Browsing by Author "Thapa, Kanchan"
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- Assessing global patterns in mammalian carnivore occupancy and richness by integrating local camera trap surveysRich, Lindsey N.; Davis, Courtney L.; Farris, Zachary J.; Miller, David A. W.; Tucker, Jody M.; Hamel, Sandra; Farhadinia, Mohammad S.; Steenweg, Robin; Di Bitetti, Mario S.; Thapa, Kanchan; Kane, Mamadou D.; Sunarto, Sunarto; Robinson, Nathaniel P.; Paviolo, Agustin; Cruz, Paula; Martins, Quinton; Gholikhani, Navid; Taktehrani, Atieh; Whittington, Jesse; Widodo, Febri A.; Yoccoz, Nigel G.; Wultsch, Claudia; Harmsen, Bart J.; Kelly, Marcella J. (2017-08)Aim: Biodiversity loss is a major driver of ecosystem change, yet the ecological data required to detect and mitigate losses are often lacking. Recently, camera trap surveys have been suggested as a method for sampling local wildlife communities, because these observations can be collated into a global monitoring network. To demonstrate the potential of camera traps for global monitoring, we assembled data from multiple local camera trap surveys to evaluate the interchange between fine- and broad-scale processes impacting mammalian carnivore communities. Location: Argentina, Belize, Botswana, Canada, Indonesia, Iran, Madagascar, Nepal, Norway, Senegal, South Africa, and the U.S.A. Methods: We gathered camera trap data, totalling >100,000 trap nights, from across five continents. To analyse local and species-specific responses to anthropogenic and environmental variables, we fitted multispecies occurrence models to each study area. To analyse global-level responses, we then fitted a multispecies, multi-area occurrence model. Results: We recorded 4,805 detections of 96 mammalian carnivore species photographed across 1,714 camera stations located in 12 countries. At the global level, our models revealed that carnivore richness and occupancy within study areas was positively associated with prey availability. Occupancy within study areas also tended to increase with greater protection and greater distances to roads. The strength of these relationships, however, differed among countries. Main conclusions: We developed a research framework for leveraging global camera trap data to evaluate patterns of mammalian carnivore occurrence and richness across multiple spatial scales. Our research highlights the importance of intact prey populations and protected areas in conserving carnivore communities. Our research also highlights the potential of camera traps for monitoring wildlife communities and provides a case study for how this can be achieved on a global scale. We encourage greater integration and standardization among camera trap studies worldwide, which would help inform effective conservation planning for wildlife populations both locally and globally.
- Assessment of genetic diversity, population structure, and gene flow of tigers (Panthera tigris tigris) across Nepal's Terai Arc LandscapeThapa, Kanchan; Manandhar, Sulochana; Bista, Manisha; Shakya, Jivan; Sah, Govind; Dhakal, Maheshwar; Sharma, Netra; Llewellyn, Bronwyn; Wultsch, Claudia; Waits, Lisette P.; Kelly, Marcella J.; Hero, Jean-Marc; Hughes, Jane; Karmacharya, Dibesh (PLOS, 2018-03-21)With fewer than 200 tigers (Panthera tigris tigris) left in Nepal, that are generally confined to five protected areas across the Terai Arc Landscape, genetic studies are needed to provide crucial information on diversity and connectivity for devising an effective country-wide tiger conservation strategy. As part of the Nepal Tiger Genome Project, we studied landscape change, genetic variation, population structure, and gene flow of tigers across the Terai Arc Landscape by conducting Nepal's first comprehensive and systematic scat-based, non-invasive genetic survey. Of the 770 scat samples collected opportunistically from five protected areas and six presumed corridors, 412 were tiger (57%). Out of ten microsatellite loci, we retain eight markers that were used in identifying 78 individual tigers. We used this data set to examine population structure, genetic variation, contemporary gene flow, and potential population bottlenecks of tigers in Nepal. We detected three genetic clusters consistent with three demographic sub-populations and found moderate levels of genetic variation (H-e = 0.61, A(R) = 3.51) and genetic differentiation (F-ST = 0.14) across the landscape. We detected 3-7 migrants, confirming the potential for dispersal-mediated gene flow across the landscape. We found evidence of a bottleneck signature likely caused by large-scale land-use change documented in the last two centuries in the Terai forest. Securing tiger habitat including functional forest corridors is essential to enhance gene flow across the landscape and ensure long-term tiger survival. This requires cooperation among multiple stakeholders and careful conservation planning to prevent detrimental effects of anthropogenic activities on tigers.
