@article {164005, title = {EMBO Press co-evolves with molecular ecology and evolutionary biology.}, journal = {EMBO J}, year = {2026}, month = {2026 Feb 18}, issn = {1460-2075}, doi = {10.1038/s44318-026-00723-1}, url = {https://pubmed.ncbi.nlm.nih.gov/41708875/}, author = {Moran, Yehu and Coelho, Susana M and Ettema, Thijs J G and Feschotte, Cedric and Kaltenpoth, Martin and Khila, Abderrahman and Laine, Anna-Liisa and Liow, Lee Hsiang and Petrov, Dmitri and Ramakrishnan, Uma and Sarkies, Peter and Srivastava, Mansi and Voolstra, Christian and Pulverer, Bernd} } @article {162686, title = {Conservation Genomics-Making a Difference.}, journal = {Mol Ecol}, volume = {34}, year = {2025}, month = {2025 Dec}, pages = {e70191}, abstract = {

Conservation genomics has increasingly transitioned from a promising concept to a science that integrates a range of advanced analytical approaches, providing new insights into inbreeding, genetic load, demographic history and adaptive divergence in species of conservation concern. Yet, questions remain about how effectively these advances translate into practical conservation action. This Special Issue, Conservation Genomics-Making a Difference, brings together 37 papers that collectively assess how genomic data are contributing to conservation science and management. The contributions encompass empirical studies, reviews, and perspectives that together demonstrate how genomic tools are now used to identify management units, quantify inbreeding, analyse inbreeding depression, reveal adaptive variation, forecast genomic vulnerability under climate change, and guide genetic rescue and assisted migration. Several papers show direct integration of genomics into conservation planning, including fisheries management, guiding restoration of endangered or habitat-forming species, and monitoring of genetic indicators under the Convention on Biological Diversity. Others highlight emerging questions in conservation, such as the significance of structural variation, and the genomic basis of invasiveness. However, persistent challenges remain, notably in bridging the gap between research and policy, uneven global distribution of genomic resources, and translating complex analyses into practical management advice. Nevertheless, the advances presented in the 37 papers show that conservation genomics is moving beyond its early theoretical and technical focus towards real-world applications. The field is maturing and is increasingly fulfilling its promise to make a real difference for populations, species, and ecosystems.

}, keywords = {Animals, Conservation of Natural Resources, Endangered Species, Genetics, Population, Genomics, Inbreeding}, issn = {1365-294X}, doi = {10.1111/mec.70191}, author = {Hansen, Michael M and Edwards, Christine and Grossen, Christine and Kardos, Marty and Laikre, Linda and Ramakrishnan, Uma} } @article {160477, title = {Conservation: Sequencing and saving the Saola?}, journal = {Curr Biol}, volume = {35}, year = {2025}, month = {2025 Sep 22}, pages = {R878-R880}, abstract = {

The Critically Endangered Saola is a unique and cryptic Asian member of the cattle family. A new study analyses its genome, identifying evolutionary affinities, genetic variation and a possible path for conservation through captive breeding. But saving the Saola from extinction will require much more.

}, keywords = {Animals, Cattle, Conservation of Natural Resources, Endangered Species, Genetic Variation, Genome}, issn = {1879-0445}, doi = {10.1016/j.cub.2025.07.086}, author = {Ramakrishnan, Uma} } @article {161128, title = {Exceedingly low genetic diversity in snow leopards due to persistently small population size.}, journal = {Proc Natl Acad Sci U S A}, volume = {122}, year = {2025}, month = {2025 Oct 14}, pages = {e2502584122}, abstract = {

Snow leopards () serve as an umbrella species whose conservation benefits their high-elevation Asian habitat. Their numbers are believed to be in decline due to numerous anthropogenic threats; however, their conservation is hindered by numerous knowledge gaps. In particular, the dearth of genetic data, unique among all big cat species, hinders a full understanding of their population structure, historical population size, and current levels of genetic diversity. Here, we use whole-genome sequencing data for 41 snow leopards (37 newly sequenced) to offer insights into these unresolved aspects of snow leopard biology. Among our samples, we find evidence of a primary genetic divide between the northern and southern part of the range around the Dzungarian Basin-as previously identified using landscape models and fecal microsatellite markers-and a secondary divide south of Kyrgyzstan around the Taklamakan Desert. Most noteworthy, we find that snow leopards have the lowest genetic diversity of any big cat species, likely due to a persistently small population size throughout their evolutionary history rather than recent inbreeding. We also find that snow leopards have significantly less highly deleterious homozygous load compared to numerous species, suggesting effective purging during their evolutionary history at small population sizes. Without a large population size or ample standing genetic variation to help buffer them from any forthcoming anthropogenic challenges, snow leopard persistence may be more tenuous than currently appreciated.

}, keywords = {Animals, Conservation of Natural Resources, Ecosystem, Felidae, Genetic Variation, Microsatellite Repeats, Panthera, Population Density}, issn = {1091-6490}, doi = {10.1073/pnas.2502584122}, author = {Solari, Katherine A and Morgan, Simon and Poyarkov, Andrey D and Weckworth, Byron and Samelius, Gustaf and Sharma, Koustubh and Ostrowski, Stephane and Ramakrishnan, Uma and Kubanychbekov, Zairbek and Kachel, Shannon and Johansson, {\"O}rjan and Lkhagvajav, Purevjav and Hemmingmoore, Heather and Alexandrov, Dmitry Y and Bayaraa, Munkhtsog and Grachev, Alexey and Korablev, Miroslav P and Hernandez-Blanco, Jose A and Munkhtsog, Bariushaa and Rosenbaum, Barry and Rozhnov, Viatcheslav V and Madad Rajabi, Ali and Noori, Hafizullah and Suryawanshi, Kulbhushansingh R and Armstrong, Ellie E and Petrov, Dmitri A} } @article {156894, title = {Host-Pathogen-Vector Continuum in a Changing Landscape: Potential Transmission Pathways for in a Small Mammal Community.}, journal = {Ecol Evol}, volume = {15}, year = {2025}, month = {2025 Apr}, pages = {e71085}, abstract = {

Bacterial infections account for a large proportion of zoonoses. Our current understanding of zoonotic spillover, however, is largely based on studies from viral systems. Small mammals such as rodents and their ectoparasites present a unique system for studying several bacterial pathogens and mapping their spillover pathways. Using spp. (a Gram-negative bacteria) as a model system within a rainforest human-use landscape, we investigated (1) ecological correlates of prevalence in small mammal hosts and (2) evolutionary relationships between spp. and various hosts and ectoparasites to gain insight into pathogen movement pathways within ecological communities. We detected in five out of eight small mammal species and in 86 (40.56\%) out of 212 individuals, but prevalence varied widely among species (0\%-75.8\%). Seven of the ten ectoparasite species found on these small mammals were positive for . Interestingly, while genotypes (15) in small mammals were host-specific, ectoparasites had nonspecific associations, suggesting the possibility for vector-mediated cross-species transmission. We also found that prevalence in hosts was positively correlated with their aggregated ectoparasite loads, further emphasizing the crucial role that ectoparasites may play in these transmission pathways. Our cophylogenetic analysis and ancestral trait (host) reconstruction revealed incongruence between small mammal and phylogenies, indicating historic host shifts and validating the potential for contemporary spillover events. We found that small mammal hosts in this fragmented landscape often move across habitat boundaries, creating a transmission pathway (via shared ectoparasites) to novel hosts, which may include synanthropic species like . Our results highlight the necessity to disentangle the complex relationship among hosts, ectoparasites, and bacterial pathogens to understand the implications of undetected spillover events.

}, keywords = {bacterial zoonosis; coevolution; ectoparasites; host shifts; vector-borne pathogens.}, issn = {2045-7758}, doi = {10.1002/ece3.71085}, url = {https://pubmed.ncbi.nlm.nih.gov/40177689/}, author = {Ansil, B R and Viswanathan, Ashwin and Ramachandran, Vivek and Yeshwanth, H M and Sanyal, Avirup and Ramakrishnan, Uma} } @article {154152, title = {Identification of Distinct Rodent-Associated Adenovirus Lineages from Mixed-Use Landscape.}, journal = {Ecohealth}, year = {2025}, month = {2025 Feb 04}, abstract = {

Land-use change and increased human-livestock-wildlife interactions have generated numerous possibilities for viral spillover, demanding enhanced surveillance in biodiverse regions. We investigated adenovirus diversity in small mammals, an understudied host taxon, from a forest-plantation mosaic in the Western Ghats biodiversity hotspot. We observed high prevalence (up to 39.39\%) and identified five lineages of adenoviruses with unique mutations in the dominant small mammal species,\ Rattus satarae. These lineages significantly differed from other known murine adenoviruses (p-distance \> 25\%), indicating the likelihood of novel adenoviruses in this endemic small mammal and suggesting potential for unexplored DNA virus diversity in the region.

}, keywords = {DNA viruses; India; small mammals; surveillance.}, issn = {1612-9210}, doi = {10.1007/s10393-025-01700-6}, url = {https://pubmed.ncbi.nlm.nih.gov/39903359/}, author = {Ansil, B R and Sanyal, Avirup and Sreenivas, Darshan and Garg, Kritika M and Ramakrishnan, Uma and Chattopadhyay, Balaji} } @article {156895, title = {Tiger turnaround as populations grow in India.}, journal = {Nature}, volume = {640}, year = {2025}, month = {2025 Apr}, pages = {603-604}, abstract = {

Until a few tens of thousands of years ago, Earth harboured a remarkable collection of large animals1, including giant ground sloths (Megatherium), woolly mammoths (Mammuthus primigenius) and elephant birds (Mullerornis\ and\ Aepyornis). Most of these iconic beasts are now extinct, and many large mammals are vanishingly rare following widespread human persecution and habitat disruption. Yet in India, a nation with a burgeoning human population, good news is reverberating about the population of wild tigers (Panthera tigris).\ Writing in\ Science, Jhala\ et al.2\ present findings about tigers that provide key lessons for conserving imperilled large animals elsewhere in the world.

}, issn = {1476-4687}, doi = {10.1038/d41586-025-01027-w}, url = {https://www.nature.com/articles/d41586-025-01027-w}, author = {Laurance, William F and Ramakrishnan, Uma} } @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 {152147, title = {Genetic load.}, journal = {Curr Biol}, volume = {34}, year = {2024}, month = {2024 Dec 16}, pages = {R1216-R1220}, abstract = {

We tend to assume that all genetic variation is good: the higher the variation in a population, the more diverse its gene pool, the more secure its future. Unfortunately, the relationship between genetic variation and survival of a population or a species is more complex. Some genetic variants are advantageous, increasing the survival and reproductive output of an individual, while others may be neutral now (but potentially advantageous in the future), and finally, some genetic variants are disadvantageous. All organisms carry a burden of disadvantageous genetic variants, called {\textquoteright}genetic load{\textquoteright}. This genetic load can lead to diseases or morphological abnormalities and reduce survival or reproduction. Although genetic load has been studied for decades, recent technological advances now enable a more detailed understanding of its characteristics and potential consequences in wild species.

}, keywords = {Animals, Genetic Load, Genetic Variation, Reproduction}, issn = {1879-0445}, doi = {10.1016/j.cub.2024.11.004}, author = {Grossen, Christine and Ramakrishnan, Uma} } @article {145429, title = {On the road to losing connectivity: Faecal samples provide genome-wide insights into anthropogenic impacts on two large herbivore species in central India.}, journal = {Mol Ecol}, year = {2024}, month = {2024 Jul 03}, pages = {e17461}, abstract = {

Humans have impacted most of the planet, and the ensuing fragmentation results in small, isolated habitat patches posing a risk of genetic diversity loss, inbreeding, and genetic load. Understanding how natural and anthropogenic landscape features affect gene flow among habitat patches is critical for maintaining connectivity. Genome-wide data are required to comprehend the impacts of recent fragmentation, which can be challenging when only non-invasive samples are available. Here, we build upon advancements in conservation genomics to address connectivity of two large herbivores, gaur (Bos gaurus) and sambar (Rusa unicolor) in central India. Given their habitat associations, we expected these species to respond similarly to habitat fragmentation. We used faecal-DNA and methylation-based host-DNA enrichment with modified ddRAD protocol to generate genome-wide single-nucleotide polymorphism (SNP) data for 124 gaur and 99 sambar individuals. Our findings reveal that gaur populations in central India are fragmented, displaying high genetic differentiation, with drift significantly affecting small populations like Umred Karhandla Wildlife Sanctuary. Although sambar shows low genetic structure, another small population, Bor Tiger Reserve is genetically differentiated. Our results suggest that although land cover change and roads restrict animal movement, the extent of this impact varies across the two species. We show that different species respond differently to landscape features, even with similar habitat associations. We highlight small and isolated populations requiring urgent conservation intervention. Such multi-species approaches enhance our understanding of cross-species connectivity patterns. We suggest shifting from single-species to multi-species holistic conservation approach in rapidly developing landscapes to better manage co-occurring endangered species.

