Genetic structure of tigers (Panthera tigris tigris) in India and its implications for conservation

Temporal Changes in Tasmanian Devil Genetic Diversity at Sites With and Without Supplementation

Management interventions for threatened species are well documented with genetic data now playing a pivotal role in informing their outcomes. However, in situ actions like supplementations (releasing individuals into an existing population) are often restricted to a singular site. Considerable research and management effort have been dedicated to conserving the Tasmanian devil (Sarcophilus harrisii), offering a unique opportunity to investigate the temporal genetic consequences of supplementation at multiple sites, in comparison to outcomes observed in the absence of management interventions. Using 1,778 genome-wide SNPs across 1,546 individuals, we compared four wild-supplemented sites to four monitoring-only sites (not supplemented; control sites) over 9 years (2014-2022). At the study completion, genetic differentiation among supplemented sites had significantly decreased compared to among not-supplemented sites. We found statistically significant variation in genetic change over time between sites using linear mixed-effects modelling with random slopes. Investigating this among-site variation showed that three of the supplemented sites conformed to predictions that supplementations would have a positive impact on the genetic diversity of devils at these sites. We predicted no change over time at our fourth site due to the observed relatively high gene flow, however, this site did not align with predictions, instead showing decreased genetic diversity and increased relatedness. Amongst not supplemented sites, there was no consistent pattern of temporal genetic change, suggesting devil sites across Tasmania are highly heterogeneous, likely reflecting variation in site connectivity and genetic drift. Our study demonstrates that long-term concurrent monitoring of multiple sites, including controls, is necessary to contextualise the influence of management interventions on natural species fluctuations.

Heterozygosity is low where rare color variants in wild carnivores prevail

Coat color and pattern are a distinguished feature in mammalian carnivores, shaped by climatic cycles and habitat type. It can be expressed in various ways, such as gradients, polymorphisms, and rare color variants. Although natural selection explains much of the phenotypic variation found in the wild, genetic drift and heterozygote deficiency, as prominent in small and fragmented populations, may also affect phenotypic variability through the fixation of recessive alleles. The aim of this study was to test whether rare color variants in the wild could relate to a deficiency of heterozygotes, resulting from habitat fragmentation and small population size. We present an overview of all rare color variants in the order Carnivora, and compiled demographic and genetic data of the populations where they did and did not occur, to test for significant correlations. We also tested how phylogeny and body weight influenced the presence of color variants with phylogenetic generalized linear mixed models (PGLMMs). We found 40 color-variable species and 59 rare color variants. In 17 variable phenotypic populations for which genetic diversity was available, the average A R was 4.18, H O = 0.59, and H E = 0.66, and F IS = 0.086. We found that variable populations displayed a significant reduction in heterozygosity and allelic richness compared to non-variable populations across species. We also found a significant negative correlation between population size and inbreeding coefficients. Therefore, it is possible that small effective size had phenotypic consequences on the extant populations. The high frequency of the rare color variants (averaging 20%) also implies that genetic drift is locally overruling natural selection in small effective populations. As such, rare color variants could be added to the list of phenotypic consequences of inbreeding in the wild.

The tide of tiger poaching in India is rising! An investigation of the intertwined facts with a focus on conservation

Poaching and illegal trafficking are major threats to biodiversity, especially when endangered felids are concerned. Tigers are iconic animals, and there is huge demand for their body parts both in the national and international illegal markets. India forms the largest tiger conservation unit in the world and poaching is at its peak even though there are stringent laws and strict enforcement. In the present study, we analytically estimated the tiger seizure cases in India from 2001-2021 using newspaper archives as the main source of data. The data was geo-referenced to understand the details of seizure, demand, and locality. We statistically correlated the seizure rate with the density of tigers, tiger reserves, and various other socio-economic factors. Our result shows that skin, claws, bones, and teeth have more demand, with nails and teeth being the most preferred in local markets. The bones, flesh, and other parts were mostly seized in the border states of the north and eastern states. The intensity of seizures is very high in the states of Maharashtra, Karnataka, Tamil Nadu, and Assam. From our analysis, we predict four trade routes for the export of the seized parts: the Nepal-Bhutan border, Assam border, the Brahmaputra, and the Mumbai port. This corresponds to the five tiger conservation blocks in India, and we observed the seizure rate is high near the Western Ghats region, which has not yet been noticed. Apart from the seizure, we are unconcerned with the seizure's origin or the local trading routes. The study demonstrates the importance of identifying the source population using DNA methods and carefully enforcing the rules in area of poaching. We assert that current approaches are incapable of resolving the issue and that a more precise and effective forensic procedure capable of resolving the issue at the minute local level is critical for precisely tracing trade channels.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10708-022-10633-4.

