Landscape genomic signatures indicate reduced gene flow and forest-associated adaptive divergence in an endangered neotropical turtle.

Human-induced transformations of ecosystems usually result in fragmented populations subject to increased extinction risk. Fragmentation is also often associated with novel environmental heterogeneity, which in combination with restricted gene flow may increase the opportunity for local adaptation. To manage at-risk populations in these landscapes, it is important to understand how gene flow is changing, and how populations respond to habitat loss. We conducted a landscape genomics analysis using Restriction-site Associated DNA sequencing to investigate the evolutionary response of the critically endangered Dahl's Toad-headed turtle (Mesoclemmys dahli) to severe habitat modification. The species has lost almost all of its natural habitat in the southwestern part of its range and about 70% in the northeast. Based on least cost path analysis across different resistance surfaces for 3,211 SNPs, we found that the landscape matrix is restricting gene flow, causing the fragmentation of the species into at least six populations. Genome scans and allele-environment association analyses indicate that the population fragments in the deforested grasslands of the southwest are adaptively different from those in the more forested northeast. Populations in areas with no forest had low levels of adaptive genetic diversity and the fixation of ancestrally-polymorphic SNPs, consistent with directional selection in this novel environment. Our results suggest that this forest-stream specialist is adapting to pond-grassland conditions, but it is also suffering from negative consequences of habitat loss, including genetic erosion, isolation, small effective population sizes, and inbreeding. We recommend gene flow restoration via genetic rescue to counteract these threats, and provide guidance for this strategy.

Constraints to species' elevational range shifts as climate changes.

Predicting whether the ranges of tropical species will shift to higher elevations in response to climate change requires models that incorporate data on topography and land use. We incorporated temperature gradients and land-cover data from the current ranges of species in a model of range shifts in response to climate change. We tested four possible scenarios of amphibian movement on a tropical mountain: movement upslope through and to land cover suitable for the species; movement upslope to land-cover types that will not sustain survival and reproduction; movement upslope to areas that previously were outside the species' range; and movement upslope to cooler areas within the current range. Areas in the final scenario will become isolated as climate continues to change. In our scenarios more than 30% of the range of 21 of 46 amphibian species in the tropical Sierra Nevada de Santa Marta is likely to become isolated as climate changes. More than 30% of the range of 13 amphibian species would shift to areas that currently are unlikely to sustain survival and reproduction. Combined, over 70% of the current range of seven species would become thermally isolated or shift to areas that currently are unlikely to support survival and reproduction. The constraints on species' movements to higher elevations in response to climate change can increase considerably the number of species threatened by climate change in tropical mountains.

Movement behaviour within and beyond perceptual ranges in three small mammals: effects of matrix type and body mass.

1. For animal species inhabiting heterogeneous landscapes, the tortuosity of the dispersal path is a key determinant of the success in locating habitat patches. Path tortuosity within and beyond perceptual range must differ, and may be differently affected by intrinsic attributes of individuals and extrinsic environmental factors. Understanding how these factors interact to determine path tortuosity allows more accurate inference of successful movements between habitat patches. 2. We experimentally determined the effects of intrinsic (body mass and species identity) and extrinsic factors (distance to nearest forest fragment and matrix type) on the tortuosity of movements of three forest-dwelling didelphid marsupials, in a fragmented landscape of the Atlantic Forest, Brazil. 3. A total of 202 individuals were captured in forest fragments and released in three unsuitable matrix types (mowed pasture, abandoned pasture and manioc plantation), carrying spool-and-line devices. 4. Twenty-four models were formulated representing a priori hypotheses of major determinants of path tortuosity, grouped in three scenarios (only intrinsic factors, only extrinsic factors and models with combinations of both), and compared using a model selection approach. Models were tested separately for individuals released within the perceptual range of the species, and for individuals released beyond the perceptual range. 5. Matrix type strongly affected path tortuosity, with more obstructed matrix types hampering displacement of animals. Body mass was more important than species identity to determine path tortuosity, with larger animals moving more linearly. Increased distance to the fragment resulted in more tortuous paths, but actually reflects a threshold in perceptual range: linear paths within perceptual range, tortuous paths beyond. 6. The variables tested explained successfully path tortuosity, but only for animals released within the perceptual range. Other factors, such as wind intensity and direction of plantation rows, may be more important for individuals beyond their perceptual range. 7. Simplistic scenarios considering only intrinsic or extrinsic factors are inadequate to predict path tortuosity, and to infer dispersal success in heterogeneous landscapes. Perceptual range represents a fundamental threshold where the effects of matrix type, body mass and individual behaviour change drastically.

Turtles and Tortoises Are in Trouble.

Turtles and tortoises (chelonians) have been integral components of global ecosystems for about 220 million years and have played important roles in human culture for at least 400,000 years. The chelonian shell is a remarkable evolutionary adaptation, facilitating success in terrestrial, freshwater and marine ecosystems. Today, more than half of the 360 living species and 482 total taxa (species and subspecies combined) are threatened with extinction. This places chelonians among the groups with the highest extinction risk of any sizeable vertebrate group. Turtle populations are declining rapidly due to habitat loss, consumption by humans for food and traditional medicines and collection for the international pet trade. Many taxa could become extinct in this century. Here, we examine survival threats to turtles and tortoises and discuss the interventions that will be needed to prevent widespread extinction in this group in coming decades.