}, issn = {1365-294X}, doi = {10.1111/mec.17461}, author = {Tyagi, Abhinav and Yadav, Nidhi and Pandit, Awadhesh and Ramakrishnan, Uma} } @article {145412, title = {Spatial patterns in the diet of Gyps vultures in India and their implications for conservation}, journal = {BIOLOGICAL CONSERVATION}, volume = {292}, year = {2024}, month = {04/2024}, abstract = {

Dietary analyses are particularly useful for developing conservation programmes for species threatened by resource depletion, poisoning and environmental pollution. Gyps vultures in South Asia represent one such case, having undergone a population collapse caused by feeding on carcasses of cattle treated with the non-steroidal anti-inflammatory drug diclofenac. Following a ban on the veterinary use of diclofenac, populations of vultures remain low and mostly concentrated near protected areas. Understanding the role of protected areas in the recovery of these critically endangered species requires analyses of spatial variation in their diet. We used faecal metabarcoding to investigate the spatial variation in the diet of Gyps vultures across four landscapes from sites located inside and outside protected areas. We collected faecal 642 samples, of which 419 yielded adequate molecular data to identify the vulture species and 30 molecular operational taxonomic units corresponding to at least 28 diet species. The diet was dominated by large ungulates and varied across landscapes, protection status and vulture species, with the observed variation largely explained by differential intake of wild and domestic species. Domestic livestock was present in \>95 \% of the samples from Central, West and North India, but 77 \% of the samples had only wild species in South India. This variation was explained by livestock density within 100 km radius of the sampling site. Our results imply that protected areas may not offer a respite from possibility of diclofenac-poisoning across most parts of the country and efforts should continue unabated to remove nephrotoxic drugs from veterinary use.

}, doi = {10.1016/j.biocon.2024.110551}, author = {Ghosh-Harihar, Mousumi and Yadav, Nidhi and Gurung, Nehal and Darshan, C. S. and Shashikumar, B. and Vishnudas, C. K. and Prakash, Vibhu and Green, Rhys E. and Ramakrishnan, Uma} } @article {149377, title = {Unraveling the genomic diversity and admixture history of captive tigers in the United States.}, journal = {Proc Natl Acad Sci U S A}, volume = {121}, year = {2024}, month = {2024 Sep 24}, pages = {e2402924121}, abstract = {

Genomic studies of endangered species have primarily focused on describing diversity patterns and resolving phylogenetic relationships, with the overarching goal of informing conservation efforts. However, few studies have investigated genomic diversity housed in captive populations. For tigers (), captive individuals vastly outnumber those in the wild, but their diversity remains largely unexplored. Privately owned captive tiger populations have remained an enigma in the conservation community, with some believing that these individuals are severely inbred, while others believe they may be a source of now-extinct diversity. Here, we present a large-scale genetic study of the private (non-zoo) captive tiger population in the United States, also known as "Generic" tigers. We find that the Generic tiger population has an admixture fingerprint comprising all six extant wild tiger subspecies. Of the 138 Generic individuals sequenced for the purpose of this study, no individual had ancestry from only one subspecies. We show that the Generic tiger population has a comparable amount of genetic diversity relative to most wild subspecies, few private variants, and fewer deleterious mutations. We observe inbreeding coefficients similar to wild populations, although there are some individuals within both the Generic and wild populations that are substantially inbred. Additionally, we develop a reference panel for tigers that can be used with imputation to accurately distinguish individuals and assign ancestry with ultralow coverage (0.25{\texttimes}) data. By providing a cost-effective alternative to whole-genome sequencing (WGS), the reference panel provides a resource to assist in tiger conservation efforts for both ex- and in situ populations.

}, keywords = {Animals, Animals, Zoo, Conservation of Natural Resources, Endangered Species, Genetic Variation, Genome, Genomics, Phylogeny, Tigers, United States}, issn = {1091-6490}, doi = {10.1073/pnas.2402924121}, author = {Armstrong, Ellie E and Mooney, Jazlyn A and Solari, Katherine A and Kim, Bernard Y and Barsh, Gregory S and Grant, Victoria B and Greenbaum, Gili and Kaelin, Christopher B and Panchenko, Katya and Pickrell, Joseph K and Rosenberg, Noah and Ryder, Oliver A and Yokoyama, Tsuya and Ramakrishnan, Uma and Petrov, Dmitri A and Hadly, Elizabeth A} } @article {129159, title = {Citizen science facilitates first ever genetic detection of wolf-dog hybridization in Indian savannahs.}, journal = {Ecol Evol}, volume = {13}, year = {2023}, month = {2023 May}, pages = {e10100}, abstract = {

Human demographic expansion has confined wildlife to fragmented habitats, often in proximity to human-modified landscapes. Such interfaces facilitate increased interactions between feral or domesticated animals and wildlife, posing a high risk to wild species. This is especially relevant for free-ranging dogs () and wild canids like gray wolves () and golden jackals (). Wolf-dog hybridization may lead to a significant reduction of specific adaptations in wolves that could result in the decline of wolf populations. Detection and genetic discrimination of hybrids between dogs and wolves are challenging because of their complex demographic history and close ancestry. Citizen scientists identified two phenotypically different-looking individuals and subsequently collected non-invasive samples that were used by geneticists to test wolf-dog hybridization. Genomic data from shed hair samples of suspected hybrid individuals using double-digest restriction-site-associated DNA (ddRAD) sequencing resulted in 698 single nucleotide polymorphism (SNP) markers. We investigated the genetic origin of these two individuals analyzed with genetically known dogs, wolves, and other canid species including jackals and dholes (). Our results provide the first genetic evidence of one F2 hybrid and the other individual could be a complex hybrid between dogs and wolves. Our results re-iterate the power of next-generation sequencing (NGS) for non-invasive samples as an efficient tool for detecting hybrids. Our results suggest the need for more robust monitoring of wolf populations and highlight the tremendous potential for collaborative approaches between citizens and conservation scientists to detect and monitor threats to biodiversity.

}, issn = {2045-7758}, doi = {10.1002/ece3.10100}, author = {Tyagi, Abhinav and Godbole, Mihir and Vanak, Abi Tamim and Ramakrishnan, Uma} } @article {129167, title = {Gene flow drives genomic diversity in Asian Pikas distributed along the core and range-edge habitats in the Himalayas.}, journal = {Ecol Evol}, volume = {13}, year = {2023}, month = {2023 May}, pages = {e10129}, abstract = {

Studying the genetic variation among different species distributed across their core and range-edge habitats can provide valuable insights into how genetic variation changes across the species{\textquoteright} distribution range. This information can be important for understanding local adaptation, as well as for conservation and management efforts. In this study, we have carried out genomic characterization of six species of Asian Pikas distributed along their core and range-edge habitats in the Himalayas. We utilized a population genomics approach using ~28,000 genome-wide SNP markers obtained from restriction-site associated DNA sequencing. We identified low nucleotide diversity and high inbreeding coefficients in all six species across their core and range-edge habitats. We also identified evidence of gene flow among genetically diverse species. Our results provide evidence of reduced genetic diversity in Asian pikas distributed across the Himalayas and the neighboring regions and indicate that recurrent gene flow is possibly a key mechanism for maintaining genetic diversity and adaptive potential in these pikas. However, full-scale genomics studies that utilize whole-genome sequencing approaches will be needed to quantify the direction and timing of gene flow and functional changes associated with introgressed regions in the genome. Our results represent an important step toward understanding the patterns and consequences of gene flow in species, sampled at the least studied, yet climatically vulnerable part of their habitat that can be further used to inform conservation strategies that promote connectivity and gene flow between populations.

}, issn = {2045-7758}, doi = {10.1002/ece3.10129}, author = {Dahal, Nishma and Romine, Melia G and Khatiwara, Sunita and Ramakrishnan, Uma and Lamichhaney, Sangeet} } @article {125196, title = {Prioritizing India{\textquoteright}s landscapes for biodiversity, ecosystem services and human well-being}, journal = {NATURE SUSTAINABILITY }, year = {2023}, month = {02/2023}, abstract = {

Biodiversity conservation and human well-being are tightly interlinked. Yet, mismatches in the scale at which these two priority issues are planned and implemented have exacerbated biodiversity loss, erosion of ecosystem services and declining human quality of life. India houses the second largest human population on the planet, while \< 5\% of the country{\textquoteright}s land area is effectively protected for conservation. This warrants landscape-level conservation planning through a judicious mix of land-sharing and land-sparing approaches combined with the co-production of ecosystem services. Through a multifaceted assessment, we prioritize spatial extents of land parcels that, in the face of anthropogenic threats, can safeguard conservation landscapes across India{\textquoteright}s biogeographic zones. We found that only a fraction (similar to 15\%) of the priority areas identified here are encompassed under India{\textquoteright}s extant Protected Area network, and furthermore, that several landscapes of high importance were omitted from all previous global-scale assessments. We then examined the spatial congruence of priority areas with administrative units earmarked for economic development by the Indian government and propose management zoning through state-driven and participatory approaches. Our spatially explicit insights can help meet the twin goals of biodiversity conservation and sustainable development in India and other countries across the Global South.

Biodiversity conservation is critical for promoting ecosystem services and human well-being, but current conservation efforts fail to protect most high priority zones. A mix of land-sparing and land-sharing is needed to safeguard critical ecosystems in India and across the Global South.

}, doi = {10.1038/s41893-023-01063-2}, author = {Srivathsa, Arjun and Vasudev, Divya and Nair, Tanaya and Chakrabarti, Stotra and Chanchani, Pranav and DeFries, Ruth and Deomurari, Arpit and Dutta, Sutirtha and Ghose, Dipankar and Goswami, Varun R. and Nayak, Rajat and Neelakantan, Amrita and Thatte, Prachi and Vaidyanathan, Srinivas and Verma, Madhu and Krishnaswamy, Jagdish and Sankaran, Mahesh and Ramakrishnan, Uma} } @article {123072, title = {SARS-CoV-2 infection dynamics and genomic surveillance to detect variants in wastewater - a longitudinal study in Bengaluru, India.}, journal = {Lancet Reg Health Southeast Asia}, year = {2023}, month = {2023 Jan 18}, pages = {100151}, abstract = {

BACKGROUND: Environmental surveillance (ES) of a pathogen is crucial for understanding the community load of disease. As an early warning system, ES for SARS-CoV-2 has complemented routine diagnostic surveillance by capturing near real-time virus circulation at a population level.

METHODS: In this longitudinal study conducted between January 2022 and June 2022 in 28 sewershed sites in Bengaluru city (\~{}11 million inhabitants), we quantified weekly SARS-CoV-2 RNA concentrations to track infection dynamics and provide evidence of change in the relative abundance of emerging variants.

FINDINGS: We describe an early warning system using the exponentially weighted moving average control chart and demonstrate how SARS-CoV-2 RNA concentrations in wastewater correlated with clinically diagnosed new COVID-19 cases, with the trends appearing 8-14 days earlier in wastewater than in clinical data. This was further corroborated by showing that the estimated number of infections is strongly correlated with SARS-CoV-2 RNA copies detected in the wastewater. Using a deconvolution matrix, we detected emerging variants of concern up to two months earlier in wastewater samples. In addition, we found a huge diversity in variants detected in wastewater compared to clinical samples. The findings from this study have been discussed regularly with local authorities to inform policy-making decisions.

INTERPRETATION: Our study highlights that quantifying viral titre, correlating it with a known number of cases in the area, and combined with genomic surveillance helps in tracking variants of concern (VOC) over time and space, enabling timely and making informed policy decisions.

FUNDING: This work has been supported by funding from the Rockefeller Foundation grant to National Centre for Biological Sciences (TIFR) and the Indian Council of Medical Research grant to (FI) Tata Institute for Genetics and Society and Tata Trusts.