How methodological changes have influenced our understanding of population structure in threatened species: insights from tiger populations across India

Unprecedented advances in sequencing technology in the past decade allow a better understanding of genetic variation and its partitioning in natural populations. Such inference is critical to conservation: to understand species biology and identify isolated populations. We review empirical population genetics studies of Endangered Bengal tigers within India, where 60-70% of wild tigers live. We assess how changes in marker type and sampling strategy have impacted inferences by reviewing past studies, and presenting three novel analyses including a single-nucleotide polymorphism (SNP) panel, genome-wide SNP markers, and a whole-mitochondrial genome network. At a broad spatial scale, less than 100 SNPs revealed the same patterns of population clustering as whole genomes (with the exception of one additional population sampled only in the SNP panel). Mitochondrial DNA indicates a strong structure between the northeast and other regions. Two studies with more populations sampled revealed further substructure within Central India. Overall, the comparison of studies with varied marker types and sample sets allows more rigorous inference of population structure. Yet sampling of some populations is limited across all studies, and these should be the focus of future sampling efforts. We discuss challenges in our understanding of population structure, and how to further address relevant questions in conservation genetics. This article is part of the theme issue 'Celebrating 50 years since Lewontin's apportionment of human diversity'.

Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers

Increasing habitat fragmentation leads to wild populations becoming small, isolated, and threatened by inbreeding depression. However, small populations may be able to purge recessive deleterious alleles as they become expressed in homozygotes, thus reducing inbreeding depression and increasing population viability. We used whole-genome sequences from 57 tigers to estimate individual inbreeding and mutation load in a small-isolated and two large-connected populations in India. As expected, the small-isolated population had substantially higher average genomic inbreeding (FROH = 0.57) than the large-connected (FROH = 0.35 and FROH = 0.46) populations. The small-isolated population had the lowest loss-of-function mutation load, likely due to purging of highly deleterious recessive mutations. The large populations had lower missense mutation loads than the small-isolated population, but were not identical, possibly due to different demographic histories. While the number of the loss-of-function alleles in the small-isolated population was lower, these alleles were at higher frequencies and homozygosity than in the large populations. Together, our data and analyses provide evidence of 1) high mutation load, 2) purging, and 3) the highest predicted inbreeding depression, despite purging, in the small-isolated population. Frequency distributions of damaging and neutral alleles uncover genomic evidence that purifying selection has removed part of the mutation load across Indian tiger populations. These results provide genomic evidence for purifying selection in both small and large populations, but also suggest that the remaining deleterious alleles may have inbreeding-associated fitness costs. We suggest that genetic rescue from sources selected based on genome-wide differentiation could offset any possible impacts of inbreeding depression.

High frequency of an otherwise rare phenotype in a small and isolated tiger population

Most endangered species exist today in small populations, many of which are isolated. Evolution in such populations is largely governed by genetic drift. Empirical evidence for drift affecting striking phenotypes based on substantial genetic data are rare. Approximately 37% of tigers (Panthera tigris) in the Similipal Tiger Reserve (in eastern India) are pseudomelanistic, characterized by wide, merged stripes. Camera trap data across the tiger range revealed the presence of pseudomelanistic tigers only in Similipal. We investigated the genetic basis for pseudomelanism and examined the role of drift in driving this phenotype's frequency. Whole-genome data and pedigree-based association analyses from captive tigers revealed that pseudomelanism cosegregates with a conserved and functionally important coding alteration in Transmembrane Aminopeptidase Q (Taqpep), a gene responsible for similar traits in other felid species. Noninvasive sampling of tigers revealed a high frequency of the Taqpep p.H454Y mutation in Similipal (12 individuals, allele frequency = 0.58) and absence from all other tiger populations (395 individuals). Population genetic analyses confirmed few (minimal number) tigers in Similipal, and its genetic isolation, with poor geneflow. Pairwise FST (0.33) at the mutation site was high but not an outlier. Similipal tigers had low diversity at 81 single nucleotide polymorphisms (mean heterozygosity = 0.28, SD = 0.27). Simulations were consistent with founding events and drift as possible drivers for the observed stark difference of allele frequency. Our results highlight the role of stochastic processes in the evolution of rare phenotypes. We highlight an unusual evolutionary trajectory in a small and isolated population of an endangered species.

