Human footprint differentially impacts genetic connectivity of four wide‐ranging mammals in a fragmented landscape

Corridor-based approach with spatial cross-validation reveals scale-dependent effects of geographic distance, human footprint and canopy cover on grizzly bear genetic connectivity

Understanding how human infrastructure and other landscape attributes affect genetic differentiation in animals is an important step for identifying and maintaining dispersal corridors for these species. We built upon recent advances in the field of landscape genetics by using an individual-based and multiscale approach to predict landscape-level genetic connectivity for grizzly bears (Ursus arctos) across ~100,000 km2 in Canada's southern Rocky Mountains. We used a genetic dataset with 1156 unique individuals genotyped at nine microsatellite loci to identify landscape characteristics that influence grizzly bear gene flow at multiple spatial scales and map predicted genetic connectivity through a matrix of rugged terrain, large protected areas, highways and a growing human footprint. Our corridor-based modelling approach used a machine learning algorithm that objectively parameterized landscape resistance, incorporated spatial cross validation and variable selection and explicitly accounted for isolation by distance. This approach avoided overfitting, discarded variables that did not improve model performance across withheld test datasets and spatial predictive capacity compared to random cross-validation. We found that across all spatial scales, geographic distance explained more variation in genetic differentiation in grizzly bears than landscape variables. Human footprint inhibited connectivity across all spatial scales, while open canopies inhibited connectivity at the broadest spatial scale. Our results highlight the negative effect of human footprint on genetic connectivity, provide strong evidence for using spatial cross-validation in landscape genetics analyses and show that multiscale analyses provide additional information on how landscape variables affect genetic differentiation.

The genetic structure and connectivity in two sympatric rodent species with different life histories are similarly affected by land use disturbances

The negative impact of habitat fragmentation due to human activities may be different in different species that co-exist in the same area, with consequences on the development of environmental protection plans. Here we aim at understanding the effects produced by different natural and anthropic landscape features on gene flow patterns in two sympatric species with different specializations, one generalist and one specialist, sampled in the same locations. We collected and genotyped 194 wood mice (generalist species) and 199 bank voles (specialist species) from 15 woodlands in a fragmented landscape characterized by different potential barriers to dispersal. Genetic variation and structure were analyzed in the two species, respectively. Effective migration surfaces, isolation-by-resistance (IBR) analysis, and regression with randomization were used to investigate isolation-by-distance (IBD) and the relative importance of land cover elements on gene flow. We observed similar patterns of heterozygosity and IBD for both species, but the bank vole showed higher genetic differences among geographic areas. The IBR analysis suggests that (i) connectivity is reduced in both species by urban areas but more strongly in the specialist bank vole; (ii) cultivated areas act as dispersal corridors in both species; (iii) woodlands appear to be an important factor in increasing connectivity in the bank vole, and less so in the wood mouse. The difference in dispersal abilities between a generalist and specialist species was reflected in the difference in genetic structure, despite extensive habitat changes due to human activities. The negative effects of fragmentation due to the process of urbanization were, at least partially, mitigated by another human product, i.e., cultivated terrains subdivided by hedgerows, and this was true for both species.

Influence of land use changes on landscape connectivity for North China leopard (Panthera pardus japonensis)

North China leopard (Panthera pardus japonensis) is the most widespread subspecies of leopard and one of the rare and endangered species in China. It is currently confined to several isolated natural reserves, and little is known about its habitat network connectivity with land use changes. This study was conducted to assess the impacts of land use changes on landscape connectivity for North China leopard in the Great Taihang Region. Circuit theory‐based connectivity models and least‐cost path analyses were used to delineate pathways suitable for species movement, and evaluate the impacts of land use changes on landscape connectivity. The results revealed that there were 37 least‐cost paths in 1990 and 38 in 2020. The area of forest land increased from 57,142.74 km² to 74,836.64 km², with the percentage increasing from 26.61% to 34.85%. In general, the increase in forest land area promoted the landscape connectivity for North China leopard at broad spatial scales. The improvement of landscape connectivity was not always consistent with the land use changes, and there was a slightly decreasing trend on connectivity in some key movement barrier areas with high intensity of human activities. Improving landscape connectivity at broad spatial scales is as important as protecting the habitats (natural reserves) where the species lives. Our study can serve as an example of exploring the relationships between land use changes and landscape connectivity for species conservation at broad spatial scales with limited movement pattern data. This information is proved to be critical for enhancing landscape connectivity for the conservation concern of North China leopard and planning of natural reserves network.

