From descriptive to predictive distribution models: a working example with Iberian amphibians and reptiles

Niche suitability and spatial distribution patterns of anurans in a unique Ecoregion mosaic of Northern Pakistan

The lack of information regarding biodiversity status hampers designing and implementing conservation strategies and achieving future targets. Northern Pakistan consists of a unique ecoregion mosaic which supports a myriad of environmental niches for anuran diversity in comparison to the deserts and xeric shrublands throughout the rest of the country. In order to study the niche suitability, species overlap and distribution patterns in Pakistan, we collected observational data for nine anuran species across several distinct ecoregions by surveying 87 randomly selected locations from 2016 to 2018 in Rawalpindi District and Islamabad Capital Territory. Our model showed that the precipitation of the warmest and coldest quarter, distance to rivers and vegetation were the greatest drivers of anuran distribution, expectedly indicating that the presence of humid forests and proximity to waterways greatly influences the habitable range of anurans in Pakistan. Sympatric overlap between species occurred at significantly higher density in tropical and subtropical coniferous forests than in other ecoregion types. We found species such as Minervarya spp., Hoplobatrachus tigerinus and Euphlyctis spp. preferred the lowlands in proximal, central and southern parts of the study area proximal to urban settlements, with little vegetation and higher average temperatures. Duttaphrynus bengalensis and D. stomaticus had scattered distributions throughout the study area with no clear preference for elevation. Sphaerotheca pashchima was patchily distributed in the midwestern extent of the study area as well as the foothills to the north. Microhyla nilphamariensis was widely distributed throughout the study area with a preference for both lowlands and montane terrain. Endemic frogs (Nanorana vicina and Allopaa hazarensis) were observed only in locations with higher elevations, higher density of streams and lower average temperatures as compared to the other seven species sampled. It is recommended to provide legal protection to amphibians of Pakistan, especially endemic species, through revision in the existing wildlife laws. We suggest studying the effectiveness of existing amphibian tunnels and corridors or designing new ones tailored to the needs of our species to prevent their local extinction due to ongoing or proposed urban development which might affect their dispersal and colonization.

Distribution model transferability for a wide-ranging species, the Gray Wolf

Using existing data can be a reliable and cost-effective way to predict species distributions, and particularly useful for recovering or expanding species. We developed a current gray wolf (Canis lupus) distribution model for the western Great Lakes region, USA, and evaluated the spatial transferability of single-state models to the region. This study is the first assessment of transferability in a wide-ranging carnivore, as well as one of few developed for large spatial extents. We collected 3500 wolf locations from winter surveys in Minnesota (2017–2019), Wisconsin (2019–2020), and Michigan (2017–2020). We included 10 variables: proportion of natural cover, pastures, and crops; distance to natural cover, agriculture, developed land, and water; major and minor road density; and snowfall (1-km res.). We created a regional ensemble distribution by weight-averaging eight models based on their performance. We also developed single-state models, and estimated spatial transferability using two approaches: state cross-validation and extrapolation. We assessed performance by quantifying correlations, receiver operating characteristic curves (ROC), sensitivities, and two niche similarity indices. The regional area estimated to be most suitable for wolves during winter (threshold = maximum sensitivity/specificity) was 106,465 km² (MN = 48,083 km², WI = 27,757 km², MI = 30,625 km²) and correctly predicted 88% of wolf locations analyzed. Increasing natural cover and distance to crops were consistently important for determining regional and single-state wolf distribution. Extrapolation (vs. cross-validation) produced results with the greatest performance metrics, and were most similar to the regional model, yet good internal performance was unrelated to greater extrapolation performance. Factors influencing species distributions are scale-dependent and can vary across areas due to behavioral plasticity. When extending inferences beyond the current occurrence of individuals, assessing variation in ecology such as habitat selection, as well as methodological factors including model performance, will be critical to avoid poor scientific interpretations and develop effective conservation applications. In particular, accurate distribution models for recovering or recovered carnivores can be used to develop plans for habitat management, quantify potential of unoccupied habitat, assess connectivity modeling, and mitigate conflict, facilitating long-term species persistence.

Genetic traces of hybrid zone movement across a fragmented habitat

Theoretical and empirical studies suggest that the structure and position of hybrid zones can change over time. Evidence for moving hybrid zones has been directly inferred by repeated sampling over time, or indirectly through the detection of genetic footprints left by the receding species and the resulting asymmetric patterns of introgression across markers. We here investigate a hybrid zone formed by two subspecies of the Iberian golden-striped salamander, Chioglossa lusitanica, using a panel of 35 nuclear loci (31 SNPs and 4 allozymes) and one mitochondrial locus in a transect in central Portugal. We found concordant and coincident clines for most of the nuclear loci (n=22, 63%), defining a narrow hybrid zone of ca. 6 km wide, with the centre positioned ca. 15 km south of the Mondego river. Asymmetric introgression was observed at another 14 loci. Their clines are displaced towards the north, with positions located either close to the Mondego river (n=6), or further northwards (n=8). We interpret these profiles as genetic traces of the southward displacement of C. lusitanica lusitanica by C. l. longipes over the wider Mondego river valley. We noted the absence of significant linkage disequilibrium and we inferred low levels of effective selection per locus against hybrids, suggesting that introgression in the area of species replacement occurred under a neutral diffusion process. A species distribution model suggests that the C. lusitanica hybrid zone coincides with a narrow corridor of fragmented habitat. From the position of the displaced clines, we infer that patches of locally suitable habitat trapped some genetic variants that became disassociated from the southward moving hybrid zone. This study highlights the influence of habitat availability on hybrid zone movement.