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.

Recent Evolutionary History of Tigers Highlights Contrasting Roles of Genetic Drift and Selection

Species conservation can be improved by knowledge of evolutionary and genetic history. Tigers are among the most charismatic of endangered species and garner significant conservation attention. However, their evolutionary history and genomic variation remain poorly known, especially for Indian tigers. With 70% of the world's wild tigers living in India, such knowledge is critical. We re-sequenced 65 individual tiger genomes representing most extant subspecies with a specific focus on tigers from India. As suggested by earlier studies, we found strong genetic differentiation between the putative tiger subspecies. Despite high total genomic diversity in India, individual tigers host longer runs of homozygosity, potentially suggesting recent inbreeding or founding events, possibly due to small and fragmented protected areas. We suggest the impacts of ongoing connectivity loss on inbreeding and persistence of Indian tigers be closely monitored. Surprisingly, demographic models suggest recent divergence (within the last 20,000 years) between subspecies and strong population bottlenecks. Amur tiger genomes revealed the strongest signals of selection related to metabolic adaptation to cold, whereas Sumatran tigers show evidence of weak selection for genes involved in body size regulation. We recommend detailed investigation of local adaptation in Amur and Sumatran tigers prior to initiating genetic rescue.

An incentive-based mitigation strategy to encourage coexistence of large mammals and humans along the foothills of Indian Western Himalayas

Escalation of human–wildlife conflict (HWC) is a barrier to the conservation of ecological corridors across the globe. The existing mechanisms to counter HWC are either economically and socially taxing, or ineffective for long-term management. We assessed HWC in the corridor linking the Rajaji and Corbett Tiger Reserves in Uttarakhand, India, and its drivers, along with the benefits derived by local communities from the forest. We designed an innovative incentive-based mitigation mechanism to encourage coexistence of people and wildlife around the corridor. Costs incurred due to conflict and benefits derived from the forest were assessed using semi-structured questionnaire-based personal interviews (n = 757) with representatives from forest dependent households (hh). Fuelwood (1678.7 ± 131 kg hh⁻¹ year⁻¹), fodder (4772 ± 186 kg hh⁻¹ year⁻¹) and green/dry grass (3359 ± 104 kg hh⁻¹ year⁻¹) contributed 3 ± 1%, 6 ± 0.5% and 9 ± 1%, respectively, to the annual income of dependent households. 69% of the households practising agriculture reported crop damage by wild animals, 19% of the households that owned livestock reported livestock loss, and 1.58% reported attack on humans resulting in injuries. The cost incurred due to crop raiding and livestock depredation was US $ 159.83 ± 1.0 hh⁻¹ year⁻¹ and US $ 229.32 ± 34.0 hh⁻¹ year⁻¹, respectively. Crop loss was positively associated with the number of crops grown per season and cultivation of sugarcane, wheat and pulses, and negatively with distance from forest and cultivation of fodder and finger millet. Livestock depredation was negatively associated with distance from forest and positively with number of livestock owned, primarily calves. The accounting profit from cultivating a hectare of land, in the absence of crop depredation by wild animals, was estimated at US $ 3571.84 ha⁻¹ year⁻¹ and US $ 361.44 ha⁻¹ year⁻¹ for the plains and hills, respectively. This value can be used to calculate the payments to be paid to local communities to encourage them to adopt HWC resistant agricultural and pastoralism practices. The net present value of benefits from participating in the payments to encourage coexistence programme for 5 years, discounted at 12%, was US $ 12,875.7 ha⁻¹ for the plains and US $ 1302.9 ha⁻¹ for the hills.