Wetlands are keystone habitats for jaguars in an intercontinental biodiversity hotspot.

Agricultural development was the major contributor to South America's designation as the continent with the highest rates of forest loss from 2000-2012. As the apex predator in the Neotropics, jaguars (Panthera onca) are dependent on forest cover but the species' response to habitat fragmentation in heterogeneous agricultural landscapes has not been a subject of extensive research. We used occupancy as a measure of jaguar habitat use in Colombia's middle Magdalena River valley which, as part of the intercontinental Tumbes-Chocó-Magdalena biodiversity hotspot, is exceedingly fragmented by expanding cattle pastures and oil palm plantations. We used single-season occupancy models to analyze 9 months of data (2015-2016) from 70 camera trap sites. Given the middle Magdalena's status as a "jaguar corridor" and our possible violation of the occupancy models' demographic closure assumption, we interpreted our results as "probability of habitat use (Ψ)" by jaguars. We measured the associations between jaguar presence and coverage of forest, oil palm, and wetlands in radii buffers of 1, 3, and 5 km around each camera trap. Our camera traps recorded 77 jaguar detections at 25 of the camera trap sites (36%) during 15,305 trap nights. The probability of detecting jaguars, given their presence at a site, was 0.28 (0.03 SE). In the top-ranked model, jaguar habitat use was positively influenced by wetland coverage (ß = 7.16, 3.20 SE) and negatively influenced by cattle pastures (ß = -1.40, 0.63 SE), both in the 3 km buffers. We conclude that wetlands may serve as keystone habitats for jaguars in landscapes fragmented by cattle ranches and oil palm plantations. Greater focus on wetland preservation could facilitate jaguar persistence in one of the most important yet vulnerable areas of their distribution.

Elevational ranges of birds on a tropical montane gradient lag behind warming temperatures.

BACKGROUND: Species may respond to a warming climate by moving to higher latitudes or elevations. Shifts in geographic ranges are common responses in temperate regions. For the tropics, latitudinal temperature gradients are shallow; the only escape for species may be to move to higher elevations. There are few data to suggest that they do. Yet, the greatest loss of species from climate disruption may be for tropical montane species. METHODOLOGY/PRINCIPAL FINDINGS: We repeat a historical transect in Peru and find an average upward shift of 49 m for 55 bird species over a 41 year interval. This shift is significantly upward, but also significantly smaller than the 152 m one expects from warming in the region. To estimate the expected shift in elevation we first determined the magnitude of warming in the locality from historical data. Then we used the temperature lapse rate to infer the required shift in altitude to compensate for warming. The range shifts in elevation were similar across different trophic guilds. CONCLUSIONS: Endothermy may provide birds with some flexibility to temperature changes and allow them to move less than expected. Instead of being directly dependent on temperature, birds may be responding to gradual changes in the nature of the habitat or availability of food resources, and presence of competitors. If so, this has important implications for estimates of mountaintop extinctions from climate change.

Representation of global and national conservation priorities by Colombia's Protected Area Network.

BACKGROUND: How do national-level actions overlap with global priorities for conservation? Answering this question is especially important in countries with high and unique biological diversity like Colombia. Global biodiversity schemes provide conservation guidance at a large scale, while national governments gazette land for protection based on a combination of criteria at regional or local scales. Information on how a protected area network represents global and national conservation priorities is crucial for finding gaps in coverage and for future expansion of the system. METHODOLOGY/PRINCIPAL FINDINGS: We evaluated the agreement of Colombia's protected area network with global conservation priorities, and the extent to which the network reflects the country's biomes, species richness, and common environmental and physical conditions. We used this information to identify priority biomes for conservation. We find the dominant strategy in Colombia has been a proactive one, allocating the highest proportion of protected land on intact, difficult to access and species rich areas like the Amazon. Threatened and unique areas are disproportionately absent from Colombia's protected lands. We highlight six biomes in Colombia as conservation priorities that should be considered in any future expansion of Colombia's protected area network. Two of these biomes have less than 3% of their area protected and more than 70% of their area transformed for human use. One has less than 3% protected and high numbers of threatened vertebrates. Three biomes fall in both categories. CONCLUSIONS: Expansion of Colombia's Protected Area Network should consider the current representativeness of the network. We indicate six priority biomes that can contribute to improving the representation of threatened species and biomes in Colombia.

