Tigers of Sundarbans in India: is the population a separate conservation unit?

Does Effective Population Size Govern Evolutionary Differences in Telomere Length?

Lengths of telomeres vary by an order of magnitude across mammalian species. Similarly, age- and sex-standardized telomere lengths differ by up to 1 kb (14%) across human populations. How to explain these differences? Telomeres play a central role in senescence and aging, and genes that affect telomere length are likely under weak selection (i.e. telomere length is a trait that is subject to nearly neutral evolution). Importantly, natural selection is more effective in large populations than in small populations. Here, we propose that observed differences in telomere length across species and populations are largely due to differences in effective population sizes. In this perspective, we present preliminary evolutionary genetic evidence supporting this hypothesis and highlight the need for more data.

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’.

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.

Revisiting taxonomic disparities in the genus Naemorhedus: new insights from Indian Himalayan Region

Gorals are distributed in varied ranges of habitats in South and South–East Asia, and the existence of the number of species in the genus Naemorhedus has been greatly debated from time to time. A school of thought supports the presence of three species, while a recent genetic study recognizes five species of goral throughout their distribution range. However, the unavailability of DNA sequences of gorals from India left a gap in understanding the species occurrence in Indian Himalayan Region (IHR). We revisited goral taxonomy by sequencing mitochondrial Cytochrome b gene (∼404 bp) and control region (∼225 bp) of 75 Himalayan gorals from Western and Central Himalayas in India. Based on various species delineating methods, we suggest that Himalayan goral (N. goral) is a highly diverged species and possibly exists into two subspecies, i.e. N. g. bedfordi in Western Himalayas and N. g. goral in the Central Himalayas. We validate the presence of plausibly six species of gorals across the distribution and recognize N. griseus and N. goral are two distinct species considering the observed discrepancy in the available sequences. We also propose that goral populations distributed in Western and Central Himalayas may be considered as two evolutionary significant units (ESUs). This recognition will bring concentrated efforts in further exploring the natural populations and ecological information required for prioritizing conservation and management of Himalayan goral.

Falling "fortresses": Unlocking Governance Entanglements and Shifting Knowledge Paradigms to Counter Climate Change Threats in Biodiversity Conservation

Biodiversity conservation is facing unprecedented challenges at the intersection of rapidly changing climates, widespread ecosystem degradation under the influence of global warming and resultant human tragedies over livelihood, habitation, adaptation and coping needs. These challenges are more acute across biodiversity hotspots in the Global South. This study disentangles the complex interplay to propose alternative paradigms of governance and policy thinking necessary for sustainable biodiversity conservation. Climate change impacts are exposing critical deficiencies of 'scientific forest management' pursued for over a century. For example, recurrent disasters and ecological shifts are increasingly obfuscating cognitive and physical boundaries between the reserve forest and human habitations; putting additional stress on livelihoods which in turn escalate pressures on the forest commons and fuel further conflicts between conservation governance and local communities. Instead of assisting in adaptation, the existing conservation governance mechanisms are producing further conflicts between humans and non-humans; livelihoods and conservation; disaster management and development. Conducted in the Sundarbans Biosphere Reserve -world's largest mangrove forest ecosystem and a climate change hotspot located along the Bay of Bengal across India and Bangladesh -the study finds an urgent need of rethinking and recalibrating biodiversity conservation in the times of climate change. However, institutional and market-based approaches such as promoting ecotourism or mangrove plantations may have little impact in this regard, the study finds. Instead, integrating cultural ecosystem services and co-producing knowledge will be critical to tackle the entanglements of climate change and its impacts on local lives, livelihoods and biodiversity conservation.

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.

Electropsun Polycaprolactone Fibres in Bone Tissue Engineering: A Review

Regeneration of bone tissue requires novel load bearing, biocompatible materials that support adhesion, spreading, proliferation, differentiation, mineralization, ECM production and maturation of bone-forming cells. Polycaprolactone (PCL) has many advantages as a biomaterial for scaffold production including tuneable biodegradation, relatively high mechanical toughness at physiological temperature. Electrospinning produces nanofibrous porous matrices that mimic many properties of natural tissue extracellular matrix with regard to surface area, porosity and fibre alignment. The biocompatibility and hydrophilicity of PCL nanofibres can be improved by combining PCL with other biomaterials to form composite scaffolds for bone regeneration. This work reviews the most recent research on synthesis, characterization and cellular response to nanofibrous PCL scaffolds and the composites of PCL with other natural and synthetic materials for bone tissue engineering.