}, issn = {2772-3682}, doi = {10.1016/j.lansea.2023.100151}, author = {Lamba, Sanjay and Ganesan, Sutharsan and Daroch, Namrta and Paul, Kiran and Joshi, Soumya Gopal and Sreenivas, Darshan and Nataraj, Annamalai and Srikantaiah, Vishwanath and Mishra, Rakesh and Ramakrishnan, Uma and Ishtiaq, Farah} } @article {131295, title = {Topcats and underdogs: intraguild interactions among three apex carnivores across Asia{\textquoteright}s forestscapes.}, journal = {Biol Rev Camb Philos Soc}, year = {2023}, month = {2023 Jul 14}, abstract = {

Intraguild interactions among carnivores have long held the fascination of ecologists. Ranging from competition to facilitation and coexistence, these interactions and their complex interplay influence everything from species persistence to ecosystem functioning. Yet, the patterns and pathways of such interactions are far from understood in tropical forest systems, particularly across countries in the Global South. Here, we examined the determinants and consequences of competitive interactions between dholes Cuon alpinus and the two large felids (leopards Panthera pardus and tigers Panthera tigris) with which they most commonly co-occur across Asia. Using a combination of traditional and novel data sources (N = 118), we integrate information from spatial, temporal, and dietary niche dimensions. These three species have faced catastrophic declines in their extent of co-occurrence over the past century; most of their source populations are now confined to Protected Areas. Analysis of dyadic interactions between species pairs showed a clear social hierarchy. Tigers were dominant over dholes, although pack strength in dholes helped ameliorate some of these effects; leopards were subordinate to dholes. Population-level spatio-temporal interactions assessed at 25 locations across Asia did not show a clear pattern of overlap or avoidance between species pairs. Diet-profile assessments indicated that wild ungulate biomass consumption by tigers was highest, while leopards consumed more primate and livestock prey as compared to their co-predators. In terms of prey offtake (ratio of wild prey biomass consumed to biomass available), the three species together harvested 0.4-30.2\% of available prey, with the highest offtake recorded from the location where the carnivores reach very high densities. When re-examined in the context of prey availability and offtake, locations with low wild prey availability showed spatial avoidance and temporal overlap among the carnivore pairs, and locations with high wild prey availability showed spatial overlap and temporal segregation. Based on these observations, we make predictions for 40 Protected Areas in India where temporally synchronous estimates of predator and prey densities are available. We expect that low prey availability will lead to higher competition, and in extreme cases, to the complete exclusion of one or more species. In Protected Areas with high prey availability, we expect intraguild coexistence and conspecific competition among carnivores, with spill-over to forest-edge habitats and subsequent prey-switching to livestock. We stress that dhole-leopard-tiger co-occurrence across their range is facilitated through an intricate yet fragile balance between prey availability, and intraguild and conspecific competition. Data gaps and limitations notwithstanding, our study shows how insights from fundamental ecology can be of immense utility for applied aspects like large predator conservation and management of human-carnivore interactions. Our findings also highlight potential avenues for future research on tropical carnivores that can broaden current understanding of intraguild competition in forest systems of Asia and beyond.

}, issn = {1469-185X}, doi = {10.1111/brv.12998}, author = {Srivathsa, Arjun and Ramachandran, Vivek and Saravanan, Pooja and Sureshbabu, Abhijith and Ganguly, Divyajyoti and Ramakrishnan, Uma} } @article {131285, title = {Validating saliva as a biological sample for cost-effective, rapid and routine screening for SARS-CoV-2}, journal = {INDIAN JOURNAL OF MEDICAL MICROBIOLOGY}, volume = {45}, year = {2023}, month = {09/2023}, abstract = {

Purpose: Compared to nasopharyngeal/oropharyngeal swabs (N/OPS-VTM), non-invasive saliva samples have enormous potential for scalability and routine population screening of SARS-CoV-2. In this study, we investigate the efficacy of saliva samples relative to N/OPS-VTM for use as a direct source for RT-PCR based SARS-CoV-2 detection. Methods: We collected paired nasopharyngeal/oropharyngeal swabs and saliva samples from suspected positive SARS-CoV-2 patients and tested using RT-PCR. We used generalized linear models to investigate factors that explain result agreement. Further, we used simulations to evaluate the effectiveness of saliva-based screening in restricting the spread of infection in a large campus such as an educational institution. Results: We observed a 75.4\% agreement between saliva and N/OPS-VTM, that increased drastically to 83\% in samples stored for less than three days. Such samples processed within two days of collection showed 74.5\% test sensitivity. Our simulations suggest that a test with 75\% sensitivity, but high daily capacity can be very effective in limiting the size of infection clusters in a workspace. Guided by these results, we successfully implemented a saliva-based screening in the Bangalore Life Sciences Cluster (BLiSC) campus. Conclusion: These results suggest that saliva may be a viable alternate source for SARS-CoV-2 surveillance if samples are processed immediately. Although saliva shows slightly lower sensitivity levels when compared to N/ OPS-VTM, saliva collection is logistically advantageous. We strongly recommend the implementation of salivabased screening strategies for large workplaces and in schools, as well as for population-level screening and routine surveillance as we learn to live with the SARS-CoV-2 virus.

}, doi = {10.1016/j.ijmmb.2023.100384}, author = {Ansil, B R and George, Carolin Elizabeth and Chandrasingh, Sindhulina and Viswanathan, Ashwin and Thattai, Mukund and Raghu, Padinjat and Devadiga, Santhosha and Harikumar, Arun Geetha and Harsha, Pulleri Kandi and Nair, Indu and Ramakrishnan, Uma and Mayor, Satyajit} } @article {131287, title = {Draft genome sequence of an invasive plant .}, journal = {Bioinformation}, volume = {18}, year = {2022}, month = {2022}, pages = {739-741}, abstract = {

L. is an invasive species of global concern. An ornamental plant originating from central America, it has now spread across natural and human-dominated habitats across tropical and subtropical regions globally. Understanding the population and evolutionary genetics of this species could help gain deeper insights into invasion biology, and provide tools for more effective management. Such investigation would require a relatively good quality genome assembly. While there have been reports of a transcriptome, it has been challenging to construct the genome assembly because of the large genome size. We present here the first draft genome assembly of L. which has an N50 value of 62 Kb, genome completeness of 99.3\% and genome coverage of 74.3\%. We hope that such an assembly will help researchers study colonization history, the genetic basis of adaptation and invasiveness, and help design strategies to contain the invasiveness of this plant, allowing biodiversity recovery in several parts of the globe.

}, issn = {0973-2063}, doi = {10.6026/97320630018739}, author = {Joshi, Adwait G and Praveen, P and Ramakrishnan, Uma and Sowdhamini, Ramanathan} } @article {105477, title = {The evolutionary history of an accidental model organism, the leopard gecko Eublepharis macularius (Squamata: Eublepharidae).}, journal = {Mol Phylogenet Evol}, year = {2022}, month = {2022 Jan 12}, pages = {107414}, abstract = {

The leopard gecko, Eublepharis macularius, is a widely used model organism in laboratory and experimental studies. The high phenotypic diversity in the pet trade, the fact that the provenance of different breeding lines is unknown, and that distinct Eublepharis species are known to hybridize, implies that the continued use of E. macularius as a model requires clarity on the origin of the lineages in the pet trade. We combine multi-locus sequence data and the first range-wide sampling of the genus Eublepharis to reconstruct the evolutionary history of the Eublepharidae and Eublepharis, with an updated time-tree for the Eublepharidae. Our sampling includes five of the six recognized species and additional nominal taxa of uncertain status comprising 43 samples from 34 localities plus 48 pet-trade samples. The Eublepharidae began diversifying in the Cretaceous. Eublepharis split from its sister genera in Africa in the Palaeocene-Eocene, and began diversifying in the Oligocene-Miocene, with late Miocene-Pliocene cladogenesis giving rise to extant species. The current species diversity within this group is moderately underestimated. Our species delimitation suggests 10 species with four potentially unnamed divergent lineages in Iran, India and Pakistan. All 30 individuals of E. macularius that we sampled from the pet trade, which include diverse morphotypes, come from a few shallow E. macularius clades, confirming that lab and pet trade strains are part of a single taxon. One of the wild-caught haplotypes of E. macularius, from near Karachi, Pakistan, is identical to (10) pet-trade samples and all other captive populations are closely related to wild-caught animals from central/southern Pakistan (0.1-0.5 \% minimum pairwise uncorrected ND2 sequence divergence).

}, issn = {1095-9513}, doi = {10.1016/j.ympev.2022.107414}, author = {Agarwal, Ishan and Bauer, Aaron M and Gamble, Tony and Giri, Varad B and Jablonski, Daniel and Khandekar, Akshay and Mohapatra, Pratyush P and Masroor, Rafaqat and Mishra, Anurag and Ramakrishnan, Uma} } @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 {108060, title = {Synthesizing habitat connectivity analyses of a globally important human-dominated tiger-conservation landscape.}, journal = {Conserv Biol}, year = {2022}, month = {2022 Mar 14}, abstract = {

As ecological data and associated analyses become more widely available, synthesizing results for effective communication with stakeholders is essential. In the case of wildlife corridors, managers in human-dominated landscapes need to identify both the locations of corridors and multiple stakeholders for effective oversight. We synthesized 5 independent studies of tiger (Panthera tigris) connectivity in central India, a global priority landscape for tiger conservation, to quantify agreement on landscape permeability for tiger movement and potential movement pathways. We used the latter analysis to identify connectivity areas on which studies agreed and stakeholders associated with these areas to determine relevant participants in corridor management. Three or more of the 5 studies{\textquoteright} resistance layers agreed in 63\% of the study area. Areas in which all studies agree on resistance were of primarily low (66\%, e.g., forest) and high (24\%, e.g., urban) resistance. Agreement was lower in intermediate resistance areas (e.g., agriculture). Despite these differences, the studies largely agreed on areas with high levels of potential movement: \>40\% of high average (top 20\%) current-flow pixels were also in the top 20\% of current-flow agreement pixels (measured by low variation), indicating consensus connectivity areas (CCAs) as conservation priorities. Roughly 70\% of the CCAs fell within village administrative boundaries, and 100\% overlapped forest department management boundaries, suggesting that people live and use forests within these priority areas. Over 16\% of total CCAs{\textquoteright} area was within 1 km of linear infrastructure (437 road, 170 railway, 179 transmission line, and 339 canal crossings; 105 mines within 1 km of CCAs). In 2019, 78\% of forest land diversions for infrastructure and mining in Madhya Pradesh (which comprises most of the study region) took place in districts with CCAs. Acute competition for land in this landscape with globally important wildlife corridors calls for an effective comanagement strategy involving local communities, forest departments, Appendix 1 and infrastructure planners. This article is protected by copyright. All rights reserved.

}, issn = {1523-1739}, doi = {10.1111/cobi.13909}, author = {Schoen, Jay M and Neelakantan, Amrita and Cushman, Samuel A and Dutta, Trishna and Habib, Bilal and Jhala, Yadvendradev V and Mondal, Indranil and Ramakrishnan, Uma and Reddy, P Anuradha and Saini, Swati and Sharma, Sandeep and Thatte, Prachi and Yumnam, Bibek and DeFries, Ruth} } @article {116715, title = {Using Environmental Sampling to Enable Zoonotic Pandemic Preparedness.}, journal = {J Indian Inst Sci}, year = {2022}, month = {2022 Sep 07}, pages = {1-20}, abstract = {

The current pandemic caused by the SARS CoV-2, tracing back its origin possibly to a coronavirus associated with bats, has ignited renewed interest in understanding zoonotic spillovers across the globe. While research is more directed towards solving the problem at hand by finding therapeutic strategies and novel vaccine techniques, it is important to address the environmental drivers of pathogen spillover and the complex biotic and abiotic drivers of zoonoses. The availability of cutting-edge genomic technologies has contributed enormously to preempt viral emergence from wildlife. However, there is still a dearth of studies from species-rich South Asian countries, especially from India. In this review, we outline the importance of studying disease dynamics through environmental sampling from wildlife in India and how ecological parameters of both the virus and the host community may play a role in mediating cross-species spillovers. Non-invasive sampling using feces, urine, shed hair, saliva, shed skin, and feathers has been instrumental in providing genetic information for both the host and their associated pathogens. Here, we discuss the advances made in environmental sampling protocols and strategies to generate genetic data from such samples towards the surveillance and characterization of potentially zoonotic pathogens. We primarily focus on bat-borne or small mammal-borne zoonoses and propose a conceptual framework for non-invasive strategies to tackle the threat of emerging zoonotic infections.

}, issn = {0970-4140}, doi = {10.1007/s41745-022-00322-z}, author = {Sanyal, Avirup and Agarwal, Sanskriti and Ramakrishnan, Uma and Garg, Kritika M and Chattopadhyay, Balaji} } @article {95905, title = {At the crossroads: molecular ecology and wildlife conservation.}, journal = {J Indian Inst Sci}, year = {2021}, month = {2021 Jul 05}, pages = {1-2}, issn = {0970-4140}, doi = {10.1007/s41745-021-00246-0}, author = {Ramakrishnan, Uma} } @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 {99107, title = {Global Commitments to Conserving and Monitoring Genetic Diversity Are Now Necessary and Feasible.}, journal = {Bioscience}, volume = {71}, year = {2021}, month = {2021 Sep}, pages = {964-976}, abstract = {

Global conservation policy and action have largely neglected protecting and monitoring genetic diversity-one of the three main pillars of biodiversity. Genetic diversity (diversity within species) underlies species{\textquoteright} adaptation and survival, ecosystem resilience, and societal innovation. The low priority given to genetic diversity has largely been due to knowledge gaps in key areas, including the importance of genetic diversity and the trends in genetic diversity change; the perceived high expense and low availability and the scattered nature of genetic data; and complicated concepts and information that are inaccessible to policymakers. However, numerous recent advances in knowledge, technology, databases, practice, and capacity have now set the stage for better integration of genetic diversity in policy instruments and conservation efforts. We review these developments and explore how they can support improved consideration of genetic diversity in global conservation policy commitments and enable countries to monitor, report on, and take action to maintain or restore genetic diversity.