Assessment of agricultural prospects in relation to land use change and population pressure on a spatiotemporal framework

The urbanisation process moves quickly in emerging nations like India and Bangladesh, transforming natural landscapes into unsustainable landscapes. Consequently, growing development has had a significant impact on agricultural land as a natural environment. Moreover, there is a scarcity of research on fragmentation probability modelling in the extant literature. Thus, by combining random forest (RF) and bagging with the datasets which are multi-temporal in a GIS framework, the probability of fragmentation of LULC at Jangipur subdivision in India and Bangladesh can be modelled. Parallelepiped, Mohalnobis distance, support vector machines (SVM), spectral angle mapper (SAM), and artificial neural networks (ANN) classifiers were used for LULC classification, where SVM (Kappa coefficient: 0.87) surpassed other classifiers. The LULC maps for 1990, 2000, 2010, and 2020 were created using the best classifier (SVM). During this time, the built-up area grew from 23.769 to 158.125 km². Then, using an ANN-based cellular automata model, the future LULC map for 2030 was predicted (CA-ANN). In 2030, the built-up area would be 201.58 km². Then the matrices of class and landscape were taken out of the LULC maps utilising FRAGSTAT software and included the patch number (NP), largest patch index (LPI), edge density (ED), contagion index (percentage) (CONTAG), perimeter and area (P/A), aggregation index (AI), landscape percentage (PLAND), the area of class (CA), patch density (PD), edge in total (TE), total core area (TCA), and largest shape index (LSI). The validation results revealed that bagging (0.915 = AUC) and RF (0.874 = AUC) are capable of assessing fragmentation probability, with the bagging model having the greatest precision level of the two. Almost 20% of the total LULC was in a high and very high zone of fragmentation vulnerability, necessitating the use of direct measures to safeguard it. As a result, adequate LULC management is required.

Movement ecology of vulnerable lowland tapirs between areas of varying human disturbance

BACKGROUND

Animal movement is a key ecological process that is tightly coupled to local environmental conditions. While agriculture, urbanisation, and transportation infrastructure are critical to human socio-economic improvement, these have spurred substantial changes in animal movement across the globe with potential impacts on fitness and survival. Notably, however, human disturbance can have differential effects across species, and responses to human activities are thus largely taxa and context specific. As human disturbance is only expected to worsen over the next decade it is critical to better understand how species respond to human disturbance in order to develop effective, case-specific conservation strategies.

METHODS

Here, we use an extensive telemetry dataset collected over 22 years to fill a critical knowledge gap in the movement ecology of lowland tapirs (Tapirus terrestris) across areas of varying human disturbance within three biomes in southern Brazil: the Pantanal, Cerrado, and Atlantic Forest.

RESULTS

From these data we found that the mean home range size across all monitored tapirs was 8.31 km² (95% CI 6.53-10.42), with no evidence that home range sizes differed between sexes nor age groups. Interestingly, although the Atlantic Forest, Cerrado, and Pantanal vary substantially in habitat composition, levels of human disturbance, and tapir population densities, we found that lowland tapir movement behaviour and space use were consistent across all three biomes. Human disturbance also had no detectable effect on lowland tapir movement. Lowland tapirs living in the most altered habitats we monitored exhibited movement behaviour that was comparable to that of tapirs living in a near pristine environment.

CONCLUSIONS

Contrary to our expectations, although we observed individual variability in lowland tapir space use and movement, human impacts on the landscape also had no measurable effect on their movement. Lowland tapir movement behaviour thus appears to exhibit very little phenotypic plasticity in response to human disturbance. Crucially, the lack of any detectable response to anthropogenic disturbance suggests that human modified habitats risk being ecological traps for tapirs and this information should be factored into conservation actions and species management aimed towards protecting lowland tapir populations.