Tigers of the World: Genomics and Conservation

Of all the big cats, or perhaps of all the endangered wildlife, the tiger may be both the most charismatic and most well-recognized flagship species in the world. The rapidly changing field of molecular genetics, particularly advances in genome sequencing technologies, has provided new tools to reconstruct what characterizes a tiger. Here we review how applications of molecular genomic tools have been used to depict the tiger's ancestral roots, phylogenetic hierarchy, demographic history, morphological diversity, and genetic patterns of diversification on both temporal and geographical scales. Tiger conservation, stabilization, and management are important areas that benefit from use of these genome resources for developing survival strategies for this charismatic megafauna both in situ and ex situ.

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

Despite massive global conservation strategies, tiger populations continued to decline until recently, mainly due to habitat loss, human-animal conflicts, and poaching. These factors are known to affect the genetic characteristics of tiger populations and decrease local effective population sizes. The Terai Arc Landscape (TAL) at the foothills of the Himalaya is one of the 42 source sites of tigers around the globe. Therefore, information on how landscape features and anthropogenic factors affect the fine-scale spatial genetic structure and variation of tigers in TAL is needed to develop proper management strategies for achieving long-term conservation goals. We document, for the first time, the genetic characteristics of this tiger population by genotyping 71 tiger samples using 13 microsatellite markers from the western region of TAL (WTAL) of 1800 km2. Specifically, we aimed to estimate the genetic variability, population structure, and gene flow. The microsatellite markers indicated that the levels of allelic diversity (MNA = 6.6) and genetic variation (Ho = 0.50, HE = 0.64) were slightly lower than those reported previously in other Bengal tiger populations. We observed moderate gene flow and significant genetic differentiation (FST= 0.060) and identified the presence of cryptic genetic structure using Bayesian and non-Bayesian approaches. There was low and significantly asymmetric migration between the two main subpopulations of the Rajaji Tiger Reserve and the Corbett Tiger Reserve in WTAL. Sibship relationships indicated that the functionality of the corridor between these subpopulations may be retained if the quality of the habitat does not deteriorate. However, we found that gene flow is not adequate in view of changing land use matrices. We discuss the need to maintain connectivity by implementing the measures that have been suggested previously to minimize the level of human disturbance, including relocation of villages and industries, prevention of encroachment, and banning sand and boulder mining in the corridors.

Estimating the Population Size and Genetic Diversity of Amur Tigers in Northeast China

Over the past century, the endangered Amur tiger (Panthera tigris altaica) has experienced a severe contraction in demography and geographic range because of habitat loss, poaching, and prey depletion. In its historical home in Northeast China, there appears to be a single tiger population that includes tigers in Southwest Primorye and Northeast China; however, the current demographic status of this population is uncertain. Information on the abundance, distribution and genetic diversity of this population for assessing the efficacy of conservation interventions are scarce. We used noninvasive genetic detection data from scats, capture-recapture models and an accumulation curve method to estimate the abundance of Amur tigers in Northeast China. We identified 11 individual tigers (6 females and 5 males) using 10 microsatellite loci in three nature reserves between April 2013 and May 2015. These tigers are confined primarily to a Hunchun Nature Reserve along the border with Russia, with an estimated population abundance of 9–11 tigers during the winter of 2014–2015. They showed a low level of genetic diversity. The mean number of alleles per locus was 2.60 and expected and observed heterozygosity were 0.42 and 0.49, respectively. We also documented long-distance dispersal (~270 km) of a male Amur tiger to Huangnihe Nature Reserve from the border, suggesting that the expansion of neighboring Russian populations may eventually help sustain Chinese populations. However, the small and isolated population recorded by this study demonstrate that there is an urgent need for more intensive regional management to create a tiger-permeable landscape and increased genetic connectivity with other populations.

Estimation of Male Gene Flow: Use Caution

Because male gene flow cannot easily be estimated directly in many organisms, Hedrick et al. (2013) provided an approach to estimate male gene flow given estimates of diploid nuclear and female differentiation. This approach appears to work well when there is lower female than male gene flow. However, in a tiger data set there was less female differentiation observed as estimated by mitochondrial DNA than expected given the observed overall nuclear diploid differentiation. To analyze these data, we suggest an alternative approach which allows incorporation of sex-specific gene flow and sex-specific effective population size. We find that the pattern of differentiation observed in tigers was consistent with a lower male than female effective population size using this alternative approach. Further, this finding is consistent with observed data in tigers where the male effective population size was 33% that of the female effective population size.