}, issn = {0006-3568}, doi = {10.1093/biosci/biab054}, author = {Hoban, Sean and Bruford, Michael W and Funk, W Chris and Galbusera, Peter and Griffith, M Patrick and Grueber, Catherine E and Heuertz, Myriam and Hunter, Margaret E and Hvilsom, Christina and Stroil, Belma Kalamujic and Kershaw, Francine and Khoury, Colin K and Laikre, Linda and Lopes-Fernandes, Margarida and MacDonald, Anna J and Mergeay, Joachim and Meek, Mariah and Mittan, Cinnamon and Mukassabi, Tarek A and O{\textquoteright}Brien, David and Ogden, Rob and Palma-Silva, Clarisse and Ramakrishnan, Uma and Segelbacher, Gernot and Shaw, Robyn E and Sj{\"o}gren-Gulve, Per and Veli{\v c}kovi{\'c}, Nevena and Vernesi, Cristiano} } @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 {90599, title = {High prevalence and diversity of Bartonella in small mammals from the biodiverse Western Ghats.}, journal = {PLoS Negl Trop Dis}, volume = {15}, year = {2021}, month = {2021 Mar}, pages = {e0009178}, abstract = {

Bartonella species are recognized globally as emerging zoonotic pathogens. Small mammals such as rodents and shrews are implicated as major natural reservoirs for these microbial agents. Nevertheless, in several tropical countries, like India, the diversity of Bartonella in small mammals remain unexplored and limited information exists on the natural transmission cycles (reservoirs and vectors) of these bacteria. Using a multi-locus sequencing approach, we investigated the prevalence, haplotype diversity, and phylogenetic affinities of Bartonella in small mammals and their associated mites in a mixed-use landscape in the biodiverse Western Ghats in southern India. We sampled 141 individual small mammals belonging to eight species. Bartonella was detected in five of the eight species, including three previously unknown hosts. We observed high interspecies variability of Bartonella prevalence in the host community. However, the overall prevalence (52.5\%) and haplotype diversity (0.9) was high for the individuals tested. Of the seven lineages of Bartonella identified in our samples, five lineages were phylogenetically related to putative zoonotic species-B. tribocorum, B. queenslandensis, and B. elizabethae. Haplotypes identified from mites were identical to those identified from their host species. This indicates that these Bartonella species may be zoonotic, but further work is necessary to confirm whether these are pathogenic and pose a threat to humans. Taken together, these results emphasize the presence of hitherto unexplored diversity of Bartonella in wild and synanthropic small mammals in mixed-use landscapes. The study also highlights the necessity to assess the risk of spillover to humans and other incidental hosts.

}, issn = {1935-2735}, doi = {10.1371/journal.pntd.0009178}, author = {Ansil, B R and Mendenhall, Ian H 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} } @article {90237, title = {Securing biodiversity, securing our future: A national mission on biodiversity and human well-being for India}, journal = {BIOLOGICAL CONSERVATION}, volume = {253}, year = {2021}, month = {01/2021}, abstract = {

Highly populated tropical countries face tremendous pressures in reconciling the needs for improved economic security and the protection of declining biodiversity. India is no exception and its biodiversity is under severe pressure due to complex interactions among land use change, other human economic activities, and climate change. Preservation and restoration of biodiversity is perhaps the cheapest and least risky way to mitigate the impacts of threats such as climate change, diminishing food and nutritional security, declining economy, absence of affordable healthcare, rising zoonotic diseases and lack of capacity to address these issues. Here we describe a framework for biodiversity conservation - the National Mission on Biodiversity and Human Well-Being (NMBHWB) for India - which integrates biodiversity, ecosystem services, climate change, agriculture, health, bio-economy and capacity building in the realm of biodiversity science. We provide an overview of the seven Programs of the Mission which make it interdisciplinary, integrative, and comprehensive in its approach. The Mission explicitly links research with policy-making and implementation for effective management of biodiversity with sustainable development. With its emphasis on convergence and synergies among various goals, themes and project sites, the Mission will further develop new models for stakeholder consultations and co-production of knowledge. We posit that the NMBHWB will enable India to realize the United Nations Sustainable Development Goals and Targets while advancing India{\textquoteright}s commitments to the Paris Agreement on climate change and other international environmental conventions and treaties.

}, doi = {10.1016/j.biocon.2020.108867}, author = {Bawa, Kamaljit S and Sengupta, Asmita and Chavan, Vishwas and Chellam, Ravi and Ganesan, R. and Krishnaswamy, Jagdish and Mathur, Vinod B. and Nawn, Nandan and Olsson, Shannon B and Pandit, Nitin and Quader, Suhel and Rajagopal, Prabhakar and Ramakrishnan, Uma and Ravikanth, G. and Sankaran, Mahesh and Shankar, Darshan and Seidler, Reinmar and Shaanker, R. Uma and Vanak, Abi Tamim} } @article {93661, title = {The truth about scats and dogs: Next-generation sequencing and spatial capture-recapture models offer opportunities for conservation monitoring of an endangered social canid}, journal = {BIOLOGICAL CONSERVATION}, year = {2021}, month = {04/2021}, abstract = {

Obtaining accurate population counts of endangered species is central to conservation biology, with implications for gaining ecological insights, informing management strategies, and judicial use of conservation funds. Despite decades of progress in methodological developments in the realm of population ecology, reliable density estimates are unavailable for many species of conservation concern. The dhole (Asiatic wild dog Cuon alpinus) is one such endangered large carnivore found in the tropical forests of south and southeast Asia. Here, we (i) develop next-generation sequencing resources to identify individual dholes from genetic samples, (ii) apply these methods to identify individuals in the wild, from scat (fecal) samples collected through systematic field surveys and (iii) generate reliable estimates of dhole densities in Wayanad Wildlife Sanctuary (Western Ghats, India) using Spatial Capture-Recapture {\textquoteright}SCR{\textquoteright} models. We estimate dhole densities to be 12-14.2 individuals/100 sq. km based on a set of SCR models, with similar to 50 individuals within Wayanad{\textquoteright}s administrative boundary. Our study presents a methodological improvement in generating population estimates of an important apex predator while also offering ecologically informative insights on a species in dire need of science-based management efforts. Replicating this study across connected reserves and over time can serve as a unified framework for understanding population dynamics, population structures, landscape connectivity and metapopulation-level conservation requirements. We propose that the approach presented here may be adopted as an economically and logistically feasible protocol for conservation monitoring of dholes and other ecologically important species plagued by similar issues of data-deficiency, and insufficient funding and resources.

}, doi = {10.1016/j.biocon.2021.109028}, author = {Srivathsa, Arjun and Rodrigues, Ryan G and Toh, Kok Ben and Zachariah, Arun and Taylor, Ryan W and Oli, Madan K and Ramakrishnan, Uma} } @article {79864, title = {Assessing the status of critically endangered Kondana soft-furred rat (Millardia kondana) using integrative taxonomy: combining evidence from morphological, molecular and environmental niche modeling}, journal = {MAMMALIA}, volume = {84}, year = {2020}, month = {07/2020}, pages = {392-406}, abstract = {

Kondana soft-furred rat is a critically endangered (CR) species, known from a single locality - Sinhgad in the northern Western Ghats, India. However, the taxonomic status of this species is uncertain due to its close resemblance to the widely distributed soft-furred field rat Millardia meltada, which has serious implications on the conservation status of Millardia kondana. In this study, we assessed the current taxonomic status of M. kondana through an integrative approach combining morphological, molecular and environmental niche modeling analyses. We collected morphological data from the specimens around Sinhgad as well as preserved specimens in the museum. Both morphological and two-dimensional (2D) morphometrical analyses showed a significant difference between M. kondana and M. meltada. Molecular phylogeny based on cytochrome b gene revealed a sister relationship between M. kondana and M. meltada, and both species form distinct well-supported monophyletic clades. Niche modeling also predicted niche segregation between the two species: M. kondana preferred areas with a high elevation and precipitation seasonality while M. meltada favored regions with a low elevation and precipitation. We confirmed that M. kondana is taxonomically distinct from M. meltada, and based on our estimates of its occurrence and occupancy, M. kondana continues to be treated as CR until further detailed investigations.

}, doi = {10.1515/mammalia-2019-0056}, author = {Bajaru, Sameer B and Lajmi, Aparna and Manakadan, Ranjit and Kulavmode, Amol R. and Ramakrishnan, Uma} } @article {84578, title = {Closely related species show species-specific environmental responses and different spatial conservation needs: Prionailurus cats in the Indian subcontinent.}, journal = {Sci Rep}, volume = {10}, year = {2020}, month = {2020 Oct 30}, pages = {18705}, abstract = {

Phylogenetically closely related species are often assumed to have similar responses to environmental conditions, but species-specific responses have also been described. These two scenarios may have different conservation implications. We tested these two hypotheses for Prionailurus cats (P. rubiginosus, P. bengalensis, P. viverrinus) in the Indian subcontinent and show its implications on species current protected area coverage and climatic suitability trends through time. We fitted ecological niche models with current environmental conditions and calculated niche overlap. In addition, we developed a model for the Jungle Cat Felis chaus to compare species responses and niche overlap estimates within Prionailurus with those for a related sympatric small cat species. Then we estimated the proportion of current suitable environment covered by protected area and projected climatic models from past (last interglacial) to future (2070; RCP4.5 and RCP8.5) conditions to show implications on population management and conservation. The hypothesis of a similar response and niche overlap among closely related species is not supported. Protected area coverage was lowest for P. viverrinus (mean = 0.071, SD = 0.012) and highest for P. bengalensis (mean = 0.088, SD = 0.006). In addition, the proportion of the subcontinent with suitable climate varied through time and was species-specific. For P. bengalensis, climatic suitability shrunk since at least the mid-Holocene, a trend that can be intensified by human-induced climate warming. Concerning P. viverrinus, most predictions show stable future climatic suitability, but a few indicated potential loss. Climatic suitability for P. rubiginous was predicted to remain stable but the species exhibited a negative association with intensive agriculture. Similar responses to environmental change by phylogenetically closely related species should not be assumed and have implications on protected area coverage and natural trends of species climatic suitability over time. This should be taken into account during conservation and management actions.

}, issn = {2045-2322}, doi = {10.1038/s41598-020-74684-8}, author = {Silva, Andr{\'e} P and Mukherjee, Shomita and Ramakrishnan, Uma and Fernandes, Carlos and Bj{\"o}rklund, Mats} } @article {79863, title = {The desert hamster Phodopus roborovskii (Satunin, 1903) (Rodentia, Cricetidae) from north-western Tibetan plateau, Ladakh, India: an addition to the mammalian fauna of the Indian subcontinent}, journal = {MAMMALIA}, volume = {84}, year = {2020}, month = {05/2020}, pages = {253-258}, abstract = {

During a systematic survey of the small mammals in the relatively unexplored north-western regions of the Tibetan plateau in India, we captured and identified the desert hamster Phodopus roborovskii using molecular phylogenetic methods. We also provide revised distributional estimates for this species using niche modelling (Maxent and 19 bioclimatic variables), taking into account sampling bias. We evaluated suitable habitats for the species, identifying regions in the Trans-Himalayas that may harbour this species. This study improves the knowledge of the desert hamster{\textquoteright}s range and is a new record and an addition to the Indian sub-continental mammalian fauna, similar to 750 km southward extension from its known range.

}, doi = {10.1515/mammalia-2018-0199}, author = {Ramachandran, Vivek and Joshi, Mukta and Ambekar, Mayuresh and Charoo, Samina Amin and Ramakrishnan, Uma} } @article {81504, title = {Genetic diversity targets and indicators in the CBD post-2020 Global Biodiversity Framework must be improved}, journal = {BIOLOGICAL CONSERVATION}, volume = {248}, year = {2020}, month = {08/2020}, abstract = {

The 196 parties to the Convention on Biological Diversity (CBD) will soon agree to a post-2020 global framework for conserving the three elements of biodiversity (genetic, species, and ecosystem diversity) while ensuring sustainable development and benefit sharing. As the most significant global conservation policy mechanism, the new CBD framework has far-reaching consequences- it will guide conservation actions and reporting for each member country until 2050. In previous CBD strategies, as well as other major conservation policy mechanisms, targets and indicators for genetic diversity (variation at the DNA level within species, which facilitates species adaptation and ecosystem function) were undeveloped and focused on species of agricultural relevance. We assert that, to meet global conservation goals, genetic diversity within all species, not just domesticated species and their wild relatives, must be conserved and monitored using appropriate metrics. Building on suggestions in a recent Letter in Science (Laikre et al., 2020) we expand argumentation for three new, pragmatic genetic indicators and modifications to two current indicators for maintaining genetic diversity and adaptive capacity of all species, and provide guidance on their practical use. The indicators are: 1) the number of populations with effective population size above versus below 500, 2) the proportion of populations maintained within species, 3) the number of species and populations in which genetic diversity is monitored using DNA-based methods. We also present and discuss Goals and Action Targets for post-2020 biodiversity conservation which are connected to these indicators and underlying data. These pragmatic indicators and goals have utility beyond the CBD; they should benefit conservation and monitoring of genetic diversity via national and global policy for decades to come.

}, doi = {10.1016/j.biocon.2020.108654}, author = {Hoban, Sean and Bruford, Michael and Jackson, JD and Lopes-Fernandes, M and ....... and Ramakrishnan, Uma and et al} } @article {84573, title = {Health Heatmap of India: An Open Data Platform.}, journal = {J Indian Inst Sci}, year = {2020}, month = {2020 Oct 18}, pages = {1-16}, abstract = {

Health Heatmap of India is an open data platform built for bringing together data from diverse sources and facilitating visualization, analysis, and insight building from such data. In this paper, we describe the context and need for such an open data platform and describe the technical aspects of building it. The beta site of the portal is available at https://healthheatmapindia.org.

