Browsing by Author "Waits, Lisette P."
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- 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.
- Feeding ecological knowledge: the underutilised power of faecal DNA approaches for carnivore diet analysisMonterroso, P.; Godinho, R.; Oliveira, T.; Ferreras, P.; Kelly, Marcella J.; Morin, D.J.; Waits, Lisette P.; Alves, P.C.; Mills, L.S. (Blackwell Publishing Ltd, 2018-12-22)Accurate analyses of the diets of predators are key to understand trophic interactions and defining conservation strategies. Diets are commonly assessed through analysis of non-invasively collected scats, and the use of faecal DNA (fDNA) analysis can reduce the species misidentifications that could lead to biased ecological inference. We review the scientific literature since publication of the first paper on amplifying fDNA, in order to assess trends in the use of genetic non-invasive sampling (gNIS) for predator species identification in scat-based diet studies of North American and European terrestrial mammalian carnivores (Carnivora). We quantify error rates in morphology-based predator species identification. We then provide an overview of how applying gNIS would improve research on trophic interactions and other areas of carnivore ecology. We found that carnivore species identity was verified by using gNIS in only 8% of 400 studies of carnivore diets based on scats. The median percentage of false positives (i.e. samples wrongly identified as belonging to the target species) in morphology-based studies was 18%, and was consistent regardless of species’ body size. We did not find an increasing trend in the use of gNIS over time, despite the existing technical capability to identify almost all carnivore species. New directions for fDNA studies include employing high-throughput sequencing (HTS) and DNA metabarcoding to identify the predator species, the individual predator, the entire assemblage of consumed items, and the microbiome of the predator and pathogens. We conclude that HTS protocols and metagenomic approaches hold great promise for elevating gNIS as a fundamental cornerstone for future research in ecology and conservation biology of mammals. © 2018 The Authors. Mammal Review published by Mammal Society and John Wiley & Sons Ltd.
- 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.
- Integrating multiple genetic detection methods to estimate population density of social and territorial carnivoresMurphy, Sean M.; Augustine, Ben C.; Adams, Jennifer R.; Waits, Lisette P.; Cox, John J. (Ecological Society of America, 2018-10)Spatial capture-recapture models can produce unbiased estimates of population density, but sparse detection data often plague studies of social and territorial carnivores. Integrating multiple types of detection data can improve estimation of the spatial scale parameter (sigma), activity center locations, and density. Noninvasive genetic sampling is effective for detecting carnivores, but social structure and territoriality could cause differential detectability among population cohorts for different detection methods. Using three observation models, we evaluated the integration of genetic detection data from noninvasive hair and scat sampling of the social and territorial coyote (Canis latrans). Although precision of estimated density was improved, particularly if sharing sigma between detection methods was appropriate, posterior probabilities of sigma and posterior predictive checks supported different sigma for hair and scat observation models. The resulting spatial capture-recapture model described a scenario in which scat-detected individuals lived on and around scat transects, whereas hair-detected individuals had larger sigma and mostly lived off of the detector array, leaving hair but not scat samples. A more supported interpretation is that individual heterogeneity in baseline detection rates (lambda(0)) was inconsistent between detection methods, such that each method disproportionately detected different population cohorts. These findings can be attributed to the sociality and territoriality of canids: Residents may be more likely to strategically mark territories via defecation (scat deposition), and transients may be more likely to exhibit rubbing (hair deposition) to increase mate attraction. Although this suggests that reliance on only one detection method may underestimate population density, integrating multiple sources of genetic detection data may be problematic for social and territorial carnivores. These data are typically sparse, modeling individual heterogeneity in lambda(0) and/or sigma with sparse data is difficult, and positive bias can be introduced in density estimates if individual heterogeneity in detection parameters that is inconsistent between detection methods is not appropriately modeled. Previous suggestions for assessing parameter consistency of sigma between detection methods using Bayesian model selection algorithms could be confounded by individual heterogeneity in lambda(0) in noninvasive detection data. We demonstrate the usefulness of augmenting those approaches with calibrated posterior predictive checks and plots of the posterior density of activity centers for key individuals.
- A multiscale analysis and quantification of human impacts on Sumatran tiger (Panthera tigris sumatrae) habitat in Riau, SumatraPoor, Erin Elizabeth (Virginia Tech, 2018-09-25)Worldwide, we are losing biodiversity at unprecedented rates, and due to deforestation, degradation and poaching, Southeast Asian wildlife is facing extreme threats. Indonesia recently eclipsed Brazil in having the world's highest deforestation rate, largely due to the rise of the palm oil industry. Indonesia contains multiple biodiversity hotspots and endangered species such as the Sumatran tiger (Panthera tigris sumatrae). While Riau Province, Sumatra, produces approximately 20% of the world's palm oil, tigers still inhabit parts of Riau, though their habitat and prey are understudied. Thus, in this research, I aim to assess and quantify how tiger habitat has changed, how it will continue to change, and provide recommendations on how to improve the landscape for tigers. I create the first accuracy-assessed land cover maps of Riau, and then predict land cover change from 2016 – 2050. Using this newly created land cover map, I assess whether Tesso Nilo National Park, Bukit Tigapuluh National Park, and Rimbang Baling Wildlife Reserve are effective at preventing deforestation. Next, I examine human impacts within Tesso Nilo specifically, due to its suitability for oil palm and its potential as a stepping stone for wildlife movement from the western, mountains to the eastern peatlands of Sumatra. Finally, I examine impacts of human presence within Rimbang Baling on felid-prey relationships. I predict that by 2050, over 60% of natural forest in Riau will be lost, and all protected areas only confer low levels of protection. I determined that Tesso Nilo National Park has nearly 2500 km of roads within it and no areas within the park are untouched by humans. Wildlife detections were low near the boundary of Rimbang Baling and there was evidence of humans negatively impacting mousedeer (Tragulus spp) behavior. I suggest focusing on securing the habitat within Rimbang Baling and Bukit Tigapuluh to ensure habitat for dispersing tigers from the western mountains, in addition to, and perhaps before focusing on restoring Tesso Nilo and creating wildlife corridors. While tiger recovery in Riau will be difficult, with education, dedication, persistence and intelligent planning, tigers may be able to persist in this unique ecosystem in the long-term.
- 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.