Browsing by Author "Wultsch, Claudia"
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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.
- A Comparative Analysis of Genetic Diversity and Structure in Jaguars (Panthera onca), Pumas (Puma concolor), and Ocelots (Leopardus pardalis) in Fragmented Landscapes of a Critical Mesoamerican Linkage ZoneWultsch, Claudia; Waits, Lisette P.; Kelly, Marcella J. (PLOS, 2016-03-14)With increasing anthropogenic impact and landscape change, terrestrial carnivore populations are becoming more fragmented. Thus, it is crucial to genetically monitor wild carnivores and quantify changes in genetic diversity and gene flow in response to these threats. This study combined the use of scat detector dogs and molecular scatology to conduct the first genetic study on wild populations of multiple Neotropical felids coexisting across a fragmented landscape in Belize, Central America. We analyzed data from 14 polymorphic microsatellite loci in 1053 scat samples collected from wild jaguars (Panthera onca), pumas (Puma concolor), and ocelots (Leopardus pardalis). We assessed levels of genetic diversity, defined potential genetic clusters, and examined gene flow for the three target species on a countrywide scale using a combination of individual- and population-based analyses. Wild felids in Belize showed moderate levels of genetic variation, with jaguars having the lowest diversity estimates (HE = 0.57 ± 0.02; AR = 3.36 ± 0.09), followed by pumas (HE = 0.57 ± 0.08; AR = 4.20 ± 0.16), and ocelots (HE = 0.63 ± 0.03; AR = 4.16 ± 0.08). We observed low to moderate levels of genetic differentiation for all three target species, with jaguars showing the lowest degree of genetic subdivision across the country, followed by ocelots and pumas. Although levels of genetic diversity and gene flow were still fairly high, we detected evidence of fine-scale genetic subdivision, indicating that levels of genetic connectivity for wild felids in Belize are likely to decrease if habitat loss and fragmentation continue at the current rate. Our study demonstrates the value of understanding fine-scale patterns of gene flow in multiple co-occurring felid species of conservation concern, which is vital for wildlife movement corridor planning and prioritizing future conservation and management efforts within human-impacted landscapes.
- Determining habitat and biotic factors driving puma (Puma concolor) space use and underlying dynamic processes (colonization and extinction) over 20 years in protected and private areas throughout Belize, Central AmericaMcPhail, Darby K. (Virginia Tech, 2024-07-01)Despite being a top carnivore, there is relatively scant information on pumas (Puma concolor) in the neotropics especially compared to the more well-studied jaguar (Panthera onca). Understanding long-term puma distribution can affect land management decisions such as appropriate size of buffer zones around protected areas since pumas influence, and are influenced by, sympatric carnivore populations, lower trophic levels, and habitat. We used single-species, single-season and multi-season occupancy modeling to explore factors influencing distribution and persistence of pumas across the country of Belize. We used camera trapping data from 7 protected areas over 20 years with 2,198 camera stations covering ~5,000 km2. For both approaches, detection was mostly affected by distance to roads, enhanced vegetation index (EVI), and elevation, with variable directionality depending on site. In single season modeling, Occupancy increased at lower elevations and intermediate EVI in one site, and closer to water sources at another, while in multi-season modeling, intermediate EVI and canopy cover influenced occupancy. Biotic covariates were highly variable across sites and methods, but detection and occupancy were generally positively associated with prey, jaguar and ocelot trap rates, canopy cover, and elevation, while human trap rates negatively affected occupancy at one site. Colonization was positively affected by deer (Odocoileus virginianus and Mazama americana) trap rates while extinction had no supported covariates. Puma occupancy ranged from 0.41-0.96 in single season models and 0.55-0.90 in multi-season models across all site/years. Compared to other single-season studies, Belize generally had higher occupancy, even in areas of selective logging, however there are no other multi-season studies to compare. While sites with heavy human impacts had lowest occupancy, these areas are still used and likely serve as steppingstones between protected areas of higher occupancy. Such areas could be targets for protection to preserve landscape connectivity. Additionally, due to high occupancy and colonization across varying habitat and biotic factors the jaguar is likely an effective umbrella species for puma space use, however more analysis on other species is needed to ensure efficiency for more than just pumas.