}, issn = {0970-4140}, doi = {10.1007/s41745-020-00196-z}, author = {Dinesh, Akshay S and Mathur, Varnita and Ansil, B R and Chandru, Vijay and Chellam, Ravi and Vanak, Abi Tamim and Ramakrishnan, Uma and Rajagopal, Prabhakar} } @article {83633, title = {Metabarcoding for parallel identification of species, sex and diet of obligate scavengers: an application to globally-threatened Gyps vultures}, journal = {CONSERVATION GENETICS RESOURCES}, year = {2020}, month = {2020}, abstract = {

After suffering a massive decline (similar to 99\%) in numbers caused by feeding on livestock carcasses containing the nephrotoxic drug diclofenac, critically endangeredGypsvultures now persist in low numbers in the Indian subcontinent. Most are concentrated near National Parks, likely due to availability of wild carcasses free from toxic veterinary drugs. Quantification of vulture diets is critical to test this hypothesis. We describe a validated "field-to-benchtop-to-desktop" metabarcoding workflow for assessing species- and sex-specific diet of these obligate scavengers from non-invasively collected faecal samples. Seven metabarcodes were designed to simultaneouslsy identify the vulture species, sex and diet. Amplicons generated from multiplex PCRs were indexed and sequenced on an Illumina Miseq platform. We included controls and three replicates per sample to establish a series of non-arbitrary thresholds to filter the sequence data and eliminate cross-contamination, PCR/sequencing errors and false positives. This strategy enabled identification of species and sex for all samples and diet-specific sequences with high taxonomic resolution for 97\% of samples. Just four (two for diet, one each for vulture species and sexing) metabarcodes were sufficient to meet the objectives. This preliminary analysis suggests that domestic livestock is the most frequently consumed diet item across samples from inside and outside protected habitats. Our method provides a rapid and reliable tool for describing large-scale variation in consumption of domestic versus wild species in the diet of these scavengers, paving the way for a better understanding of the role protected areas play in persistence and recovery of the remainingGypsvultures in the wild.

}, doi = {10.1007/s12686-020-01171-7}, author = {Ghosh-Harihar, Mousumi and Gurung, Nehal and Shukla, Harsh and Sinha, Ishani and Pandit, Awadhesh and Prakash, Vibhu and Green, Rhys E. and Ramakrishnan, Uma} } @article {83636, title = {Opinion: Envisioning a biodiversity science for sustaining human well-being.}, journal = {Proc Natl Acad Sci U S A}, year = {2020}, month = {2020 Sep 30}, issn = {1091-6490}, doi = {10.1073/pnas.2018436117}, author = {Bawa, Kamaljit S and Nawn, Nandan and Chellam, Ravi and Krishnaswamy, Jagdish and Mathur, Vinod and Olsson, Shannon B and Pandit, Nitin and Rajagopal, Prabhakar and Sankaran, Mahesh and Shaanker, R Uma and Shankar, Darshan and Ramakrishnan, Uma and Vanak, Abi Tamim and Quader, Suhel} } @article {72071, title = {The role of geography, environment, and genetic divergence on the distribution of pikas in the Himalaya}, journal = {ECOLOGY AND EVOLUTION}, year = {2020}, month = {01/2020}, abstract = {

Pikas (Ochotona Link, 1795) are high-altitude specialist species making them a useful bioindicator species to warming in high-altitude ecosystem. The Himalayan Mountains are an important part of their range, supporting approximately 23\%{\textendash}25\% of total pika species worldwide, yet we lack basic information on the distribution patterns. We combine field-based surveys with genetics-based identification and phylogeny to identify differences in species-environment relationships. Further, we suggest putative evolutionary causes for the observed niche patterns.

}, doi = {10.1002/ece3.6007}, author = {Dahal, Nishma and Kumar, Sunil and Noon, Barry R and Nayak, Rajat and Lama, Rinzin Phunjok and Ramakrishnan, Uma} } @article {59705, title = {Coalescent theory of migration network motifs.}, journal = {Mol Biol Evol}, year = {2019}, month = {2019 Jun 04}, abstract = {

Natural populations display a variety of spatial arrangements, each potentially with a distinctive impact on genetic diversity and genetic differentiation among subpopulations. Although the spatial arrangement of populations can lead to intricate migration networks, theoretical developments have focused mainly on a small subset of such networks, emphasizing the island-migration and stepping-stone models. In this study, we investigate all small network motifs: the set of all possible migration networks among populations subdivided into at most four subpopulations. For each motif, we use coalescent theory to derive expectations for three quantities that describe genetic variation: nucleotide diversity, FST, and half-time to equilibrium diversity. We describe the impact of network properties on these quantities, finding that motifs with a high mean node degree have the largest nucleotide diversity and the longest time to equilibrium, whereas motifs with low density have the largest FST. In addition, we show that the motifs whose pattern of variation is most strongly influenced by loss of a connection or a subpopulation are those that can be split easily into disconnected components. We illustrate our results using two example datasets-sky island birds of genus Sholicola and Indian tigers-identifying disturbance scenarios that produce the greatest reduction in genetic diversity; for tigers, we also compare the benefits of two assisted gene flow scenarios. Our results have consequences for understanding the effect of geography on genetic diversity, and they can assist in designing strategies to alter population migration networks toward maximizing genetic variation in the context of conservation of endangered species.

}, issn = {1537-1719}, doi = {10.1093/molbev/msz136}, author = {Alcala, Nicolas and Goldberg, Amy and Ramakrishnan, Uma and Rosenberg, Noah A} } @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 {67828, title = {Filovirus-reactive antibodies in humans and bats in Northeast India imply zoonotic spillover.}, journal = {PLoS Negl Trop Dis}, volume = {13}, year = {2019}, month = {2019 Oct}, pages = {e0007733}, abstract = {

Bats are reservoirs for several zoonotic pathogens, including filoviruses. Recent work highlights the diversity of bat borne filoviruses in Asia. High risk activities at the bat-human interface pose the threat of zoonotic virus transmission. We present evidence for prior exposure of bat harvesters and two resident fruit bat species to filovirus surface glycoproteins by screening sera in a multiplexed serological assay. Antibodies reactive to two antigenically distinct filoviruses were detected in human sera and to three individual filoviruses in bats in remote Northeast India. Sera obtained from Eonycteris spelaea bats showed similar patterns of cross-reactivity as human samples, suggesting them as the species responsible for the spillover. In contrast, sera from Rousettus leschenaultii bats reacted to two different virus glycoproteins. Our results indicate circulation of several filoviruses in bats and the possibility for filovirus transmission from bats to humans.

}, issn = {1935-2735}, doi = {10.1371/journal.pntd.0007733}, author = {Dovih, Pilot and Laing, Eric D and Chen, Yihui and Low, Dolyce H W and Ansil, B R and Yang, Xinglou and Shi, Zhengli and Broder, Christopher C and Smith, Gavin J D and Linster, Martin and Ramakrishnan, Uma and Mendenhall, Ian H} } @article {60613, title = {Geographical and host species barriers differentially affect generalist and specialist parasite community structure in a tropical sky-island archipelago.}, journal = {Proc Biol Sci}, volume = {286}, year = {2019}, month = {2019 Jun 12}, pages = {20190439}, abstract = {

Understanding why some parasites emerge in novel host communities while others do not has broad implications for human and wildlife health. In the case of haemosporidian blood parasites, epidemic wild bird mortalities on oceanic islands have been linked to Plasmodium spp., but not genera like Haemoproteus. Indeed, Haemoproteus is absent from many oceanic islands. By contrast, birds on continental islands share long coevolutionary histories with both Plasmodium and Haemoproteus, and are thus ideal model systems to elucidate eco-evolutionary endpoints associated with these parasites in oceanic islands. Here, we examine eco-evolutionary dynamics of avian haemosporidian in the Shola sky-island archipelago of the Western Ghats, India. Our analyses reveal that compared to Plasmodium, Haemoproteus lineages were highly host-specific and diversified via co-speciation with their hosts. We show that community structure of host-generalist Plasmodium was primarily driven by geographical factors (e.g. biogeographic barriers), while that of host-specialist Haemoproteus was driven by host species barriers (e.g. phylogenetic distance). Consequently, a few host species can harbour a high diversity of Plasmodium lineages which, in turn, are capable of infecting multiple host species. These two mechanisms can act in concert to increase the risk of introduction, establishment, and emergence of novel Plasmodium lineages in island systems.

}, issn = {1471-2954}, doi = {10.1098/rspb.2019.0439}, author = {Gupta, Pooja and Vishnudas, C K and Ramakrishnan, Uma and Robin, V V and Dharmarajan, Guha} } @article {59739, title = {The hills are alive with geckos! A radiation of a dozen species on sky islands across peninsular India (Squamata: Gekkonidae, Hemiphyllodactylus) with the description of three new species}, journal = {Organisms Diversity \& Evolution}, volume = {19}, year = {2019}, month = {06/2019}, pages = {341{\textendash}361}, abstract = {

Sky Islands are high-elevation environments that are separated by warmer, low elevations, forming natural patches of unique montane habitat that often persist through changing climates. Peninsular India was ancestrally forested and has gradually become more arid since at least the Oligocene, and open landscapes have dominated since the middle-late Miocene. Mesic forests today are largely restricted to coastal mountains and some other montane habitats. A mitochondrial phylogeny and fossil-calibrated timetree of Indian Hemiphyllodactylus reveal an Indochinese origin and an endemic radiation with 12 species-level lineages, where a single species was known, that diversified in the Oligocene-Miocene across montane forest habitats in the Eastern Ghats and south India. The phylogeny also suggests the discontinuous Eastern Ghats mountain range encompasses two distinct biogeographic entities: north and south of the Pennar/Krishna-Godavari River basins. This study\ highlights the deep history of the region and the importance of montane habitats as islands of unique biodiversity that have persisted through millions of years of changing climates. We describe three new species: Hemiphyllodactylus arakuensis sp. nov., H. jnana sp. nov. and H. kolliensis sp. nov. from montane habitats above 1000\ m. The montane habitats of these species are emerging hotspots of reptile endemism, and this study emphasizes the need for systematic biodiversity inventory across India to uncover basic patterns of diversity and distribution.

}, doi = {10.1007/s13127-019-00392-5}, author = {Agarwal, Ishan and Khandekar, A and Giri, Varad B. and Ramakrishnan, Uma and Karanth, Praveen} } @article {45447, title = {Comparative Population Structure in Species of Bats Differing in Ecology and Morphology in the Andaman Islands, India}, journal = {Acta Chiropterologica}, volume = {20}, year = {2018}, month = {06/2018}, pages = {85-98}, abstract = {

Gene flow results from movement between populations, homogenising gene pools and impacting genetic variation and evolution. Growing evidence suggests that movement of individuals among populations may be more strongly determined by ecological traits. We compared genetic and morphometric differentiation in four species of bats {\textemdash} Eonycteris spelaea, Cynopterus sphinx, Rhinolophus affinis and Hipposideros pomona {\textemdash} which differ in their flight capability and roosting requirement to understand their effects in shaping genetic structure. Hypervariable region I of the mitochondrial control region was amplified from 40 E. spelaea, 28 C. sphinx, 44 R. affinis and 57 H. pomona sampled from locations spread across the Andaman archipelago. Populations of E. spelaea were nearly panmictic; R. affinis were differentiated into two clusters, and H. pomona were differentiated into three clusters. Consistent genetic and morphometric clusters were obtained for C. sphinx and the genetic break for C. sphinx occurs between Middle and South Andaman Islands, coincided with the Jarawa Tribal Reserve. In conclusion, poorly-dispersing, caveroosting species show high population structure, but when flight capability is very well-developed, the effect of disjunct roost availability is offset. The genetic structure of C. sphinx where we expected panmixia, is possibly confounded by the colonization history of its two genetic lineages and its habitat use which may prevent significant gene flow between the two lineages.

}, doi = {10.3161/15081109ACC2018.20.1.006}, author = {Chakravarty, R and Chattopadhyay, Balaji and Ramakrishnan, Uma} } @article {36276, title = {The critically endangered forest owlet Heteroglaux blewitti is nested within the currently recognized Athene clade: A century-old debate addressed.}, journal = {PLoS One}, volume = {13}, year = {2018}, month = {2018}, pages = {e0192359}, abstract = {

Range-restricted species generally have specific niche requirements and may often have unique evolutionary histories. Unfortunately, many of these species severely lack basic research, resulting in poor conservation strategies. The phylogenetic relationship of the Critically Endangered Forest Owlet Heteroglaux blewitti has been the subject of a century-old debate. The current classifications based on non-phylogenetic comparisons of morphology place the small owls of Asia into three genera, namely, Athene, Glaucidium, and Heteroglaux. Based on morphological and anatomical data, H. blewitti has been alternatively hypothesized to belong within Athene, Glaucidium, or its own monotypic genus Heteroglaux. To test these competing hypotheses, we sequenced six loci (~4300 bp data) and performed phylogenetic analyses of owlets. Mitochondrial and nuclear trees were not congruent in their placement of H. blewitti. However, both mitochondrial and nuclear combined datasets showed strong statistical support with high maximum likelihood bootstrap (\>/ = 90) and Bayesian posterior probability values (\>/ = 0.98) for H. blewitti being nested in the currently recognized Athene group, but not sister to Indian A. brama. The divergence of H. blewitti from its sister taxa was between 4.3 and 5.7 Ma coinciding with a period of drastic climatic changes in the Indian subcontinent. This study presented the first genetic analysis of H. blewitti, a Critically Endangered species, and addressed the long debate on the relationships of the Athene-Heteroglaux-Glaucidium complex. We recommend further studies with more data and complete taxon sampling to understand the biogeography of Indian Athene species.