- Ecological correlates of the spatial co-occurrence of sympatric mammalian carnivores worldwideDavis, Courtney L.; Rich, Lindsey N.; Farris, Zachary J.; Kelly, Marcella J.; Di Bitetti, Mario S.; Di Blanco, Yamil; Albanesi, Sebastian; Farhadinia, Mohammad S.; Gholikhani, Navid; Hamel, Sandra; Harmsen, Bart J.; Wultsch, Claudia; Kane, Mamadou D.; Martins, Quinton; Murphy, Asia J.; Steenweg, Robin; Sunarto, Sunarto; Taktehrani, Atieh; Thapa, Kanchan; Tucker, Jody M.; Whittington, Jesse; Widodo, Febri A.; Yoccoz, Nigel G.; Miller, David A. W. (2018-09)The composition of local mammalian carnivore communities has far-reaching effects on terrestrial ecosystems worldwide. To better understand how carnivore communities are structured, we analysed camera trap data for 108087 trap days across 12 countries spanning five continents. We estimate local probabilities of co-occurrence among 768 species pairs from the order Carnivora and evaluate how shared ecological traits correlate with probabilities of co-occurrence. Within individual study areas, species pairs co-occurred more frequently than expected at random. Co-occurrence probabilities were greatest for species pairs that shared ecological traits including similar body size, temporal activity pattern and diet. However, co-occurrence decreased as compared to other species pairs when the pair included a large-bodied carnivore. Our results suggest that a combination of shared traits and top-down regulation by large carnivores shape local carnivore communities globally.
- Ecology of Tigers in Churia Habitat and a Non-Invasive Genetic Approach to Tiger Conservation in Terai Arc, NepalThapa, Kanchan (Virginia Tech, 2014-10-13)Tigers (Panthera tigris tigris) can be viewed as a proxy for intact and healthy ecosystems. Their wild populations have plummeted to fewer than 3,200 individuals in the last four decades and threats to these apex predators are mounting rather than diminishing. Global conservation bodies (Global Tiger Initiative, World Wildlife Fund, Wildlife Conservation Society, Panthera etc.) have recently called for solidarity and scaling up of conservation efforts to save tigers from extinction. In South Asia, tiger habitat ranges from tropical evergreen forests, dry arid regions and sub-tropical alluvial floodplains, to temperate mixed deciduous forest. The churia habitat is relatively unstudied and is considered a young and geologically fragile mountain range in Nepal. The contribution of the churia habitat to tiger conservation has not been considered, since modern conservation started in 1970's. This study focuses on the ecology of the tiger with respect to population density, habitat use, and prey occupancy and density, in the churia habitat of Chitwan National Park. This study also includes the first assessment of genetic diversity, genetic structure, and gene flow of tigers across the Terai Arc Landscape- Nepal. The Terai Arc Landscape harbors the only remaining tiger population found across the foothills of the Himalayas in Nepal and northwest India. I used a combination of camera-trapping techniques, which have been a popular and robust method for monitoring tiger populations across the landscape, combined with a noninvasive genetic approach to gain information on tigers, thus adding new information relevant to global tiger conservation. I investigated tiger, leopard (Panthera pardus fusca), and prey densities, and predicted the tiger density across the Churia habitat in Chitwan National Park. I used a camera-trap grid with 161 locations accumulating 2,097 trap-nights in a 60 day survey period during the winter season of 2010-2011. Additionally, I used distance sampling techniques for estimating prey density in the churia habitat by walking 136 km over 81 different line transects. The team photographed 31 individual tigers and 28 individual leopards along with 25 mammalian species from a sampling area of 536 km² comprising Churia and surrounding areas. Density estimates of tigers and