- 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.
- 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.
- Long‐term monitoring of ocelot densities in BelizeSatter, Christopher B.; Augustine, Ben C.; Harmsen, Bart J.; Foster, Rebecca J.; Sanchez, Emma E.; Wultsch, Claudia; Davis, Miranda L.; Kelly, Marcella J. (The Wildlife Society, 2019-01)Ocelots (Leopardus pardalis) are listed as least concern on the International Union for Conservation of Nature (IUCN) Red list of Threatened Species, yet we lack knowledge on basic demographic parameters across much of the ocelot's geographic range, including population density. We used camera‐trapping methodology and spatially explicit capture‐recapture (SECR) models with sex‐specific detection function parameters to estimate ocelot densities across 7 field sites over 1 to 12 years (from data collected during 2002–2015) in Belize, Central America. Ocelot densities in the broadleaf rainforest sites ranged between 7.2 and 22.7 ocelots/100 km2, whereas density in the pine (Pinus spp.) forest site was 0.9 ocelots/100 km2. Applying an inverse‐variance weighted average over all years for each broadleaf site increased precision and resulted in average density ranging from 8.5 to 13.0 ocelots/100 km2. Males often had larger movement parameter estimates and higher detection probabilities at their activity centers than females. In most years, the sex ratio was not significantly different from 50:50, but the pooled sex ratio estimated using an inverse weighted average over all years indicated a female bias in 1 site, and a male bias in another. We did not detect any population trends as density estimates remained relatively constant over time; however, the power to detect such trends was generally low. Our SECR density estimates were lower but more precise than previous estimates and indicated population stability for ocelots in Belize.
- Noninvasive tracking of jaguars (Panthera onca) and co-occurring Neotropical felids in Belize, Central America by genotyping feces and remote camera trappingWultsch, Claudia (Virginia Tech, 2013-04-30)The elusive jaguar (Panthera onca) is extremely difficult to study due to its wide-ranging behavior, crepuscular activity peaks and its occurrence in low population densities in often dense forest habitats. Jaguars are also a species of concern, but our ability to provide for their survival is hampered by our inability to obtain reliable information on the status of their wild populations. This study combines innovative noninvasive research techniques such as scat detector dogs and molecular scatology to conduct the first genetic study on wild populations of Neotropical felids coexisting across fragmented forest habitats in Belize, Central America. Specifically, we analyzed multi-locus data in jaguars (Panthera onca), pumas (Puma concolor) and ocelots (Leopardus pardalis) collected from 1053 scat samples across their range in the country. First, we optimized 14 polymorphic microsatellite loci for jaguars (Panthera onca), pumas (Puma concolor), and ocelots (Leopardus pardalis), and assessed their utility for cross-species amplification. Additionally, we tested their reliability for species and individual identification using fecal DNA as he primary DNA source. All microsatellite loci examined successfully cross-amplified in the three target species, and were polymorphic. Second, to maximize PCR amplification success and genotyping accuracy rates, and to minimize genotyping error rates for fecal DNA samples, we evaluated the performance of two fecal DNA storage techniques (dimethyl sulfoxide saline solution/DET buffer, 95% EtOH) suitable for long-term preservation at remote tropical sites. Additionally, we tested fecal DNA samples collected from four different scat locations (top, side, bottom, inside). DET buffer was the superior fecal DNA preservation method and collecting fecal DNA from side and top locations of the scat resulted in the highest PCR success rates. For the main genetic study, we assessed the genetic conservation status of all three target species across the country of Belize. We examined levels of genetic diversity within different sites, (2) defined potential genetic clusters/populations, (3) and examined levels of gene flow and population structure for all three target species on a countrywide scale. Furthermore, we compared genetic diversity and gene flow levels among the three target species. Wild felids in Belize showed moderate levels of heterozygosity (HE = 0.60 - 0.70) with jaguars having the lowest genetic diversity with average expected heterozygosities of HE = 0.60 ± 0.05 and allelic richness (AR) of 4.94 ± 0.44 followed by pumas with HE = 0.65 ± 0.06 and AR of 7.52 ± 0.86 and ocelots with HE = 0.70 ± 0.05 and AR of 3.89 ± 0.23. We observed low to moderate levels of differentiation (FST = 0.00 - 0.15) and weak population structure using spatial Bayesian clustering