}, keywords = {Animals, Bayes Theorem, Conservation of Natural Resources, Endangered Species, Fossils, Phylogeny, Strigiformes}, issn = {1932-6203}, doi = {10.1371/journal.pone.0192359}, author = {Koparde, Pankaj and Mehta, Prachi and Reddy, Sushma and Ramakrishnan, Uma and Mukherjee, Shomita and Robin, V V} } @article {48888, title = {Gene expression is implicated in the ability of pikas to occupy Himalayan elevational gradient.}, journal = {PLoS One}, volume = {13}, year = {2018}, month = {2018}, pages = {e0207936}, abstract = {

Species are shifting their ranges due to climate change, many moving to cooler and higher locations. However, with elevation increase comes oxygen decline, potentially limiting a species{\textquoteright} ability to track its environment depending on what mechanisms it has available to compensate for hypoxic stress. Pikas (Family Ochotonidae), cold-specialist small mammal species, are already undergoing elevational range shifts. We collected RNA samples from one population of Ochotona roylei in the western Himalaya at three sites- 3,600, 4,000, and 5,000 meters-and found no evidence of significant population genetic structure nor positive selection among sites. However, out of over 10,000 expressed transcripts, 26 were significantly upregulated at the 5,000 m site and were significantly enriched for pathways consistent with physiological compensation for limited oxygen. These results suggest that differences in gene expression may play a key role in enabling hypoxia tolerance on this local scale, indicating elevational flexibility that may facilitate successful range shifts in response to climate change.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0207936}, author = {Solari, Katherine A and Ramakrishnan, Uma and Hadly, Elizabeth A} } @article {39421, title = {Gut microflora may facilitate adaptation to anthropic habitat: A comparative study in .}, journal = {Ecol Evol}, volume = {8}, year = {2018}, month = {2018 Jul}, pages = {6463-6472}, abstract = {

Anthropophilic species ("commensal" species) that are completely dependent upon anthropic habitats experience different selective pressures particularly in terms of food than their noncommensal counterparts. Using a next-generation sequencing approach, we characterized and compared the gut microflora community of 53 commensal and 59 noncommensal captured in 10 locations in the Western Ghats, India. We observed that, while species identity was important in characterizing the microflora communities of the two hosts, environmental factors also had a significant effect. While there was significant geographic variation in the microflora of the noncommensal , there was no effect of geographic distance on gut microflora of the commensal . Interestingly, host genetic distance did not significantly influence the community in either hosts. Collectively, these results indicate that a shift in habitat is likely to result in a change in the gut microflora community and imply that the gut microflora is a complex trait, influenced by various parameters in different habitats.

}, issn = {2045-7758}, doi = {10.1002/ece3.4040}, author = {Varudkar, Amruta and Ramakrishnan, Uma} } @article {36661, title = {Maintaining tiger connectivity and minimizing extinction into the next century: Insights from landscape genetics and spatially-explicit simulations }, journal = {BIOLOGICAL CONSERVATION }, volume = {218}, year = {2018}, month = {02/2018}, pages = {181-191 }, doi = {10.1016/j.biocon.2017.12.022 }, author = {Thatte, Prachi and Joshi, A and Vaidyanathan, S and Landguth, E and Ramakrishnan, Uma} } @article {45449, title = {An optimized protocol for large-scale in situ sampling and analysis of volatile organic compounds}, journal = {Ecology and Evolution}, volume = {8}, year = {2018}, month = {06/2018}, pages = {59242-5935}, abstract = {

Chemical ecology is an ever-expanding field with a growing interest in population- and community-level studies. Many such studies are hindered due to lack of an efficient and accelerated protocol for large-scale sampling and analysis of chemical compounds. Here, we present an optimized protocol for such large-scale study of volatiles. A large-scale in situ study to understand role of semiochemicals in variation in mating success of lekking blackbuck was conducted. Suitable methods for sampling and statistical analysis were identified by testing and comparing the efficiencies of available techniques to reduce analysis time while retaining sensitivity and comprehensiveness. Solid-phase extraction using polydimethylsiloxane, analysis using a semiautomated detection of retention time and base peak, and statistical analysis using random forest algorithm were identified as the most efficient methods for large-scale in situ sampling and analysis of volatiles. The protocol for large-scale volatile analysis can facilitate evolutionary and metaecological studies of volatiles in situ from all types of biological samples. The protocol has potential for wider application with the analysis and interpretation methods being suitable for all kinds of semiochemicals, including nonvolatile chemicals.

}, doi = {10.1002/ece3.4138}, author = {Nair, Jyothi and Sanmugam, PV and Karpe, Snehal D and Ramakrishnan, Uma and Olsson, Shannon B} } @article {79777, title = {An optimized protocol for large-scale in situ sampling and analysis of volatile organic compounds }, journal = {Ecology and Evolution}, volume = {8}, year = {2018}, month = {06/2018}, pages = {5924-5936}, abstract = {

Chemical ecology is an ever-expanding field with a growing interest in population- and community-level studies. Many such studies are hindered due to lack of an efficient and accelerated protocol for large-scale sampling and analysis of chemical compounds. Here, we present an optimized protocol for such large-scale study of volatiles. A large-scale in situ study to understand role of semiochemicals in variation in mating success of lekking blackbuck was conducted. Suitable methods for sampling and statistical analysis were identified by testing and comparing the efficiencies of available techniques to reduce analysis time while retaining sensitivity and comprehensiveness. Solid-phase extraction using polydimethylsiloxane, analysis using a semiautomated detection of retention time and base peak, and statistical analysis using random forest algorithm were identified as the most efficient methods for large-scale in situ sampling and analysis of volatiles. The protocol for large-scale volatile analysis can facilitate evolutionary and metaecological studies of volatiles in situ from all types of biological samples. The protocol has potential for wider application with the analysis and interpretation methods being suitable for all kinds of semiochemicals, including nonvolatile chemicals.

}, doi = {10.1002/ece3.4138}, author = {Nair, Jyothi and Pragadheesh, V S and Karpe, Snehal D and Ramakrishnan, Uma and Olsson, SB} } @article {31393, title = {Social structure of the harem-forming promiscuous fruit bat,, is the harem truly important?}, journal = {R Soc Open Sci}, volume = {5}, year = {2018}, month = {2018 Feb}, pages = {172024}, abstract = {

Bats are social animals and display a diverse variety of mating and social systems, with most species exhibiting some form of polygyny. Their social organization is fluid and individuals frequently switch partners and roosting sites. While harem-like social organization is observed in multiple tropical species, its importance is contested in many of them. In this study, we investigated the role of harems in the social organization of the old world fruit bat. Based on regular behavioural observations over a period of 20 months and genetic data from microsatellite markers, we observed that the social organization is flexible, individuals regularly shift between roosts and the social organization resembles a fission-fusion society. Behavioural and genetic analyses suggest that the harems are not strict units of social structure, and the colony does not show signatures of subdivision with harems as behavioural units. We also observed that there was no correlation between individuals with high association index and pairwise relatedness. Our findings indicate that similar to the mating system, the social organization ofcan also be categorized as a fission-fusion society, and hence the term {\textquoteright}harem{\textquoteright} is a misnomer. We conclude that the social system ofis flexible, with multi-male multi-female organization, and individuals tend to be loyal to a given area rather than a roost.

}, issn = {2054-5703}, doi = {10.1098/rsos.172024}, author = {Garg, Kritika M and Chattopadhyay, Balaji and Ramakrishnan, Uma} } @article {26659, title = {Climatic and geographic barriers drive distributional patterns of bird phenotypes within peninsular India}, journal = {Journal of Avian Biology}, volume = {48}, year = {2017}, month = {05/2017}, pages = {620-630}, abstract = {

Modern phylogenetic data provide unparalleled ability to test biogeographic paradigms, often suggested by differences in species distribution patterns. However, such approaches have been applied less at regional scales, particularly in Asia. In the absence of such data, we examine if concordance of distributional patterns for phenotypes (subspecies) suggest potential biogeographic barriers for birds in peninsular India. Specifically, we examine climatic and physical factors that might limit phenotype distributions in this region.

Various physical, vegetation and climatic barriers were demarcated to identify potential biogeographic units within peninsular India. We then collated occurrence of endemic or disjunctly distributed species and subspecies within these units using published range maps. We also quantified turnover between potential units, allowing us to identify significant biogeographic barriers. Three time-step climate data (Last Glacial Maxima, mid-Holocene and present) enabled us to examine differences between these potential biogeographic regions through time.

The Palk Straits, followed by the Goa Gap (\~{} 16{\textdegree}N) and the Godavari River emerged as the major barriers in this region. The Palk Straits and Godavari are physical barriers while Goa Gap appears to be a climate-mediated ecological divide. Mountain barriers like the Palghat Gap are not the most significant barriers as previously thought. Climatically intermediate regions appeared unstable in the past and showed inconsistent affinities to different geographic units across families. We suggest that relative climatic stability of the wet regions of the southern western Ghats could be responsible for high subspecies endemism here. Our approach provides hypotheses that can be tested with comparative multi-species phylogeographic data in the future.

}, doi = {10.1111/jav.01278}, author = {Ramachandran, V and Robin, V V and Tamma, Krishnapriya 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} } @article {25260, title = {Genetic Structure and Phylogeography of the Leopard Cat (Prionailurus bengalensis) Inferred from Mitochondrial Genomes.}, journal = {J Hered}, volume = {108}, year = {2017}, month = {2017 06 01}, pages = {349-360}, abstract = {

The Leopard cat Prionailurus bengalensis is a habitat generalist that is widely distributed across Southeast Asia. Based on morphological traits, this species has been subdivided into 12 subspecies. Thus far, there have been few molecular studies investigating intraspecific variation, and those had been limited in geographic scope. For this reason, we aimed to study the genetic structure and evolutionary history of this species across its very large distribution range in Asia. We employed both PCR-based (short mtDNA fragments, 94 samples) and high throughput sequencing based methods (whole mitochondrial genomes, 52 samples) on archival, noninvasively collected and fresh samples to investigate the distribution of intraspecific genetic variation. Our comprehensive sampling coupled with the improved resolution of a mitochondrial genome analyses provided strong support for a deep split between Mainland and Sundaic Leopard cats. Although we identified multiple haplogroups within the species{\textquoteright} distribution, we found no matrilineal evidence for the distinction of 12 subspecies. In the context of Leopard cat biogeography, we cautiously recommend a revision of the Prionailurus bengalensis subspecific taxonomy: namely, a reduction to 4 subspecies (2 mainland and 2 Sundaic forms).

}, keywords = {Animals, Asia, Southeastern, Biological Evolution, Cytochromes b, DNA, Mitochondrial, Felidae, Genetic Variation, Genetics, Population, Genome, Mitochondrial, Haplotypes, Phylogeography, Sequence Analysis, DNA}, issn = {1465-7333}, doi = {10.1093/jhered/esx017}, author = {Patel, Riddhi P and Wutke, Saskia and Lenz, Dorina and Mukherjee, Shomita and Ramakrishnan, Uma and Veron, G{\'e}raldine and Fickel, J{\"o}rns and Wilting, Andreas and F{\"o}rster, Daniel W} } @article {8059, title = {Genetics, morphology and ecology reveal a cryptic pika lineage in the Sikkim Himalaya.}, journal = {Mol Phylogenet Evol}, volume = {106}, year = {2017}, month = {09/2016}, pages = {55-60}, abstract = {

Asian pika species are morphologically \~{}similar and have overlapping ranges. This leads to uncertainty and species misidentification in the field. Phylogenetic analyses of such misidentified samples leads to taxonomic ambiguity. The ecology of many pika species remains understudied, particularly in the Himalaya, where sympatric species could be separated by elevation and/or substrate. We sampled, measured, and acquired genetic data from pikas in the Sikkim Himalaya. Our analyses revealed a cryptic lineage, Ochotona sikimaria, previously reported as a subspecies of O. thibetana. The results support the elevation of this lineage to the species level, as it is genetically divergent from O. thibetana, as well as sister species, O. cansus (endemic to central China) and O. curzoniae (endemic to the Tibetan plateau). The Sikkim lineage diverged from its sister species{\textquoteright} about 1.7-0.8 myr ago, coincident with uplift events in the Himalaya. Our results add to the recent spate of cryptic diversity identified from the eastern Himalaya and highlight the need for further study within the Ochotonidae.