leopards were 2.2 (SE 0.42) tigers and 4.0 (SE 1.00) leopards per 100 km². Prey density was estimated at 62.7 prey animals per 100 km² with contributions from forest ungulates to be 47% (sambar Rusa unicolor, chital Axis axis, barking deer Muntiacus muntjak, and wild pigs Sus scrofa). Churia habitat within Chitwan National Park is capable of supporting 5.86 tigers per 100 km² based on applying models developed to predict tiger density from prey density. My density estimates from camera-traps are lower than that predicted based on prey availability, which indicates that the tiger population may be below the carrying capacity. Nonetheless, the churia habitat supports 9 to 36 tigers, increasing estimates of current population size in Chitwan National Park. Based on my finding, the Churia habitat should no longer remain ignored because it has great potential to harbor tigers. Conservation efforts should focus on reducing human disturbance to boost prey populations to potentially support higher predator numbers in Churia. I used sign surveys within a rigorous occupancy framework to estimate probability of occupancy for 5 focal prey species of the tiger (gaur Bos gaurus, sambar, chital, wild pig, and barking deer); as well as probability of tiger habitat use within 537 km² of churia habitat in Chitwan National Park. Multi-season, auto-correlation models allowed me to make seasonal (winter versus summer) inferences regarding changes in occupancy or habitat use based on covariates influencing occupancy and detection. Sambar had the greatest spatial distribution across both seasons, occupying 431-437 km² of the churia habitat, while chital had the lowest distribution, occupying only 100-158 km². The gaur population showed the most seasonal variation from 318- 413 km² of area occupied, with changes in occupancy suggesting their migration out of the lowland areas in the summer and into the churia in the winter. Wild pigs showed the opposite, moving into the churia in the summer (444 km² area occupied) and having lower occupancy in the winter (383 km²). Barking deer were widespread in both seasons (329 - 349 km²). Tiger probability of habitat use Ψ SE(Ψ) was only slightly higher in winter 0.63 (SE 0.11) than in summer 0.54 (SE 0.21), but confidence intervals overlapped and area used was very similar across seasons, from 337 - 291 km². Fine-scale variation in tiger habitat use showed that tigers intensively use certain areas more often than others across the seasons. The proportion of available habitat positively influenced occupancy for the majority of prey species and tigers. Human disturbance had a strong negative influence on the distribution of the majority of prey species but was positively related to tiger habitat use. Tigers appear to live in areas with high disturbance, thus increasing the risk of human-tiger conflict in the churia habitat. Thus, efforts to reduce human disturbance would be beneficial to reducing human wildlife conflict, enriching prey populations, and would potentially support more tigers in churia habitat of Nepal. Overall, I found high prey occupancy and tiger habitat use, suggesting that the churia is highly valuable habitat for tigers and should no longer be neglected or forgotten in tiger conservation planning. Thirdly, I assessed genetic variation, genetic structure, and gene flow of the tigers in the Terai Arc Landscape, Nepal. I opportunistically collected 770 scat samples from 4 protected areas and 5 hypothesized corridors across the Terai Arc Landscape. Historical landuse change in the Terai Arc was extracted from Anthrome data sets to relate landuse change to potential barriers and subsequent hypothesized bottleneck events in the landscape. I used standard genetic metrics (allelic diversity and heterozygosity) to estimate genetic variation in the tiger population. Using program Structure (non-spatial) and TESS (spatial), I defined the putative genetic clusters present in the landscape. Migrant analysis was carried