techniques for all three target species. Although levels of genetic diversity and gene flow across the country are still fairly high, we did detect evidence of fragmentation indicating the risk of further habitat loss and fragmentation for wild felids. Felids were simultaneously monitored across all study sites by remote sensing camera traps, which allows for a comparison of density estimates obtained from two different noninvasive survey approaches. Furthermore, analytical methods for density estimation are advancing rapidly, making it difficult to choose the optimal technique. Thus, we compared a variety of density estimators including the conventional approach of estimating abundance ( ) in programs CAPTURE and MARK and dividing abundance by the effective trapping area (ETA), the recently developed spatially explicit capture-recapture (SECR) models, both the likelihood-based approach (ML-SECR) in program DENSITY and the Bayesian approach (B-SECR) in program SPACECAP, and finally the genetic-based mark-recapture one sampling occasion estimator in program CAPWIRE. Although different survey methods using various density estimators produced similar density estimates, confidence levels and coefficients of variation varied, with SECR methods resulting in the least precise estimates. Detection probabilities were generally higher for noninvasive genetic sampling than for camera trapping. Both techniques were shown to be reliable and highly efficient survey methods for density estimation of low-density Neotropical felids living in challenging environments such as the tropics. While less precise, SECR CMR models are probably a more realistic reflection of our uncertainty. They hold great promise for density estimation studies for wide-ranging and territorial carnivore species, especially if precision can be improved through study design or analysis advancements in the future. In conclusion, our results demonstrated that noninvasive sampling techniques such as molecular scatology and remote camera trapping are efficient research approaches to study multiple Neotropical felids in a multifaceted way and on a countrywide scale. We believe that the techniques and analyses developed in this study are widely applicable and relevant to the conservation and management of other elusive and difficult to study wild felids worldwide.
- Species, sex and geo-location identification of seized tiger (Panthera tigris tigris) parts in Nepal—A molecular forensic approachKarmacharya, Dibesh; Sherchan, Adarsh M.; Dulal, Santosh; Manandhar, Prajwol; Manandhar, Sulochana; Joshi, Jyoti; Bhattarai, Susmita; Bhatta, Tarka R.; Awasthi, Nagendra P.; Sharma, Ajay N.; Bista, Manisha; Silwal, Nawa R.; Pokharel, Pravin; Lamichhane, Rom R.; Sharma, Netra; Llewellyn, Bronwyn; Wultsch, Claudia; Kelly, Marcella J.; Gour, Digpal; Waits, Lisette P.; Hero, Jean-Marc; Hughes, Jane (PLOS, 2018-08-23)Tiger (Panthera tigris) populations are in danger across their entire range due to habitat loss, poaching and the demand for tiger parts. The Bengal tiger (Panthera tigris tigris) is an endangered apex predator with a population size estimated to be less than 200 in Nepal. In spite of strict wildlife protection laws, illegal trade of tiger parts is increasing; and Nepal has become one of the major sources and transit routes for poached wildlife parts. Identification of wildlife parts is often challenging for law enforcement officials due to inadequate training and lack of available tools. Here, we describe a molecular forensic approach to gain insight into illegally trafficked tiger parts seized across Nepal. We created Nepal’s first comprehensive reference genetic database of wild tigers through the Nepal Tiger Genome Project (2011–2013). This database has nuclear DNA microsatellite genotype and sex profiles, including geo-spatial information, of over 60% (n = 120) of the wild tigers of Nepal. We analyzed 15 putative cases of confiscated poached tiger parts and all were confirmed to be of tiger. Ten samples were identified as male and five were female. We determined probable geo-source location for 9 of the 14 samples with 6–8 nuclear DNA microsatellite loci using inferences from four different statistical assignment methods. Six samples were assigned to Bardia National Park and one of these was an exact match to a female tiger previously profiled in our fecal DNA reference database. Two tiger samples were assigned to Shuklaphanta Wildlife Reserve and one to Chitwan National Park. We are unable to definitively assign five tiger samples which could be offspring dispersers or might have come from tiger population outside of Nepal. Our study revealed that the western region, particularly Bardia National Park, is a poaching hotspot for illegal tiger trade in Nepal. We present feasibility of using molecular forensic based evidence to incriminate criminals in a court of law in the fight against wildlife crime.