Synthesizing habitat connectivity analyses of a globally important human-dominated tiger-conservation landscape

As ecological data and associated analyses become more widely available, synthesizing results for effective communication with stakeholders is essential. In the case of wildlife corridors, managers in human-dominated landscapes need to identify both the locations of corridors and multiple stakeholders for effective oversight. We synthesized 5 independent studies of tiger (Panthera tigris) connectivity in central India, a global priority landscape for tiger conservation, to quantify agreement on landscape permeability for tiger movement and potential movement pathways. We used the latter analysis to identify connectivity areas on which studies agreed and stakeholders associated with these areas to determine relevant participants in corridor management. Three or more of the 5 studies' resistance layers agreed in 63% of the study area. Areas in which all studies agree on resistance were of primarily low (66%, e.g., forest) and high (24%, e.g., urban) resistance. Agreement was lower in intermediate resistance areas (e.g., agriculture). Despite these differences, the studies largely agreed on areas with high levels of potential movement: >40% of high average (top 20%) current-flow pixels were also in the top 20% of current-flow agreement pixels (measured by low variation), indicating consensus connectivity areas (CCAs) as conservation priorities. Roughly 70% of the CCAs fell within village administrative boundaries, and 100% overlapped forest department management boundaries, suggesting that people live and use forests within these priority areas. Over 16% of total CCAs' area was within 1 km of linear infrastructure (437 road, 170 railway, 179 transmission line, and 339 canal crossings; 105 mines within 1 km of CCAs). In 2019, 78% of forest land diversions for infrastructure and mining in Madhya Pradesh (which comprises most of the study region) took place in districts with CCAs. Acute competition for land in this landscape with globally important wildlife corridors calls for an effective comanagement strategy involving local communities, forest departments, Appendix 1 and infrastructure planners. This article is protected by copyright. All rights reserved.

Habitat occupancy of sloth bear Melursus ursinus in Chitwan National Park, Nepal

Mammals have experienced a massive decline in their populations and geographic ranges worldwide. The sloth bear, Melursus ursinus (Shaw, 1791), is one of many species facing conservation threats. Despite being endangered in Nepal, decades of inattention to the situation have hindered their conservation and management. We assessed the distribution and patterns of habitat use by sloth bears in Chitwan National Park (CNP), Nepal. We conducted sign surveys from March to June, 2020, in 4 × 4 km grids (n = 45). We collected detection/non-detection data along a 4-km trail that was divided into 20 continuous segments of 200 m each. We obtained environmental, ecological, and anthropogenic covariates to understand determinants of sloth bear habitat occupancy. The data were analyzed using the single-species single-season occupancy method, with a spatially correlated detection. Using repeated observations, these models accounted for the imperfect detectability of the species to provide robust estimates of habitat occupancy. The model-averaged occupancy estimate for the sloth bear was 69% and the detection probability was 0.25. The probability of habitat occupancy by sloth bears increased with the presence of termites and fruits and in rugged, dry, open, undisturbed habitats. Our results indicate that the sloth bear is elusive, functionally unique, and widespread in CNP. Future conservation interventions and action plans aimed at sloth bear management must adequately consider their habitat requirements.

Understanding Species–Habitat Associations: A Case Study with the World’s Bears

Habitat modeling is one of the most common practices in ecology today, aimed at understanding complex associations between species and an array of environmental, bioclimatic, and anthropogenic factors. This review of studies of seven species of terrestrial bears (Ursidae) occupying four continents examines how habitat models have been employed, and the functionality of their predictions for management and conservation. Bear occurrence data have been obtained at the population level, as presence points (e.g., sign surveys or camera trapping), or as locations of individual radio-collared animals. Radio-collars provide greater insights into how bears interact with their environment and variability within populations; they are more commonly used in North America and Europe than in South America and Asia. Salient problematic issues apparent from this review included: biases in presence data; predictor variables being poor surrogates of actual behavioral drivers; predictor variables applied at a biologically inappropriate scale; and over-use of data repositories that tend to detach investigators from the species. In several cases, multiple models in the same area yielded different predictions; new presence data occurred outside the range of predicted suitable habitat; and future range projections, based on where bears presently exist, underestimated their adaptability. Findings here are likely relevant to other taxa.