out in Geneclass and Bayesass for estimating contemporary gene flow. I tested for a recent population bottleneck with the heterozygosity test using program Bottleneck. Of the 700 samples, 396 were positive for tiger (57% success). Using an 8 multilocus microsatellite assay, I identified 78 individual tigers. I found large scale landuse changes across the Terai Arc Landscape due to conversion of forest into agriculture in last two centuries and I identified areas of suspected barriers. I found low levels of genetic variation (expected heterozygosity = 0.61) and moderate genetic differentiation (FST = 0.14) across the landscape, indicative of sub-population structure and potential isolation of sub-populations. I detected three genetic clusters across the landscape consistent with three demographic tiger sub-populations occurring in Chitwan-Parsa, Bardia, and Suklaphanta protected areas. I detected 10 migrants across all study sites confirming there is still some dispersal mediated gene flow across the landscape. I found evidence of a bottleneck signature, especially around the lowland forests in the Terai, likely caused by large scale landuse change in last two centuries, which could explain the low levels of genetic variation detected at the sub-population level. These findings are highly relevant to tiger conservation indicating that efforts to protect source sites and to improve connectivity are needed to augment gene flow and genetic diversity across the landscape. Finally, I compared the abundance and density of tigers obtained using two non-invasive sampling techniques: camera-trapping and fecal DNA sampling. For cameras: I pooled the 2009 camera-trap data from the core tiger population across the lowland areas of Chitwan National Park. I sampled 359 km² of the core area with 187 camera-trap locations spending 2,821 trap-nights of effort. I obtained 264 identifiable photographs and identified a total of 41 individual tigers. For genetics, I sampled 325 km² of the core area along three spatial routes, walking a total of 1,173 km, collecting a total of 420 tiger fecal samples in 2011. I identified 36 tigers using the assay of 8 multilocus genotypes and captured them 42 times. I analyzed both data types separately for estimating density and jointly in an integrated model using both traditional, and spatial, capture-recapture frameworks. Using Program MARK and the model averaged results, my abundance estimates were 46 (SE 1.86) and 44 (SE 9.83) individuals from camera and genetic data, respectively. Density estimates (tigers per 100 km²) via traditional buffer strip methods using half of the Mean Maximum Distance Moved (½ MMDM) as the buffer surrounding survey grids, were 4.01 (SE 0.64) for camera data and 3.49 (SE 1.04) for genetic data. Spatially explicit capture recapture models resulted in lower density estimates both in the likelihood based program DENSITY at 2.55 (SE 0.59) for camera-trap data and 2.57 (SE 0.88) for genetic data, while the Bayesian based program SPACECAP estimates were 2.44 (SE 0.30) for camera-trap data and 2.23 (SE 0.46) for genetic data. Using a spatially explicit, integrated model that combines data from both cameras and genetics, density estimates were 1.47 (SD 0.20) tigers per 100 km² for camera-trap data and 1.89 (SD 0.36) tigers per 100 km² for genetic data. I found that the addition of camera-trap data improved precision in genetic capture-recapture estimates, but not visa-versa, likely due to low numbers of recaptures in the genetic data. While a non-invasive genetic approach can be used as a stand-alone capture-recapture method, it may be necessary to increase sample size to obtain more recaptures. Camera-trap data may provide a more precise estimates, but genetic data returns more information on other aspect of genetic health and connectivity. Combining data sets in an integrated modeling framework, aiding in pinpointing strengths and weaknesses in data sets, thus ultimately improving modeling inference.
