@article {109678, title = {How methodological changes have influenced our understanding of population structure in threatened species: insights from tiger populations across India.}, journal = {Philos Trans R Soc Lond B Biol Sci}, volume = {377}, year = {2022}, month = {2022 Jun 06}, pages = {20200418}, abstract = {

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 {\textquoteright}Celebrating 50 years since Lewontin{\textquoteright}s apportionment of human diversity{\textquoteright}.

}, keywords = {Animals, Conservation of Natural Resources, Endangered Species, Genetic Variation, Genetics, Population, India, Prospective Studies, Tigers}, issn = {1471-2970}, doi = {10.1098/rstb.2020.0418}, author = {Aylward, Megan and Sagar, Vinay and Natesh, Meghana and Ramakrishnan, Uma} } @article {99113, title = {High frequency of an otherwise rare phenotype in a small and isolated tiger population.}, journal = {Proc Natl Acad Sci U S A}, volume = {118}, year = {2021}, month = {2021 Sep 28}, abstract = {

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 () 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{\textquoteright}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 (), 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 F (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.

}, issn = {1091-6490}, doi = {10.1073/pnas.2025273118}, author = {Sagar, Vinay and Kaelin, Christopher B and Natesh, Meghana and Reddy, P Anuradha and Mohapatra, Rajesh K and Chhattani, Himanshu and Thatte, Prachi and Vaidyanathan, Srinivas and Biswas, Suvankar and Bhatt, Supriya and Paul, Shashi and Jhala, Yadavendradev V and Verma, Mayank M and Pandav, Bivash and Mondol, Samrat and Barsh, Gregory S and Swain, Debabrata and Ramakrishnan, Uma} } @article {95517, title = {Trends in Wildlife Connectivity Science from the Biodiverse and Human-Dominated South Asia}, journal = {JOURNAL OF THE INDIAN INSTITUTE OF SCIENCE}, year = {2021}, month = {06/2021}, abstract = {

The threat of habitat fragmentation and population isolation looms large over much of biodiversity in this human-dominated epoch. Species-rich South Asia is made particularly vulnerable by its high human density and anthropogenic habitat modification. Therefore, reliably estimating wildlife connectivity and the factors underpinning it become crucial in mitigating extinction risk due to isolation. We analysed peer-reviewed literature on connectivity and corridors for terrestrial mammals in South Asia to identify trends in connectivity research. We identify key research gaps and highlight future directions that may aid efforts to robustly study connectivity. We found a significant bias towards charismatic megafauna and their habitats. Methodologically, although we observed a range of approaches reflecting some of the advances and innovations in the field, several studies lacked data on animal movement/behaviour, leading to potentially biased inferences of how species disperse through human-modified landscapes. New avenues for connectivity research, though currently under-explored in South Asia, offer alternatives to the heavily used but less-reliable habitat suitability models. We highlight the advantages of landscape genetic methods that reflect effective dispersal and are made feasible through non-invasive and increasingly more cost-effective sampling methods. We also identify important gaps or areas of focus that need to be addressed going forward, including accounting for animal movement/behaviour, human impacts and landscape change for dynamic and adaptive connectivity planning for the future.

}, doi = {10.1007/s41745-021-00240-6}, author = {Thatte, Prachi and Tyagi, Abhinav and Neelakantan, Amrita and Natesh, Meghana and Sen, Mihika and Thekaekara, Tarsh} } @article {65295, title = {Empowering conservation practice with efficient and economical genotyping from poor quality samples.}, journal = {Methods Ecol Evol}, volume = {10}, year = {2019}, month = {2019 Jun}, pages = {853-859}, abstract = {

Moderate- to high-density genotyping (100 + SNPs) is widely used to determine and measure individual identity, relatedness, fitness, population structure and migration in wild populations.However, these important tools are difficult to apply when high-quality genetic material is unavailable. Most genomic tools are developed for high-quality DNA sources from laboratory or medical settings. As a result, most genetic data from market or field settings is limited to easily amplified mitochondrial DNA or a few microsatellites.To enable genotyping in conservation contexts, we used next-generation sequencing of multiplex PCR products from very low-quality DNA extracted from faeces, hair and cooked samples. We demonstrated utility and wide-ranging potential application in endangered wild tigers and tracking commercial trade in Caribbean queen conch.We genotyped 100 SNPs from degraded tiger samples to identify individuals, discern close relatives and detect population differentiation. Co-occurring carnivores do not amplify (e.g. Indian wild dog/dhole) or are monomorphic (e.g. leopard). Sixty-two SNPs from conch fritters and field-collected samples were used to test relatedness and detect population structure.We provide proof of concept for a rapid, simple, cost-effective and scalable method (for both samples and number of loci), a framework that can be applied to other conservation scenarios previously limited by low-quality DNA samples. These approaches provide a critical advance for wildlife monitoring and forensics, open the door to field-ready testing, and will strengthen the use of science in policy decisions and wildlife trade.

}, issn = {2041-210X}, doi = {10.1111/2041-210X.13173}, author = {Natesh, Meghana and Taylor, Ryan W and Truelove, Nathan K and Hadly, Elizabeth A and Palumbi, Stephen R and Petrov, Dmitri A and Ramakrishnan, Uma} } @article {25708, title = {Conservation priorities for endangered Indian tigers through a genomic lens.}, journal = {Sci Rep}, volume = {7}, year = {2017}, month = {2017 Aug 29}, pages = {9614}, abstract = {

Tigers have lost 93\% of their historical range worldwide. India plays a vital role in the conservation of tigers since nearly 60\% of all wild tigers are currently found here. However, as protected areas are small (\<300 km(2) on average), with only a few individuals in each, many of them may not be independently viable. It is thus important to identify and conserve genetically connected populations, as well as to maintain connectivity within them. We collected samples from wild tigers (Panthera tigris tigris) across India and used genome-wide SNPs to infer genetic connectivity. We genotyped 10,184 SNPs from 38 individuals across 17 protected areas and identified three genetically distinct clusters (corresponding to northwest, southern and central India). The northwest cluster was isolated with low variation and high relatedness. The geographically large central cluster included tigers from central, northeastern and northern India, and had the highest variation. Most genetic diversity (62\%) was shared among clusters, while unique variation was highest in the central cluster (8.5\%) and lowest in the northwestern one (2\%). We did not detect signatures of differential selection or local adaptation. We highlight that the northwest population requires conservation attention to ensure persistence of these tigers.

}, issn = {2045-2322}, doi = {10.1038/s41598-017-09748-3}, author = {Natesh, Meghana and Atla, Goutham and Nigam, Parag and Jhala, Yadvendradev V and Zachariah, Arun and Borthakur, Udayan and Ramakrishnan, Uma} }