@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 {99334, title = {Expansion~of the evolutionarily conserved network of J-domain proteins in the Arabidopsis mitochondrial import complex.}, journal = {Plant Mol Biol}, volume = {105}, year = {2021}, month = {2021 Mar}, pages = {385-403}, abstract = {

KEY MESSAGE: We report that discriminate interaction between the expanded mitochondrial chaperone network and variability in their expression might determine their functional specificities and impart robustness to mitochondrial import processes in plants. Mitochondrial Hsp70 (mtHsp70), the central component of the pre-sequence associated motor (PAM) complex, is crucial for the import of proteins to the mitochondrial matrix. Activity of mtHsp70 is regulated by a heterodimeric complex of two J-domain proteins (JDPs), Pam18 and Pam16. Compared to other eukaryotes, plants harbor multiple copies of these JDPs, which posit that plants have an increasingly complex mtHsp70: JDP\ network in their mitochondrial matrix. Here, we show that although highly similar in sequence, some of the plant JDPs are functionally different. Protein: protein interaction studies including yeast two-hybrid and Bimolecular Fluorescence Complementation revealed that while all the AtPam18s interacted with AtPam16s, the strengths of these promiscuous interactions are variable. Further, down-regulation of\ AtPAM16L affected seed germination, even in the presence of its seemingly identical paralog, AtPAM16. Knockdown of\ AtPAM16L caused reduction in mitochondrial number and deregulation of several mitochondrial genes, suggesting towards a specific role of\ AtPam16L in maintaining mitochondrial homeostasis, especially under stress conditions. Our findings suggest that variations in the spatio-temporal expression, accompanied by discriminate interactions between the JDPs, might be defining the functional specificity of the mtHsp70 co-chaperone machinery and providing resilience to mitochondrial import processes in plants, especially under stress conditions.

}, keywords = {Arabidopsis, Arabidopsis Proteins, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, HSP70 Heat-Shock Proteins, Mitochondria, Mitochondrial Membrane Transport Proteins, Mitochondrial Proteins, Mutation, Plants, Genetically Modified, Protein Binding, Protein Domains, Protein Transport}, issn = {1573-5028}, doi = {10.1007/s11103-020-01095-8}, author = {Tamadaddi, Chetana and Sagar, Vinay and Verma, Amit K and Afsal, Fathima and Sahi, Chandan} } @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} }