- Elephant (Elephas maximus) temporal activity, distribution, and habitat use patterns on the tiger's forgotten trails across the seasonally dry, subtropical, hilly Churia forests of NepalThapa, Kanchan; Kelly, Marcella J.; Pradhan, Narendra Man Babu (PLOS, 2019-05-13)Understanding spatial distribution, habitat use, and temporal activity patterns is important for species conservation planning. This information especially is crucial for mega herbivores like elephants as their ranging patterns encompass a myriad of habitats types. Churia habitat is geological fragile yet important for wildlife in Nepal and India. We used camera trapping and sign surveys covering 536 km(2) of Churia and surrounding areas within Chitwan National Park. Across 152 trapping locations, we accumulated 2,097 trap nights in a 60-day survey during the winter season of 2010-11. We used a non-parametric kernel density function to analyze winter activity patterns of elephants detected in camera-traps. Additionally, we walked 643 km over 76 grid cells in two surveys (winter and summer) to estimate elephant distribution and intensity of habitat use using an occupancy framework. Multi-season models allowed us to make seasonal (winter versus summer) inferences regarding changes in habitat use based on covariates influencing use and detection. We photographed 25 mammalian species including elephants with calves with a trapping rate of 2.72 elephant photos events per 100 trap nights. Elephant winter activity pattern was found to be mainly nocturnal, with crepuscular peaks. Covariates such as normalized differential vegetation index and terrain ruggedness positively influenced elephant spatial distribution and habitat use patterns within the Churia habitat. We also found lower elephant habitat use ((Psi) over cap SE((Psi) over cap)) of Churia in winter 0.51 (0.02) than in summer 0.57 (0.02). Elephants heavily used the eastern portion of Churia in both seasons (67-69%). Overall, Churia habitat, which is often ignored, clearly is used by elephants, with increases in summer use in the west and high use year-round in the east, and thus should no longer be neglected or forgotten in species conservation planning.
- Gut microbiota and their putative metabolic functions in fragmented Bengal tiger population of NepalKarmacharya, Dibesh; Manandhar, Prajwol; Manandhar, Sulochana; Sherchan, Adarsh M.; Sharma, Ajay N.; Joshi, Jyoti; Bista, Manisha; Bajracharya, Shailendra; Awasthi, Nagendra P.; Sharma, Netra; Llewellyn, Bronwyn; Waits, Lisette P.; Thapa, Kanchan; Kelly, Marcella J.; Vuyisich, Momchilo; Starkenburg, Shawn R.; Hero, Jean-Marc; Hughes, Jane; Wultsch, Claudia; Bertola, Laura; Fountain-Jones, Nicholas M.; Sinha, Amit K. (PLOS, 2019-08-29)Bengal tigers (Panthera tigris tigris) serve a pivotal role as an apex predator in forest ecosystems. To increase our knowledge on factors impacting the viability and health of this endangered species, we studied the gut microbiota in 32 individual Bengal tigers from three geographically separated areas (Chitwan National Park (CNP), Bardia National Park (BNP) and Suklaphanta Wildlife Reserve (SWR)) in Nepal, using noninvasive genetic sampling methods. Gut microbiota influence the immune system, impact various physiological functions, and modulates metabolic reactions, that ultimately impact the host health, behavior and development. Across the tiger populations in Nepal, we found significant differences in the composition of microbial communities based on their geographic locations. Specifically, we detected significant differences between CNP and the other two protected areas (CNP vs BNP: pseudo t = 1.944, P = 0.006; CNP vs SWR: pseudo t = 1.9942, P = 0.0071), but no differences between BNP and SWR. This mirrors what has been found for tiger gene flow in the same populations, suggesting gut microbiota composition and host gene flow may be linked. Furthermore, predictive metagenome functional content analysis (PICRUSt) revealed a higher functional enrichment and diversity for significant gut microbiota in the Chitwan tiger population and the lowest enrichment and diversity in Suklaphanta. The CNP tiger population contained higher proportions of microbiota that are associated with predicted functions relevant for metabolism of amino acid, lipid, xenobiotics biodegradation, terpenoides and polyketides than the SWR population. We conclude the tiger population structure, gut microbiota profile and associated functional metabolic categories are correlated, with geographically most separated CNP and SWR tiger population having the most distinct and different host genotype and microbiota profiles. Our work dramatically expands the understanding of tiger microbiota in wild populations and provides a valuable case study on how to investigate genetic diversity at different hierarchical levels, including hosts as well as their microbial communities.
