@article {149386, title = {Divergence and serial colonization shape genetic variation and define conservation units in Asian elephants.}, journal = {Curr Biol}, year = {2024}, month = {2024 Sep 27}, abstract = {

Asian elephants (Elephas maximus) are the largest extant terrestrial megaherbivores native to Asia, with 60\% of their wild population found in India. Despite ecological and cultural importance, their population genetic structure and diversity, demographic history, and ensuing implications for management/conservation remain understudied. We analyzed 34 whole genomes (between 11{\texttimes} and 32{\texttimes}) from most known elephant landscapes in India and identified five management/conservation units corresponding to elephants in Northern (Northwestern/Northeastern), Central, and three in Southern India. Our data reveal signatures of divergence and serial colonization and a potential dilution of genetic diversity from north to south of India. The northern populations diverged from others more than 70,000 years ago, have higher genetic diversity, and have low inbreeding (pi\ = 0.0016\ {\textpm} 0.0001; F\ = 0.09\ {\textpm} 0.03). Two of three populations in Southern India have low diversity and are inbred, with very low effective population sizes compared with census sizes (pi\ = 0.0014\ {\textpm} 0.00009 and 0.0015\ {\textpm} 0.0001; F\ = 0.25\ {\textpm} 0.09 and 0.17\ {\textpm} 0.02). Analyses of genetic load reveal the purging of potentially high-effect insertion/deletion (indel) deleterious alleles in the southern populations and a decreasing number of deleterious alleles from north to south in India. However, despite dilution and purging for the damaging mutation load in Southern India, the load that remains is homozygous. High homozygosity of deleterious alleles, coupled with low neutral genetic diversity, make southernmost populations high priority for conservation attention. Most surprisingly, our study suggests that patterns of genetic diversity and genetic load can correspond to genomic signatures of serial founding events, even in large, highly mobile, endangered mammals.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2024.08.062}, author = {Khan, Anubhab and Sil, Maitreya and Thekaekara, Tarsh and Garg, Kritika M and Sinha, Ishani and Khurana, Rupsy and Sukumar, Raman and Ramakrishnan, Uma} } @article {95761, title = {Considerations for Initiating a Wildlife Genomics Research Project in South and South-East Asia}, journal = {JOURNAL OF THE INDIAN INSTITUTE OF SCIENCE}, year = {2021}, month = {07/2021}, abstract = {

Next-generation sequencing (NGS) based genomic studies are revolutionizing the field of wildlife biology. These methods have yielded unprecedented insights for understanding ecology, evolution and conservation of wild populations. Despite the advantages, biodiversity rich regions in the tropics need more NGS-based studies to understand their native species. However, the field has progressed very slowly in these regions due to several challenges, including that most experts in the field are not based here. In this article, we highlight the factors that need to be considered before initiating a wildlife genomics research project with a focus on south and south-east Asia, though several factors apply to other regions as well. We highlight the challenges like policy issues for collecting samples and need for better sequencing and computational infrastructure. Finally, we discuss how global initiatives can help such regions setup NGS-based studies of wildlife.

}, doi = {10.1007/s41745-021-00243-3}, author = {Khan, Anubhab and Tyagi, Abhinav} } @article {103406, title = {Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers.}, journal = {Proc Natl Acad Sci U S A}, volume = {118}, year = {2021}, month = {2021 Dec 07}, abstract = {

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 ( = 0.57) than the large-connected ( = 0.35 and = 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.

}, issn = {1091-6490}, doi = {10.1073/pnas.2023018118}, author = {Khan, Anubhab and Patel, Kaushalkumar and Shukla, Harsh and Viswanathan, Ashwin and van der Valk, Tom and Borthakur, Udayan and Nigam, Parag and Zachariah, Arun and Jhala, Yadavendradev V and Kardos, Marty and Ramakrishnan, Uma} } @article {103405, title = {Recapitulating whole genome based population genetic structure for Indian wild tigers through an ancestry informative marker panel}, journal = { Heredity (Edinb)}, year = {2021}, month = {12/2021}, abstract = {

Identification of genetic structure within wildlife populations have implications in their conservation and management. Accurately inferring population genetic structure requires whole-genome data across the geographical range of the species, which can be resource-intensive. A cheaper strategy is to employ a subset of markers that can efficiently recapitulate the population genetic structure inferred by the whole genome data. Such ancestry informative markers (AIMs), have rarely been developed for endangered species such as tigers utilizing single nucleotide polymorphisms (SNPs). Here, we first identify the population structure of the Indian tiger using whole-genome sequences and then develop an AIMs panel with a minimum number of SNPs that can recapitulate this structure. We identified four population clusters of Indian tigers with North-East, North-West, and South Indian tigers forming three separate groups, and Terai and Central Indian tigers forming a single cluster. To evaluate the robustness of our AIMs, we applied it to a separate dataset of tigers from across India. Out of 92 SNPs present in our AIMs panel, 49 were present in the new dataset. These 49 SNPs were sufficient to recapitulate the population genetic structure obtained from the whole genome data. To the best of our knowledge, this is the first-ever SNP-based AIMs panel for big cats, which can be used as a cost-effective alternative to whole-genome sequencing for detecting the biogeographical origin of Indian tigers. Our study can be used as a guideline for developing an AIMs panel for the management of other endangered species where obtaining whole genome sequences are difficult.

}, doi = {10.1038/s41437-021-00477-y}, author = {Khan, Anubhab and Krishna, S.M. and Ramakrishnan, Uma and Das, Ranajit} } @article {89659, title = {Recent evolutionary history of tigers highlights contrasting roles of genetic drift and selection.}, journal = {Mol Biol Evol}, year = {2021}, month = {2021 Feb 16}, abstract = {

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 remains poorly known, especially for Indian tigers. With 70\% of the worlds 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, while 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.

}, issn = {1537-1719}, doi = {10.1093/molbev/msab032}, author = {Armstrong, Ellie E and Khan, Anubhab and Taylor, Ryan W and Gouy, Alexandre and Greenbaum, Gili and Thi{\'e}ry, Alexandre and Kang, Jonathan T L and Redondo, Sergio A and Prost, Stefan and Barsh, Gregory and Kaelin, Christopher and Phalke, Sameer and Chugani, Anup and Gilbert, Martin and Miquelle, Dale and Zachariah, Arun and Borthakur, Udayan and Reddy, Anuradha and Louis, Edward and Ryder, Oliver A and Jhala, Y V and Petrov, Dmitri and Excoffier, Laurent and Hadly, Elizabeth and Ramakrishnan, Uma} }