortoise (Gopherus flavomarginatus).

A widespread biogeographic pattern in nature is that population abundance is not uniform across the geographic range of species: most occurrence sites have relatively low numbers, whereas a few places contain orders of magnitude more individuals. The Bolson tortoise Gopherus flavomarginatus is endemic to a small region of the Chihuahuan Desert in Mexico, where habitat deterioration threatens this species with extinction. In this study we combined field burrows counts and the approach for modeling species abundance based on calculating the distance to the niche centroid to obtain range-wide abundance estimates. For the Bolson tortoise, we found a robust, negative relationship between observed burrows abundance and distance to the niche centroid, with a predictive capacity of 71%. Based on these results we identified four priority areas for the conservation of this microendemic and threatened tortoise. We conclude that this approach may be a useful approximation for identifying key areas for sampling and conservation efforts in elusive and rare species.

The use of ecological niche modeling to infer potential risk areas of snakebite in the Mexican state of Veracruz.

BACKGROUND: Many authors have claimed that snakebite risk is associated with human population density, human activities, and snake behavior. Here we analyzed whether environmental suitability of vipers can be used as an indicator of snakebite risk. We tested several hypotheses to explain snakebite incidence, through the construction of models incorporating both environmental suitability and socioeconomic variables in Veracruz, Mexico. METHODOLOGY/PRINCIPAL FINDINGS: Ecological niche modeling (ENM) was used to estimate potential geographic and ecological distributions of nine viper species' in Veracruz. We calculated the distance to the species' niche centroid (DNC); this distance may be associated with a prediction of abundance. We found significant inverse relationships between snakebites and DNCs of common vipers (Crotalus simus and Bothrops asper), explaining respectively 15% and almost 35% of variation in snakebite incidence. Additionally, DNCs for these two vipers, in combination with marginalization of human populations, accounted for 76% of variation in incidence. CONCLUSIONS/SIGNIFICANCE: Our results suggest that niche modeling and niche-centroid distance approaches can be used to mapping distributions of environmental suitability for venomous snakes; combining this ecological information with socioeconomic factors may help with inferring potential risk areas for snakebites, since hospital data are often biased (especially when incidences are low).

Novel data on the ecology of Cochranella mache (Anura: Centrolenidae) and the importance of protected areas for this critically endangered glassfrog in the neotropics.

We studied a population of the endangered glassfrog, Cochranella mache, at Bilsa Biological Station, northwestern Ecuador, from 2008 and 2009. We present information on annual abundance patterns, behavioral ecology, habitat use and a species distribution model performed with MaxEnt. We evaluate the importance of the National System of Protected Areas (SNAP) in Colombia and Ecuador, under scenarios of climate change and habitat loss. We predicted a restricted environmental suitability area from 48,509 Km(2) to 65,147 Km(2) along western Ecuador and adjacent Colombia; ∼ 8% of the potential distribution occurs within SNAP. We examined four aspects of C. mache ecology: (1) ecological data suggests a strong correlation between relative abundance and rainfall, with a high probability to observe frogs through rainy months (February-May); (2) habitat use and the species distribution model suggest that this canopy dweller is restricted to small streams and rivulets in primary and old secondary forest in evergreen lowland and piedmont forest of western Ecuador, with predictions of suitability areas in adjacent southern Colombia; (3) the SNAP of Colombia and Ecuador harbor a minimum portion of the predicted model of distribution (<10%); and (4) synergetic effects of habitat loss and climate change reduces in about 95% the suitability areas for this endangered frog along its distributional range in Protected Areas. The resulting model allows the recognition of areas to undertake conservation efforts and plan future field surveys, as well as forecasting regions with high probability of C. mache occurrence in western Ecuador and southern Colombia. Further research is required to assess population tendencies, habitat fragmentation and target survey zones to accelerate the discovery of unknown populations in unexplored areas with high probability of suitability. We recommend that Cochranella mache must be re-categorized as "Critically Endangered" species in national and global status, according with criteria and sub-criteria A4, B1ab(i,ii,iii,iv),E.

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.