Local-scale models reveal ecological niche variability in amphibian and reptile communities from two contrasting biogeographic regions

Ecological Niche Models (ENMs) are widely used to describe how environmental factors influence species distribution. Modelling at a local scale, compared to a large scale within a high environmental gradient, can improve our understanding of ecological species niches. The main goal of this study is to assess and compare the contribution of environmental variables to amphibian and reptile ENMs in two Spanish national parks located in contrasting biogeographic regions, i.e., the Mediterranean and the Atlantic area. The ENMs were built with maximum entropy modelling using 11 environmental variables in each territory. The contributions of these variables to the models were analysed and classified using various statistical procedures (Mann-Whitney U tests, Principal Components Analysis and General Linear Models). Distance to the hydrological network was consistently the most relevant variable for both parks and taxonomic classes. Topographic variables (i.e., slope and altitude) were the second most predictive variables, followed by climatic variables. Differences in variable contribution were observed between parks and taxonomic classes. Variables related to water availability had the larger contribution to the models in the Mediterranean park, while topography variables were decisive in the Atlantic park. Specific response curves to environmental variables were in accordance with the biogeographic affinity of species (Mediterranean and non-Mediterranean species) and taxonomy (amphibians and reptiles). Interestingly, these results were observed for species located in both parks, particularly those situated at their range limits. Our findings show that ecological niche models built at local scale reveal differences in habitat preferences within a wide environmental gradient. Therefore, modelling at local scales rather than assuming large-scale models could be preferable for the establishment of conservation strategies for herptile species in natural parks.

Diversity and distribution of amphibians in Romania

Nineteen species of amphibians inhabit Romania, 9 of which reach their range limit on this territory. Based on published occurrence reports, museum collections and our own data we compiled a national database of amphibian occurrences. We georeferenced 26779 amphibian species occurrences, and performed an analysis of their spatial patterns, checking for hotspots and patterns of species richness. The results of spatial statistic analyses supported the idea of a biased sampling for Romania, with clear hotspots of increased sampling efforts. The sampling effort is biased towards species with high detectability, protected areas, and large cities. Future sampling efforts should be focused mostly on species with a high rarity score in order to accurately map their range. Our results are an important step in achieving the long-term goals of increasing the efficiency of conservation efforts and evaluating the species range shifts under climate change scenarios.

Tracing glacial refugia of Triturus newts based on mitochondrial DNA phylogeography and species distribution modeling

INTRODUCTION

The major climatic oscillations during the Quaternary Ice Age heavily influenced the distribution of species and left their mark on intraspecific genetic diversity. Past range shifts can be reconstructed with the aid of species distribution modeling and phylogeographical analyses. We test the responses of the different members of the genus Triturus (i.e. the marbled and crested newts) as the climate shifted from the previous glacial period (the Last Glacial Maximum, ~21 Ka) to the current interglacial.

RESULTS

We present the results of a dense mitochondrial DNA phylogeography (visualizing genetic diversity within and divergence among populations) and species distribution modeling (using two different climate simulations) for the nine Triturus species on composite maps.

CONCLUSIONS

The combined use of species distribution modeling and mitochondrial phylogeography provides insight in the glacial contraction and postglacial expansion of Triturus. The combined use of the two independent techniques yields a more complete understanding of the historical biogeography of Triturus than both approaches would on their own. Triturus newts generally conform to the 'southern richness and northern purity' paradigm, but we also find more intricate patterns, such as the absence of genetic variation and suitable area at the Last Glacial Maximum (T. dobrogicus), an 'extra-Mediterranean' refugium in the Carpathian Basin (T. cristatus), and areas where species displaced one another postglacially (e.g. T. macedonicus and western T. karelinii). We provide a biogeographical scenario for Triturus, showing the positions of glacial refugia, the regions that were postglacially colonized and the areas where species displaced one another as they shifted their ranges.

A quantitative climate-match score for risk-assessment screening of reptile and amphibian introductions

Assessing climatic suitability provides a good preliminary estimate of the invasive potential of a species to inform risk assessment. We examined two approaches for bioclimatic modeling for 67 reptile and amphibian species introduced to California and Florida. First, we modeled the worldwide distribution of the biomes found in the introduced range to highlight similar areas worldwide from which invaders might arise. Second, we modeled potentially suitable environments for species based on climatic factors in their native ranges, using three sources of distribution data. Performance of the three datasets and both approaches were compared for each species. Climate match was positively correlated with species establishment success (maximum predicted suitability in the introduced range was more strongly correlated with establishment success than mean suitability). Data assembled from the Global Amphibian Assessment through NatureServe provided the most accurate models for amphibians, while ecoregion data compiled by the World Wide Fund for Nature yielded models which described reptile climatic suitability better than available point-locality data. We present three methods of assigning a climate-match score for use in risk assessment using both the mean and maximum climatic suitabilities. Managers may choose to use different methods depending on the stringency of the assessment and the available data, facilitating higher resolution and accuracy for herpetofaunal risk assessment. Climate-matching has inherent limitations and other factors pertaining to ecological interactions and life-history traits must also be considered for thorough risk assessment.