- Wild carnivore habitat use and community ecology in a biodiversity hotspot and human-wildlife conflict with pumas and dogs across ChileOsorio Popiolek, Christian Thomaz (Virginia Tech, 2021-05-21)Habitat loss and fragmentation and human-wildlife conflicts, often resulting in retaliatory killing in response to livestock predation, are one of the main threats to wild felids worldwide, including pumas (Puma concolor). However, mesocarnivores are more abundant than large carnivores, live closer to human settlements, and drive community structure and processes in similar or different ways from large predators. Understanding both large and small carnivores' habitat use is key to their conservation and management. Thus, there is need to explore the ecological roles of predators (including invasive ones like free-ranging dogs [Canis lupus familiaris] and cats [Felis catus]) to examine how ecological context modulates the ecological roles of carnivores . This is especially important in my study area, which was severely burned by a catastrophic mega-wildfire in 2017. I used dynamic occupancy modeling of human-wildlife conflict (HWC) across 52 provinces for 8 years in Chile and found that free-ranging dogs outpace pumas in livestock depredation, killing substantially more livestock than pumas. Occupancy models show that HWC occurrence for both dogs and pumas increased with sheep density. Unexpectedly, dog HWC decreased with anthropogenic habitat degradation indicating that dogs may travel far to prey on livestock. The emergence of puma HWC in a site where it did not occur in the previous year was positively associated with anthropic disturbance. Countrywide, dogs HWC occurrence probability was higher than pumas in 43 out of the 49 provinces where both species occurred. I discuss livestock vulnerability, management strategies, and policy to mitigate HWC, and also highlight threats that free-ranging dogs pose to biodiversity conservation and even human public health. I also used single-species, single-season occupancy models fit to camera-trap data to investigate the patterns of site occupancy and response to mega-wildfires of native mesocarnivores in southern-central Chile: guignas (Leopardus guigna), culpeo foxes (Lycalopex culpaeus) and chilla foxes (Lycalopex griseus). I found that vulnerable guignas avoided burned sites, preferring sites with native, dense vegetation while culpeo foxes were intermediate in being able to use plantations, but avoiding burned sites. Chilla foxes were most tolerant to landscape change with no response to burns and were found closer to human habitation and rivers. Finally, I used two-species, single season occupancy models, and Kernel Density Estimation on circular data, to investigate the spatial and temporal dynamics, and overlap of native and exotic carnivores. I found that feral cats are a potential threat to pumas, guignas, and native foxes given they overlap extensively in time of activity with these species. Also, feral dogs had the widest distribution of all species indicating that their effects could be ubiquitous on the landscape. Thus, exotic species are damaging to wildlife, to livestock industry, and even to public health. I urge dialog between government authorities, wildlife managers, and scientists to generate a legal and public policy framework to properly managing habitat and HWC in southern-central Chile.