Assessing Carnivore Occurrence and Community Attitudes Towards Wildlife in a Multi-Use Arid Landscape Corridor

Small population sizes, low densities, and large area requirements make large carnivores particularly sensitive to habitat degradation and land-use change. In fragmented landscapes, many protected areas cannot accommodate viable wildlife populations in themselves, which brings the surrounding human-dominated matrix that may extend wildlife habitats or serve as corridors into focus. Such areas are typically excluded from the conservation portfolio and are subject to rapid land -use change in many areas. This study investigates the occurrence of tigers, sloth bears, leopards and striped hyenas and assesses community use of natural resources and attitudes towards wildlife in a 3,384 km2 portion of semi-arid multiple-use landscape in Western India that also serves as an important wildlife corridor. This area abuts Ranthambore Tiger Reserve, a preeminent protected area in Western India. Sign surveys spanning 1,039.22 km of trails were conducted in 94, 36 km2 grids spanning agricultural land, forests and other land use types to collate information on wildlife occurrence and associated environmental and human factors. Analysis using occupancy models revealed that tiger and sloth bear occurrence probabilities (0.093 ± 0.05), and (0.13 ± 0.02) were considerably lower than those for leopards (0.72 ± 0.22) and striped hyenas (0.91 ± 0.08). Lack of sufficient cover and limited food availability renders these multiple-use habitats poorly suited for tigers and sloth bears, while leopards and hyenas are able to adapt better to multi-use areas. Concurrently, 66 villages were surveyed across the study landscape, where data on broad socio-economic attributes of communities and their attitudes towards wildlife were assessed through questionnaire surveys. More respondents expressed negative attitudes than positive attitudes which vary as a function of education levels, occupation and land holding sizes. Ongoing landscape transformation through mining, agricultural expansion, infrastructure development, and negative attitudes towards wildlife conservation among people living in the agricultural matrix threatens the long-term functionality of these corridors. Therefore, immediate measures are needed to develop and implement corridor conservation strategies and plans, with a focus on land use planning and human-wildlife conflict mitigation. In the absence of decisive and timely action, wildlife populations may increasingly get relegated to fragmented patches, jeopardising their persistence.

Genetic analyses reveal demographic decline and population differentiation in an endangered social carnivore, Asiatic wild dog

Deforestation and agricultural intensification have resulted in an alarming change in the global land cover over the past 300 years, posing a threat to species conservation. Dhole is a monophyletic, social canid and, being an endangered and highly forest-dependent species, is more prone to the loss of favorable habitat in the Anthropocene. We determined the genetic differentiation and demographic history of dhole across the tiger reserves of Maharashtra using the microsatellite data of 305 individuals. Simulation-based analyses revealed a 77-85% decline in the major dhole sub-populations. Protected areas have provided refuge to the historically declining dhole population resulting in clustering with strong genetic structure in the remnant dhole population. The historical population decline coincides with the extreme events in the landscape over the past 300 years. The study highlights the pattern of genetic differentiation and diversity of a highly forest-dependent species which can be associated with the loss of forest cover outside tiger reserves. It also warrants attention to develop conservation plans for the remnant surviving population of dholes in India.

Assessing spatio-temporal patterns of human-leopard interactions based on media reports in northwestern India

Large carnivores in human-use areas make for sensational print media content.  We used media reports to examine human-leopard interactions in Rajasthan, India.  We extracted news reports on leopard-related incidents from January 2016 to December 2018.  Incidents (n= 338) were categorized, mapped, and analysed to understand their nature and extent.  We found leopard-related news from 26 of 33 districts; a majority of these were in the eastern region of the State.  Most of the reported interactions appeared to be non-negative, despite losses to both leopards and people.  Our results provide a synthesis of spatio-temporal patterns of leopard-related incidents, which could help wildlife managers in better addressing negative interactions.  The study also demonstrates how news reports could be useful for examining human-wildlife interactions across large spatial scales.

