Fine-scale population genetic structure of the Bengal tiger (Panthera tigris tigris) in a human-dominated western Terai Arc Landscape, India

Female-biased introductions produce higher predicted population size and genetic diversity in simulations of a small, isolated tiger (Panthera tigris) population

Isolation of wildlife populations represents a key conservation challenge in the twenty-first century. This may necessitate consideration of translocations to ensure population viability. We investigated the potential population and genetic trajectory of a small, isolated tiger (Panthera tigris) population in Thailand's Dong Phayayen-Khao Yai forest complex across a range of scenarios. Using an individual-based, spatially-explicit population modelling approach, we simulate population and genetic trajectories and evaluate the relative impact of translocations from a related population. Population and genetic trajectories in our study were most sensitive to sex and number of individuals translocated and translocation frequency. Translocation of females produced consistently higher population, allelic richness, and heterozygosity compared to equal numbers of males. Despite population increases, declines in allelic richness and heterozygosity across simulations were stark, with simulations predicting a mean decline of allelic richness and heterozygosity of 46.5% and 53.5% without intervention, respectively. Translocations of four females every generation or every other generation were required to prevent substantial heterozygosity declines. While translocations could increase population size, they may fail to prevent long-term loss of genetic diversity in small populations unless applied frequently. This reinforces the importance of incorporating realistic processes of genetic inheritance and gene flow in modelling small populations.

DNA matchmaking in captive facilities: a case study with tigers

BACKGROUND

Genetics driven interventions if adopted in conservation breeding projects may enhance the overall success by prioritizing breeding among genetically most competent individuals and delaying or completely diminishing the ill effects of inbreeding.

METHODS AND RESULTS

In the present study, we investigated genetic make-up of 15 tigers housed at five different captive facilities of West Bengal in India and report the moderate level of genetic variation. We identified five tigers based on individual genetic attributes that may be prioritized for future breeding or animal exchange programmes. The occurrence of first and second order related individuals in captivity require management attention and they should be paired considering their immediate genetic background.

CONCLUSION

Considering tiger as a case study, we highlight the use of genetic assessment and necessity to validate the studbook records in formulating adaptive management strategies for long-term conservation and management of species of interest.

Whole genome survey of big cats (Genus: Panthera) identifies novel microsatellites of utility in conservation genetic study

Big cats (Genus: Panthera) are among the most threatened mammal groups of the world, owing to hunting, habitat loss, and illegal transnational trade. Conservation genetic studies and effective curbs on poaching are important for the conservation of these charismatic apex predators. A limited number of microsatellite markers exists for Panthera species and researchers often cross-amplify domestic cat microsatellites to study these species. We conducted data mining of seven Panthera genome sequences to discover microsatellites for conservation genetic studies of four threatened big cat species. A total of 32 polymorphic microsatellite loci were identified in silico and tested with 152 big cats, and were found polymorphic in most of the tested species. We propose a set of 12 novel microsatellite markers for use in conservation genetics and wildlife forensic investigations of big cat species. Cumulatively, these markers have a high discriminatory power of one in a million for unrelated individuals and one in a thousand for siblings. Similar PCR conditions of these markers increase the prospects of achieving efficient multiplex PCR assays. This study is a pioneering attempt to synthesise genome wide microsatellite markers for big cats.

Microsatellite characterization and development of unified STR panel for big cats in captivity: a case study from a Seoul Grand Park Zoo, Republic of Korea

The zoos manage small populations of endangered big cat species like tiger, lion, and leopard for display, research, and conservation breeding. Genetic management of these populations is essential to ensure long term survival and conservation utility. Here we propose a simple and cost effective microsatellite based protocol for the genetic management of captive big cats. We sampled 36 big cat individuals from Seoul Grand Park Zoo (Republic of Korea) and amplified 33 published microsatellite loci. Overall, allelic richness and gene diversity was found highest for leopards, followed by lions and tigers. Twelve of the thirty-three markers showed a high degree of polymorphism across all target species. These microsatellites provide a high degree of discrimination for tiger (1.45 × 10^-8), lion (1.54 × 10^-10), and leopard (1.88 × 10^-12) and thus can be adopted for the genetic characterization of big cats in accredited zoos globally. During captive breeding, zoo authorities rely on pedigree records maintained in studbooks to ensure mating of genetically fit unrelated individuals. Several studies have reported errors in studbook records of big cat species. Microsatellites are simple and cost effective tool for DNA fingerprinting, estimation of genetic diversity, and paternity assessment. Our unified microsatellite panel (12-plex) for big cats is efficient and can easily be adopted by zoo authorities for regular population management.