Distribución geggráfica de las tortugas continetales de Colombia y su represenntación en áreas protegidas / Geographic Distribution of the Tortoises and Freshwater Turtles of Colombia and their Representation in the Protected Area Network

Colombia cuenta con una alta diversidad de quelonios continentales, sin embargo, un número considerable de especies se encuentran amenazadas y para otras no existe información suficiente para evaluar su estado de amenaza. Este trabajo es una aproximación cuantitativa al estudio de la distribución geográfica de las tortugas continentales de Colombia. Con base en registros de localidades con presencia de cada especie, evaluamos la distribución geográfica a partir de modelos estadísticos (Maxent), cuencas hidrográficas, extensión de presencia y área de ocupación. Estimamos la representación de cada especie en el sistema de Parques Nacionales Naturales (PNN) y en otras áreas del sistema nacional de áreas protegidas, incluyendo Reservas Naturales de la Sociedad Civil (RNSC). Se construyeron modelos de distribución geográfica y se estimó el área de distribución (km2) para 25 de las 27 especies presentes en el país. Las áreas con mayor riqueza de especies son los ecosistemas ribereños de la Amazonia, Orinoquia y el Caribe, en particular el Caribe occidental. Este último es un bioma prioritario debido a su alto número de endemismos y por la amenaza que enfrentan sus especies. Solo el 56 % de las especies estudiadas presentan registros confirmados en los PNN. Un mayor número de especies podría estar presente en los PNN de acuerdo con los resultados de los modelos, pero solo diez especies tendrían más del 10 % de su distribución representada en dichas áreas. Los modelos generados podrán ser un punto de partida para investigar la presencia de quelonios en los PNN. Las especies endémicas están pobremente representadas en las áreas protegidas, tanto en los PNN como en otras categorías, por lo que es urgente constituir nuevas áreas protegidas para asegurar la supervivencia de sus poblaciones.

Colombia has a remarkable diversity of tortoises and freshwater turtles. However, a considerable portion of these species is threatened, and for others there is not enough information to make an adequate evaluation of their conservation status. This study is a first approximation to the quantitative evaluation of the geographic distribution of Colombia's non-marine chelonians. Based on records of occurrence for each species, we evaluated the geographic distribution using statistical models (Maxent), hydrological basins, and the extent of occurrence and area of occupancy. Based on the presence data and the models, we studied the representation of each species in National Natural Parks (NNP), which correspond to the most rigorous conservation category of IUCN classification in Colombia, and other types of protected areas such as Private Reserves. We generated distribution models and estimated the area (km2) for 25 out of 27 species in the country. This information will be valuable for updating and evaluating the threat categories at the national level. The areas with the highest species richness correspond to the riverine ecosystems of the Amazon and Orinoco river basins and the Caribbean region, particularly the western Caribbean. This region is a top priority not only because of its richness but also because of the presence of endemics and its high level of threat. Only 56 % of the species have confirmed records within National Parks. A greater portion could be present in these areas according to the statistical models, but only ten of those species would have more than 10 % of their ranges within a park's boundary. Although the resulting models have certain limitations due to the nature of the data and analyses, they can be a starting point for research on the occurrence of turtles in NNP. Endemic species are poorly represented in protected areas, both in NNP and in other categories. Thus, protected areas that can assure the persistence of their populations are urgently needed.

Body size and extinction risk in Brazilian carnivores / Tamaño corporal como factor de amenaza en carnívoros brasileros

Because extinctions are not random across taxa, it is important for conservation biologists to identify the traits that make some species more vulnerable. Factors associated with vulnerability include small geographical ranges, low densities, high trophic level, "slow" life histories, body size, and tolerance to altered habitats. In this study we examined the relationship of body size, reproductive output, longevity, and extinction risk for carnivores occurring in Brazil. We used generalized linear models analyses on phylogenetically independent contrasts to test the effect of body size alone, and the combined effect of body size, litter size and longevity on extinction risk. Body size appeared in the two best models according to the selection criteria (AIC), and it was the most plausible bionomic variable associated with extinction risk. Litter size and longevity, bionomic traits previously associated with threat risk of Brazilian carnivores, were implausible. The higher extinction risk for larger species could result from body size influencing vulnerability to different human activities, such as killing, habitat destruction and fragmentation, and the small size of natural reserves.

Debido a que las extinciones no son aleatorias a través de los diferentes taxa, es importante para los biólogos de la conservación identificar las características que hacen a algunas especies más vulnerables. Los factores asociados con la vulnerabilidad incluyen distribuciones geográficas pequeñas, densidades poblacionales bajas, niveles tróficos altos, historias de vida "lentas", tamaño del cuerpo, y tolerancia a habitats alterados. En este estudio examinamos la relación del tamaño corporal, el potencial reproductivo y la longevidad con el riesgo de extinción para los carnívoros brasileros. Realizamos análisis de modelos lineares generalizados con contrastes filogenéticamente independientes para probar el efecto del tamaño corporal solo, y el efecto combinado del tamaño corporal, el tamaño de la camada y la longevidad sobre el riesgo de extinción. El tamaño del cuerpo apareció en los dos mejores modelos de acuerdo con el criterio de selección (AIC) y es la variable bionómica más plausible afectando el riesgo de extinción. El tamaño de la prole y longevidad, otras variables bionómicas que han presentado tal efecto en otros estudios, fueron implausibles. La mayor probabilidad de amenaza para las especies grandes puede deberse a que el tamaño del cuerpo afecta la vulnerabilidad a diferentes actividades humanas como la caza, la destrucción y fragmentación del hábitat, y al tamaño reducido de la mayoría de áreas protegidas.