- Leopard Panthera pardus fusca Density in the Seasonally Dry, Subtropical Forest in the Bhabhar of Terai Arc, NepalThapa, Kanchan; Shrestha, Rinjan; Karki, Jhamak; Thapa, Gokarna Jung; Subedi, Naresh; Pradhan, Narendra Man Babu; Dhakal, Maheshwar; Khanal, Pradeep; Kelly, Marcella J. (Hindawi, 2014-07-16)We estimated leopard (Panthera pardus fusca) abundance and density in the Bhabhar physiographic region in Parsa Wildlife Reserve, Nepal. The camera trap grid, covering sampling area of 289 km2 with 88 locations, accumulated 1,342 trap nights in 64 days in the winter season of 2008-2009 and photographed 19 individual leopards. Using models incorporating heterogeneity, we estimated 28 (±SE 6.07) and 29.58 (±SE 10.44) leopards in Programs CAPTURE and MARK. Density estimates via 1/2 MMDM methods were 5.61 (±SE 1.30) and 5.93 (±SE 2.15) leopards per 100 km2 using abundance estimates from CAPTURE and MARK, respectively. Spatially explicit capture recapture (SECR) models resulted in lower density estimates, 3.78 (±SE 0.85) and 3.48 (±SE 0.83) leopards per 100 km2, in likelihood based program DENSITY and Bayesian based program SPACECAP, respectively. The 1/2 MMDM methods have been known to provide much higher density estimates than SECR modelling techniques. However, our SECR models resulted in high leopard density comparable to areas considered better habitat in Nepal indicating a potentially dense population compared to other sites. We provide the first density estimates for leopards in the Bhabhar and a baseline for long term population monitoring of leopards in Parsa Wildlife Reserve and across the Terai Arc.
- On the tiger trails: Leopard occupancy decline and leopard interaction with tigers in the forested habitat across the Terai Arc Landscape of NepalThapa, Kanchan; Malla, Sabita; Subba, Samundra Ambuhang; Thapa, Gokarna Jung; Lamichhane, Babu Ram; Subedi, Naresh; Dhakal, Maheshwar; Acharya, Krishna Prasad; Thapa, Madhuri Karki; Neupane, Pramod; Poudel, Shashank; Bhatta, Shiv Raj; Jnawali, Shant Raj; Kelly, Marcella J. (2021-01)Better conservation planning requires updated information about leopard distribution to prioritize and allocate limited resources available. The long-term persistence of leopards and sympatric tigers can be compromised by linear infrastructure development such as roads that fragment habitat. We used detection and non-detection data collected along walking search paths (similar to 4140 km) in 96 grid cells (each cell 15 km by 15 km) spread across potential habitat (similar to 13,845 km(2)) in the Terai Arc Landscape, Nepal. Multi-season occupancy models allowed us to make both spatial and temporal inferences between two surveys in 2009 and 2013, based on ecologically relevant covariates recorded in the field or remotely sensed. Additionally, we used 2013 data to make inferences on co-occurrence between tigers and leopards at the landscape level. We found the additive model containing deforestation and district roads negatively influenced leopard detection across the landscape. Although weak, we found anthropogenic factors such as extent of deforestation (decrease in forest cover) negatively affected leopard occupancy. Road abundance, especially for the east-west highway and district roads, also negatively (but weakly) influenced leopard occupancy. We found substantially lower occupancy in the year 2013 (0.59 (SE 0.06)) than in 2009 (0.86 (SE 0.04)). Tigers and leopards co-occurred across the landscape based on the species interaction factor (SIF) estimated at 1.47 (0.13) but the amount of available habitat and the prey index mediated co-occurrence. The SIF decreased as habitat availability increased, reaching independence at large habitat patches, but leopard occupancy declined in sites with tigers, primarily in large patches. The prey index was substantially lower outside of protected areas and leopards and tigers co-occurred more strongly in small patches and at low prey indices, indicating potential attraction to the same areas when prey is scarce. Mitigation measures should focus on preventing loss of critical leopard, tiger, and prey habitat through appropriate wildlife-friendly underpasses and avoiding such habitat when building infrastructure. Leopard conservation has received lower priority than tigers, but our metrics show a large decline in leopard occupancy, thus conservation planning to reverse this decline should focus on measures to facilitate human-leopard coexistence to ensure leopard persistence across the landscape.