}, issn = {1095-9513}, doi = {10.1016/j.ympev.2016.09.015}, author = {Dahal, Nishma and Lissovsky, Andrey A and Lin, Zhenzhen and Solari, Katherine and Hadly, Elizabeth A and Zhan, Xiangjiang and Ramakrishnan, Uma} } @article {26571, title = {Genomic data reveal a loss of diversity in two species of tuco-tucos (genus Ctenomys) following a volcanic eruption.}, journal = {Sci Rep}, volume = {7}, year = {2017}, month = {2017 Nov 24}, pages = {16227}, abstract = {

Marked reductions in population size can trigger corresponding declines in genetic variation. Understanding the precise genetic consequences of such reductions, however, is often challenging due to the absence of robust pre- and post-reduction datasets. Here, we use heterochronous genomic data from samples obtained before and immediately after the 2011 eruption of the Puyehue-Cord{\'o}n Caulle volcanic complex in Patagonia to explore the genetic impacts of this event on two parapatric species of rodents, the colonial tuco-tuco (Ctenomys sociabilis) and the Patagonian tuco-tuco (C. haigi). Previous analyses using microsatellites revealed no post-eruption changes in genetic variation in C. haigi, but an unexpected increase in variation in C. sociabilis. To explore this outcome further, we used targeted gene capture to sequence over 2,000 putatively neutral regions for both species. Our data revealed that, contrary to the microsatellite analyses, the eruption was associated with a small but significant decrease in genetic variation in both species. We suggest that genome-level analyses provide greater power than traditional molecular markers to detect the genetic consequences of population size changes, particularly changes that are recent, short-term, or modest in size. Consequently, genomic analyses promise to generate important new insights into the effects of specific environmental events on demography and genetic variation.

}, issn = {2045-2322}, doi = {10.1038/s41598-017-16430-1}, author = {Hsu, Jeremy L and Crawford, Jeremy Chase and Tammone, Mauro N and Ramakrishnan, Uma and Lacey, Eileen A and Hadly, Elizabeth A} } @article {20349, title = {Impact of wild prey availability on livestock predation by snow leopards.}, journal = {R Soc Open Sci}, volume = {4}, year = {2017}, month = {2017 Jun}, pages = {170026}, abstract = {

An increasing proportion of the world{\textquoteright}s poor is rearing livestock today, and the global livestock population is growing. Livestock predation by large carnivores and their retaliatory killing is becoming an economic and conservation concern. A common recommendation for carnivore conservation and for reducing predation on livestock is to increase wild prey populations based on the assumption that the carnivores will consume this alternative food. Livestock predation, however, could either reduce or intensify with increases in wild prey depending on prey choice and trends in carnivore abundance. We show that the extent of livestock predation by the endangered snow leopard Panthera uncia intensifies with increases in the density of wild ungulate prey, and subsequently stabilizes. We found that snow leopard density, estimated at seven sites, was a positive linear function of the density of wild ungulates-the preferred prey-and showed no discernible relationship with livestock density. We also found that modelled livestock predation increased with livestock density. Our results suggest that snow leopard conservation would benefit from an increase in wild ungulates, but that would intensify the problem of livestock predation for pastoralists. The potential benefits of increased wild prey abundance in reducing livestock predation can be overwhelmed by a resultant increase in snow leopard populations. Snow leopard conservation efforts aimed at facilitating increases in wild prey must be accompanied by greater assistance for better livestock protection and offsetting the economic damage caused by carnivores.

}, issn = {2054-5703}, doi = {10.1098/rsos.170026}, author = {Suryawanshi, Kulbhushansingh R and Redpath, Stephen M and Bhatnagar, Yash Veer and Ramakrishnan, Uma and Chaturvedi, Vaibhav and Smout, Sophie C and Mishra, Charudutt} } @article {13267, title = {Merging paleobiology with conservation biology to guide the future of terrestrial ecosystems.}, journal = {Science}, volume = {355}, year = {2017}, month = {2017 Feb 10}, abstract = {

Conservation of species and ecosystems is increasingly difficult because anthropogenic impacts are pervasive and accelerating. Under this rapid global change, maximizing conservation success requires a paradigm shift from maintaining ecosystems in idealized past states toward facilitating their adaptive and functional capacities, even as species ebb and flow individually. Developing effective strategies under this new paradigm will require deeper understanding of the long-term dynamics that govern ecosystem persistence and reconciliation of conflicts among approaches to conserving historical versus novel ecosystems. Integrating emerging information from conservation biology, paleobiology, and the Earth sciences is an important step forward on the path to success. Maintaining nature in all its aspects will also entail immediately addressing the overarching threats of growing human population, overconsumption, pollution, and climate change.

}, issn = {1095-9203}, doi = {10.1126/science.aah4787}, author = {Barnosky, Anthony D and Hadly, Elizabeth A and Gonzalez, Patrick and Head, Jason and Polly, P David and Lawing, A Michelle and Eronen, Jussi T and Ackerly, David D and Alex, Ken and Biber, Eric and Blois, Jessica and Brashares, Justin and Ceballos, Gerardo and Davis, Edward and Dietl, Gregory P and Dirzo, Rodolfo and Doremus, Holly and Fortelius, Mikael and Greene, Harry W and Hellmann, Jessica and Hickler, Thomas and Jackson, Stephen T and Kemp, Melissa and Koch, Paul L and Kremen, Claire and Lindsey, Emily L and Looy, Cindy and Marshall, Charles R and Mendenhall, Chase and Mulch, Andreas and Mychajliw, Alexis M and Nowak, Carsten and Ramakrishnan, Uma and Schnitzler, Jan and Das Shrestha, Kashish and Solari, Katherine and Stegner, Lynn and Stegner, M Allison and Stenseth, Nils Chr and Wake, Marvalee H and Zhang, Zhibin} } @article {26575, title = {Non-sister Sri Lankan white-eyes (genus Zosterops) are a result of independent colonizations.}, journal = {PLoS One}, volume = {12}, year = {2017}, month = {2017}, pages = {e0181441}, abstract = {

Co-occurrence of closely related taxa on islands could be attributed to sympatric speciation or multiple colonization. Sympatric speciation is considered to be rare in small islands, however multiple colonizations are known to be common in both oceanic and continental islands. In this study we investigated the phylogenetic relatedness and means of origin of the two sympatrically co-occurring Zosterops white-eyes, the endemic Zosterops ceylonensis and its widespread regional congener Z. palpebrosus, in the island of Sri Lanka. Sri Lanka is a continental island in the Indian continental shelf of the Northern Indian Ocean. Our multivariate morphometric analyses confirmed the phenotypic distinctness of the two species. Maximum Likelihood and Bayesian phylogenetic analyses with ~2000bp from two mitochondrial (ND2 and ND3) and one nuclear (TGF) gene indicated that they are phylogenetically distinct, and not sister to each other. The two subspecies of the peninsula India; Z. p. egregius of Sri Lanka and India and Z. p. nilgiriensis of Western Ghats (India) clustered within the Z. palpebrosus clade having a common ancestor. In contrast, the divergence of the endemic Z. ceylonensis appears to be much deeper and is basal to the other Zosterops white-eyes. Therefore we conclude that the two Zosterops species originated in the island through independent colonizations from different ancestral lineages, and not through island speciation or multiple colonization from the same continental ancestral population. Despite high endemism, Sri Lankan biodiversity is long considered to be a subset of southern India. This study on a speciose group with high dispersal ability and rapid diversification rate provide evidence for the contribution of multiple colonizations in shaping Sri Lanka{\textquoteright}s biodiversity. It also highlights the complex biogeographic patterns of the South Asian region, reflected even in highly vagile groups such as birds.

}, keywords = {Animals, Bayes Theorem, Biodiversity, DNA, Mitochondrial, Evolution, Molecular, Genetic Speciation, Geography, Passeriformes, Phylogeny, Sri Lanka, Sympatry}, issn = {1932-6203}, doi = {10.1371/journal.pone.0181441}, author = {Wickramasinghe, Nelum and Robin, V V and Ramakrishnan, Uma and Reddy, Sushma and Seneviratne, Sampath S} } @article {25698, title = {A phylogeny of open-habitat lizards (Squamata: Lacertidae: Ophisops) supports the antiquity of Indian grassy biomes}, journal = {JOURNAL OF BIOGEOGRAPHY }, volume = {44}, year = {2017}, month = {09/2017}, pages = {2021-2032}, abstract = {

India is dominated by tropical grassy biomes (TGBs), traditionally considered seres or degraded forest, with low diversity relative to the restricted, ancestral wet zone. It is unclear if Indian grasslands and other open habitats are anthropogenically derived or native, old-growth habitats; without a clear timescale of grassland evolution. One way to understand grassland evolution is to study the diversification in taxa restricted to open habitats. We use a dated phylogeny of Ophisops to address questions related to the origin, diversification and inter-relationships of Indian and Saharo-Arabian Ophisops, and ultimately the origin of Indian grasslands and open habitats.

}, doi = {10.1111/jbi.12999}, author = {Agarwal, Ishan and Ramakrishnan, Uma} } @article {12891, title = {Two new genera of songbirds represent endemic radiations from the Shola Sky Islands of the Western Ghats, India.}, journal = {BMC Evol Biol}, volume = {17}, year = {2017}, month = {2017 Jan 23}, pages = {31}, abstract = {

BACKGROUND: A long-standing view of Indian biodiversity is that while rich in species, there are few endemics or in-situ radiations within the subcontinent. One exception is the Western Ghats biodiversity hotspot, an isolated mountain range with many endemic species. Understanding the origins of the montane-restricted species is crucial to illuminate both taxonomic and environmental history.

RESULTS: With evidence from genetic, morphometric, song, and plumage data, we show that two songbird lineages endemic to the Western Ghats montane forest each have diversified into multiple distinct species. Historically labeled as single species of widespread Asian genera, these two lineages are highly divergent and do not group with the taxa in which they were previously classified but rather are distinct early divergences in larger Asian clades of flycatchers and babblers. Here we designated two new genera, the Western Ghats shortwings as Sholicola and the laughingthrushes as Montecincla, and evaluated species-limits to reflect distinct units by revising six previously named taxa and describing one novel species. Divergence dating showed that both these montane groups split from their Himalayan relatives during the Miocene, which is coincident with a shift towards arid conditions that fragmented the previously contiguous humid forest across peninsular India and isolated these lineages in the Western Ghats. Furthermore, these two genera showed congruent patterns of diversification across the Western Ghats Sky Islands, coincident with other climatic changes.

CONCLUSION: Our study reveals the existence of two independent endemic radiations in the high montane Western Ghats or Shola Sky Islands with coincident divergence times, highlighting the role of climate in the diversification of these ancient lineages. The endemic and highly divergent nature of these previously unrecognized species underscores the dearth of knowledge about the biogeography of the Asian tropics, even for comparatively well-known groups such as birds. The substantial increase in the diversity of this region underscores the need for more rigorous systematic analysis to inform biodiversity studies and conservation efforts.

}, issn = {1471-2148}, doi = {10.1186/s12862-017-0882-6}, author = {Robin, V V and Vishnudas, C K and Gupta, Pooja and Rheindt, Frank E and Hooper, Daniel M and Ramakrishnan, Uma and Reddy, Sushma} } @article {25699, title = {Variance in Female Reproductive Success Differentially Impacts Effective Population Size in the Short-Nosed Fruit Bat, Cynopterus sphinx}, journal = {Evolutionary Biology}, volume = {44}, year = {2017}, month = {09/2017}, pages = {3066-373}, abstract = {

Effective population size (Ne) quantifies the effects of micro-evolutionary processes and the rate of loss of genetic diversity in a population. Several demographic and mating parameters reduce Ne. Theoretical studies elucidate the impacts of various demographic and mating system parameters on Ne, while empirical studies illustrate realized Ne for species with differing life histories and mating systems. However, effect of intra-specific variation in mating system on effective size remains largely unexplored. In this paper we investigated the effect of promiscuous and polygynous mating on Ne in two wild populations of the short-nosed fruit bat, Cynopterus sphinx. Ne/N (ratio of effective population size to census size) was lower than unity in both populations, and much lower for the polygynous population compared to promiscuous population. Elasticity analyses reveal that Ne/N was sensitive to deviations in the sex ratio. Variance in female reproductive success had a higher impact on Ne compared to variance in male reproductive success in the promiscuous population. However, for the polygynous population, impact of variance in male reproductive success on Ne was higher than that of variance in female reproductive success. Our results suggest that depending on mating system, different populations of the same species could have alternate evolutionary trajectories. The rate of loss of genetic diversity would be lower for the promiscuous population compared to the polygynous population. Our study is the first to highlight which parameters would most significantly impact population specific Ne under different mating systems.