Noninvasive sampling reveals population genetic structure in the Royle's pika, Ochotona roylei, in the western Himalaya

Understanding population genetic structure of climate-sensitive herbivore species is important as it provides useful insights on how shifts in environmental conditions can alter their distribution and abundance. Herbivore responses to the environment can have a strong indirect cascading effect on community structure. This is particularly important for Royle's pika (Lagomorpha: Ochotona roylei), a herbivorous talus-dwelling species in alpine ecosystem, which forms a major prey base for many carnivores in the Himalayan arc. In this study, we used seven polymorphic microsatellite loci to detect evidence for recent changes in genetic diversity and population structure in Royle's pika across five locations sampled between 8 and 160 km apart in the western Himalaya. Using four clustering approaches, we found the presence of significant contemporary genetic structure in Royle's pika populations. The detected genetic structure could be primarily attributed to the landscape features in alpine habitat (e.g., wide lowland valleys, rivers) that may act as semipermeable barriers to gene flow and distribution of food plants, which are key determinants in spatial distribution of herbivores. Pika showed low inbreeding coefficients (F IS) and a high level of pairwise relatedness for individuals within 1 km suggesting low dispersal abilities of talus-dwelling pikas. We have found evidence of a recent population bottleneck, possibly due to effects of environmental disturbances (e.g., snow melting patterns or thermal stress). Our results reveal significant evidence of isolation by distance in genetic differentiation (F ST range = 0.04-0.19). This is the first population genetics study on Royle's pika, which helps to address evolutionary consequences of climate change which are expected to significantly affect the distribution and population dynamics in this talus-dwelling species.

Species, sex and geo-location identification of seized tiger (Panthera tigris tigris) parts in Nepal-A molecular forensic approach

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.

Assessment of fine-scale resource selection and spatially explicit habitat suitability modelling for a re-introduced tiger (Panthera tigris) population in central India

BACKGROUND

Large carnivores influence ecosystem functions at various scales. Thus, their local extinction is not only a species-specific conservation concern, but also reflects on the overall habitat quality and ecosystem value. Species-habitat relationships at fine scale reflect the individuals' ability to procure resources and negotiate intraspecific competition. Such fine scale habitat choices are more pronounced in large carnivores such as tiger (Panthera tigris), which exhibits competitive exclusion in habitat and mate selection strategies. Although landscape level policies and conservation strategies are increasingly promoted for tiger conservation, specific management interventions require knowledge of the habitat correlates at fine scale.

METHODS

We studied nine radio-collared individuals of a successfully reintroduced tiger population in Panna Tiger Reserve, central India, focussing on the species-habitat relationship at fine scales. With 16 eco-geographical variables, we performed Manly's selection ratio and K-select analyses to define population-level and individual-level variation in resource selection, respectively. We analysed the data obtained during the exploratory period of six tigers and during the settled period of eight tigers separately, and compared the consequent results. We further used the settled period characteristics to model and map habitat suitability based on the Mahalanobis D² method and the Boyce index.

RESULTS

There was a clear difference in habitat selection by tigers between the exploratory and the settled period. During the exploratory period, tigers selected dense canopy and bamboo forests, but also spent time near villages and relocated village sites. However, settled tigers predominantly selected bamboo forests in complex terrain, riverine forests and teak-mixed forest, and totally avoided human settlements and agriculture areas. There were individual variations in habitat selection between exploratory and settled periods. Based on threshold limits of habitat selection by the Boyce Index, we established that 83% of core and 47% of buffer areas are now suitable habitats for tiger in this reserve.

DISCUSSION

Tiger management often focuses on large-scale measures, but this study for the first time highlights the behaviour and fine-scale individual-specific habitat selection strategies. Such knowledge is vital for management of critical tiger habitats and specifically for the success of reintroduction programs. Our spatially explicit habitat suitability map provides a baseline for conservation planning and optimizing carrying capacity of the tiger population in this reserve.