Evolutionary stability, landscape heterogeneity, and human land-usage shape population genetic connectivity in the Cape Floristic Region biodiversity hotspot

As human-induced change eliminates natural habitats, it impacts genetic diversity and population connectivity for local biodiversity. The South African Cape Floristic Region (CFR) is the most diverse extratropical area for plant biodiversity, and much of its habitat is protected as a UNESCO World Heritage site. There has long been great interest in explaining the underlying factors driving this unique diversity, especially as much of the CFR is endangered by urbanization and other anthropogenic activity. Here, we use a population and landscape genetic analysis of SNP data from the CFR endemic plant Leucadendron salignum or "common sunshine conebush" as a model to address the evolutionary and environmental factors shaping the vast CFR diversity. We found that high population structure, along with relatively deeper and older genealogies, is characteristic of the southwestern CFR, whereas low population structure and more recent lineage coalescence depict the eastern CFR. Population network analyses show genetic connectivity is facilitated in areas of lower elevation and higher seasonal precipitation. These population genetic signatures corroborate CFR species-level patterns consistent with high Pleistocene biome stability and landscape heterogeneity in the southwest, but with coincident instability in the east. Finally, we also find evidence of human land-usage as a significant gene flow barrier, especially in severely threatened lowlands where genetic connectivity has been historically the highest. These results help identify areas where conservation plans can prioritize protecting high genetic diversity threatened by contemporary human activities within this unique cultural UNESCO site.

Gene Flow in Volant Vertebrates: Species Biology, Ecology and Climate Change

Gene flow, the exchange of genetic material between populations is an important biological process, which shapes and maintains biodiversity. The successful movement of individuals between populations depends on multiple factors determined by species biology and the environment. One of the most important factors regulating gene flow is the ability to move, and flight allows individuals to easily move across geographical barriers. Volant vertebrates are found on some of the remotest islands and contribute significantly to the biodiversity and ecosystem. The availability of next-generation sequencing data for non-model animals has substantially improved our understanding of gene flow and its consequences, allowing us to look at fine-scale patterns. However, most of our understanding regarding gene flow comes from the temperate regions and the Neotropics. The lack of studies from species-rich Asia is striking. In this review, we outline the importance of gene flow and the factors affecting gene flow, especially for volant vertebrates. We especially discuss research studies from tropical biomes of South and Southeast Asia, highlight the lacuna in literature and provide an outline for future studies in this species-rich region.

Every hill has its leopard: patterns of space use by leopards (Panthera pardus) in a mixed use landscape in India

Understanding abundance and distribution of species is often necessary for wildlife conservation. However, elusive species such as the leopard (Panthera pardus) that have wide geographical distribution and typically low abundance pose a constant challenge to conservationists due to logistical and methodological constraints. Although leopard abundance has been estimated at the scale of protected areas or other smaller regions, reliable information describing leopard distribution over large spatial scales remains largely unavailable. Knowledge about space use by leopards within landscapes could help improve conservation management, reduce human-wildlife conflict, and also facilitate population status monitoring. We carried out occupancy surveys across c. 24,000 km² in southern India in a landscape that consisted a mosaic of leopards’ natural habitats and highly human-dominated areas. We investigated the effects of key ecological and anthropogenic variables in determining leopard space use patterns. We addressed imperfect detections obtained using sign surveys conducted on spatially replicated transects within sampling units by modeling detection as a function of spatial auto-correlation and covariates. Our results show that the probability of site-use by leopards across the landscape varied between 0.02 (95% CI [0.01–0.09]) and 0.99 (95% CI [0.99–1.0]) across the study area. The best model (AIC weight = 0.97) showed that the probability of leopard space use was affected by the proportion of natural habitats and the presence of large wild prey in the sampling unit. Given that India is undergoing rapid modifications due to economic changes and demand for natural resources, we emphasize the need for landscape-based approach for conserving and monitoring leopards. We argue that leopards are an indicator of functional ecosystems represented by scrub, deciduous forest and rocky outcrops that do not always get prioritized for conservation, unlike densely forested habitats. Similarly, conservation of natural large wild prey, especially outside the protected area system, should assume greater importance, which could also have a positive impact on reducing human-leopard conflict.