}, doi = {10.1007/s11692-017-9414-y}, author = {Garg, Kritika M and Ramakrishnan, Uma} } @article {3548, title = {Genome-wide data reveal cryptic diversity and genetic introgression in an Oriental cynopterine fruit bat radiation.}, journal = {BMC Evol Biol}, volume = {16}, year = {2016}, month = {2016}, pages = {41}, abstract = {

BACKGROUND: The Oriental fruit bat genus Cynopterus, with several geographically overlapping species, presents an interesting case study to evaluate the evolutionary significance of coexistence versus isolation. We examined the morphological and genetic variability of congeneric fruit bats Cynopterus sphinx and C. brachyotis using 405 samples from two natural contact zones and 17 allopatric locations in the Indian subcontinent; and investigated the population differentiation patterns, evolutionary history, and the possibility of cryptic diversity in this species pair.

RESULTS: Analysis of microsatellites, cytochrome b gene sequences, and restriction digestion based genome-wide data revealed that C. sphinx and C. brachyotis do not hybridize in contact zones. However, cytochrome b gene sequences and genome-wide SNP data helped uncover a cryptic, hitherto unrecognized cynopterine lineage in northeastern India coexisting with C. sphinx. Further analyses of shared variation of SNPs using Patterson{\textquoteright}s D statistics suggest introgression between this lineage and C. sphinx. Multivariate analyses of morphology using genetically classified grouping confirmed substantial morphological overlap between C. sphinx and C. brachyotis, specifically in the high elevation contact zones in southern India.

CONCLUSION: Our results uncover novel diversity and detect a pattern of genetic introgression in a cryptic radiation of bats, demonstrating the complicated nature of lineage diversification in this poorly understood taxonomic group. Our results highlight the importance of genome-wide data to study evolutionary processes of morphologically similar species pairs. Our approach represents a significant step forward in evolutionary research on young radiations of non-model species that may retain the ability of interspecific gene flow.

}, issn = {1471-2148}, doi = {10.1186/s12862-016-0599-y}, author = {Chattopadhyay, Balaji and Garg, Kritika M and Kumar, A K Vinoth and Doss, D Paramanantha Swami and Rheindt, Frank E and Kandula, Sripathi and Ramakrishnan, Uma} } @article {1005, title = {Deep and wide valleys drive nested phylogeographic patterns across a montane bird community.}, journal = {Proc Biol Sci}, volume = {282}, year = {2015}, month = {2015 Jul 7}, abstract = {

Montane species distributions interrupted by valleys can lead to range fragmentation, differentiation and ultimately speciation. Paleoclimatic fluctuations may accentuate or reduce such diversification by temporally altering the extent of montane habitat and may affect species differentially. We examined how an entire montane bird community of the Western Ghats--a linear, coastal tropical mountain range--responds to topographic valleys that host different habitats. Using genetic data from 23 species (356 individuals) collected across nine locations, we examined if different species in the community reveal spatial concordance in population differentiation, and whether the timing of these divergences correlate with climatic events. Our results reveal a nested effect of valleys, with several species (10 of 23) demonstrating the oldest divergences associated with the widest and deepest valley in the mountain range, the Palghat Gap. Further, a subset of these 10 species revealed younger divergences across shallower, narrower valleys. We recovered discordant divergence times for all valley-affected montane birds, mostly in the Pleistocene, supporting the Pliestocene-pump hypotheses and highlighting the role of climatic fluctuations during this period in driving species evolution. A majority of species remain unaffected by valleys, perhaps owing to geneflow or extinction-recolonization dynamics. Studying almost the entire community allowed us to uncover a range of species{\textquoteright} responses, including some generalizable and other unpredicted patterns.

}, issn = {1471-2954}, doi = {10.1098/rspb.2015.0861}, author = {Robin, V V and Vishnudas, C K and Gupta, Pooja and Ramakrishnan, Uma} } @article {875, title = {Higher speciation and lower extinction rates influence mammal diversity gradients in Asia.}, journal = {BMC Evol Biol}, volume = {15}, year = {2015}, month = {2015}, pages = {11}, abstract = {

BACKGROUND: Little is known about the patterns and correlates of mammal diversity gradients in Asia. In this study, we examine patterns of species distributions and phylogenetic diversity in Asia and investigate if the observed diversity patterns are associated with differences in diversification rates between the tropical and non-tropical regions. We used species distribution maps and phylogenetic trees to generate species and phylogenetic diversity measures for 1{\textdegree} {\texttimes} 1{\textdegree} cells across mainland Asia. We constructed lineage-through-time plots and estimated diversification shift-times to examine the temporal patterns of diversifications across orders. Finally, we tested if the observed gradients in Asia could be associated with geographical differences in diversification rates across the tropical and non-tropical biomes. We estimated speciation, extinction and dispersal rates across these two regions for mammals, both globally and for Asian mammals.

RESULTS: Our results demonstrate strong latitudinal and longitudinal gradients of species and phylogenetic diversity with Southeast Asia and the Himalayas showing highest diversity. Importantly, our results demonstrate that differences in diversification (speciation, extinction and dispersal) rates between the tropical and the non-tropical biomes influence the observed diversity gradients globally and in Asia. For the first time, we demonstrate that Asian tropics act as both cradles and museums of mammalian diversity.

CONCLUSIONS: Temporal and spatial variation in diversification rates across different lineages of mammals is an important correlate of species diversity gradients observed in Asia.

}, keywords = {Animals, Asia, Biodiversity, Genetic Speciation, Mammals, Phylogeny}, issn = {1471-2148}, doi = {10.1186/s12862-015-0289-1}, author = {Tamma, Krishnapriya and Ramakrishnan, Uma} } @article {1001, title = {Islands within islands: two montane palaeo-endemic birds impacted by recent anthropogenic fragmentation.}, journal = {Mol Ecol}, volume = {24}, year = {2015}, month = {2015 Jul}, pages = {3572-84}, abstract = {

Anthropogenic habitat fragmentation of species that live in naturally patchy metapopulations such as mountaintops or sky islands experiences two levels of patchiness. Effects of such multilevel patchiness on species have rarely been examined. Metapopulation theory suggests that patchy habitats could have varied impacts on persistence, dependent on differential migration. It is not known whether montane endemic species, evolutionarily adapted to natural patchiness, are able to disperse between anthropogenic fragments at similar spatial scales as natural patches. We investigated historic and contemporary gene flow between natural and anthropogenic patches across the distribution range of a Western Ghats sky-island-endemic bird species complex. Data from 14 microsatellites for 218 individuals detected major genetic structuring by deep valleys, including one hitherto undescribed barrier. As expected, we found strong effects of historic genetic differentiation across natural patches, but not across anthropogenic fragments. Contrastingly, contemporary differentiation (D(PS)) was higher relative to historic differentiation (F(ST)) in anthropogenic fragments, despite the species{\textquoteright} ability to historically traverse shallow valleys. Simulations of recent isolation resulted in high D(PS)/F(ST) values, confirming recent isolation in Western Ghats anthropogenic fragments and also suggesting that this ratio can be used to identifying recent fragmentation in the context of historic connectedness. We suggest that in this landscape, in addition to natural patchiness affecting population connectivity, anthropogenic fragmentation additionally impacts connectivity, making anthropogenic fragments akin to islands within natural islands of montane habitat, a pattern that may be recovered in other sky-island systems.

}, keywords = {Animal Distribution, Animals, Computer Simulation, Conservation of Natural Resources, Ecosystem, Gene Flow, Genetic Variation, Genetics, Population, Geography, India, Microsatellite Repeats, Passeriformes, Phylogeography, Sequence Analysis, DNA}, issn = {1365-294X}, doi = {10.1111/mec.13266}, author = {Robin, V V and Gupta, Pooja and Thatte, Prachi and Ramakrishnan, Uma} } @article {872, title = {Males and females gain differentially from sociality in a promiscuous fruit bat Cynopterus sphinx.}, journal = {PLoS One}, volume = {10}, year = {2015}, month = {2015}, pages = {e0122180}, abstract = {

Sociality emerges when the benefits of group living outweigh its costs. While both males and females are capable of strong social ties, the evolutionary drivers for sociality and the benefits accrued maybe different for each sex. In this study, we investigate the differential reproductive success benefits of group membership that males and females might obtain in the promiscuous fruit bat Cynopterus sphinx. Individuals of this species live in flexible social groups called colonies. These colonies are labile and there is high turnover of individuals. However, colony males sire more offspring within the colony suggesting that being part of a colony may result in reproductive benefits for males. This also raises the possibility that long-term loyalty towards the colony may confer additional advantage in terms of higher reproductive success. We used ten seasons of genetic parentage data to estimate reproductive success and relatedness of individuals in the colony. We used recapture data to identify long and short-term residents in the colony as well as to obtain rates of recapture for males and females. Our results reveal that males have a significantly higher chance of becoming long-term residents (than females), and these long-term resident males gain twice the reproductive success compared to short-term resident males. We also observed that long-term resident females are related to each other and also achieve higher reproductive success than short-term resident females. In contrast, long-term resident males do not differ from short-term resident males in their levels of relatedness. Our results re-iterate the benefits of sociality even in species that are promiscuous and socially labile and possible benefits of maintaining a colony.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0122180}, author = {Garg, Kritika M and Chattopadhyay, Balaji and Swami Doss, D P and Kumar, A K Vinoth and Kandula, Sripathi and Ramakrishnan, Uma} } @article {894, title = {Quaternary climate change and social behavior shaped the genetic differentiation of an endangered montane primate from the southern edge of the Tibetan Plateau.}, journal = {Am J Primatol}, volume = {77}, year = {2015}, month = {2015 Mar}, pages = {271-84}, abstract = {

Multiple factors, including climate change, dispersal barriers, and social behavior influence the genetic structure of natural populations. While the effects of extrinsic factors such as historical climatic change and habitat topography have been well studied, mostly in temperate habitats, the simultaneous effects of intrinsic factors such as social behavior on genetic structure have rarely been explored. Such simultaneous effect, however, may particularly be common in social mammals such as many primates. Consequently, we studied the population structure of a rare and endangered social primate, the Arunachal macaque Macaca munzala, endemic to the northeastern Indian state of Arunachal Pradesh, located on the subtropical southern edge of the Tibetan Plateau and forming part of the Eastern Himalayan biodiversity hotspot. We studied a 534 bp-long mitochondrial DNA sequence and 22 autosomal microsatellite loci in individuals from three populations, Tawang, Upper Subansiri, and West Siang. The mtDNA data revealed three major divergence events: that between the Arunachal and bonnet macaques (ca. 1.61 mya), the founding of the West Siang population and the ancestral population of the present-day bonnet macaques (ca. 1.32 mya), and the divergence between the Tawang and Upper Subansiri populations (ca. 0.80 mya) that coincided with the major glacial events in the region. Comparing mitochondrial DNA with autosomal microsatellites, we also found evidence for female philopatry and male-driven long-distance gene flow. Arunachal macaques thus appear to be characterized by groups of philopatric females separated by geographical barriers and harsh climate but with dispersing males exerting a homogenizing effect on the nuclear gene pool. Given that severe population differentiation is of major concern in species conservation, we suggest that our study populations represent significant conservation units of this rare, endangered primate but, more importantly, emphasize the complex interplay of extrinsic and intrinsic factors in shaping the population structure of a social mammalian species.

}, keywords = {Animals, Behavior, Animal, Climate Change, DNA, Mitochondrial, Ecosystem, Evolution, Molecular, Female, Gene Flow, Genetics, Population, India, Macaca, Male, Microsatellite Repeats, Phylogeography, Population Dynamics, Sequence Analysis, DNA, Social Behavior}, issn = {1098-2345}, doi = {10.1002/ajp.22343}, author = {Chakraborty, Debapriyo and Ramakrishnan, Uma and Sinha, Anindya} } @article {890, title = {Tracing the geographic origin of traded leopard body parts in the indian subcontinent with DNA-based assignment tests.}, journal = {Conserv Biol}, volume = {29}, year = {2015}, month = {2015 Apr}, pages = {556-64}, abstract = {

Illicit trade in wildlife products is rapidly decimating many species across the globe. Such trade is often underestimated for wide-ranging species until it is too late for the survival of their remaining populations. Policing this trade could be vastly improved if one could reliably determine geographic origins of illegal wildlife products and identify areas where greater enforcement is needed. Using DNA-based assignment tests (i.e., samples are assigned to geographic locations), we addressed these factors for leopards (Panthera pardus) on the Indian subcontinent. We created geography-specific allele frequencies from a genetic reference database of 173 leopards across India to infer geographic origins of DNA samples from 40 seized leopard skins. Sensitivity analyses of samples of known geographic origins and assignments of seized skins demonstrated robust assignments for Indian leopards. We found that confiscated pelts seized in small numbers were not necessarily from local leopards. The geographic footprint of large seizures appeared to be bigger than the cumulative footprint of several smaller seizures, indicating widespread leopard poaching across the subcontinent. Our seized samples had male-biased sex ratios, especially the large seizures. From multiple seized sample assignments, we identified central India as a poaching hotspot for leopards. The techniques we applied can be used to identify origins of seized illegal wildlife products and trade routes at the subcontinent scale and beyond.

}, issn = {1523-1739}, doi = {10.1111/cobi.12393}, author = {Mondol, Samrat and Sridhar, Vanjulavalli and Yadav, Prasanjeet and Gubbi, Sanjay and Ramakrishnan, Uma} }