@article {161977, title = {Three{\textquoteright}s Company: Human infrastructure and diminishing savannas accentuate meso-carnivore interactions in a shared landscape of western India.}, year = {2025}, abstract = {

Human changes to natural habitats affect carnivores differently{\textemdash}some species benefit from new resources, while others face higher risks. In semi-arid Kachchh, India, researchers studied four meso-carnivores (golden jackal, jungle cat, Indian fox, and desert cat). They mapped habitats, measured fragmentation, and used camera traps and signs to understand where each species occurs and how they interact. Despite being the most fragmented, open savanna still supported three of the four species. Larger species showed dominance patterns influencing how they share space and time. Human disturbances, especially roads, reduced how often species co-occurred. Protecting savanna habitats and considering species interactions in policy can help prevent competition-based losses and maintain healthy carnivore communities.

}, keywords = {Free-ranging dogsInterspecific interactionsHabitat useHuman impactsCarnivoresShared landscapesTropics}, doi = {https://doi.org/10.1016/j.biocon.2025.111618}, author = {Ganguly, D and Srivathsa, A and Vasudev, D and Ramakrishnan, U} } @article {121921, title = {Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex predation. }, journal = {Gigascience}, volume = {12:giac112}, year = {2022}, month = {12/2022}, abstract = {

The tiger, a poster child for conservation, remains an endangered apex predator. Continued survival and recovery will require a comprehensive understanding of genetic diversity and the use of such information for population management. A high-quality tiger genome assembly will be an important tool for conservation genetics, especially for the Indian tiger, the most abundant subspecies in the wild. Here, we present high-quality near-chromosomal genome assemblies of a female and a male wild Indian tiger (Panthera tigris tigris). Our assemblies had a scaffold N50 of \>140 Mb, with 19 scaffolds corresponding to the 19 numbered chromosomes, containing 95\% of the genome. Our assemblies also enabled detection of longer stretches of runs of homozygosity compared to previous assemblies, which will help improve estimates of genomic inbreeding. Comprehensive genome annotation identified 26,068 protein-coding genes, including several gene families involved in key morphological features such as the teeth, claws, vision, olfaction, taste, and body stripes. We also identified 301 microRNAs, 365 small nucleolar RNAs, 632 transfer RNAs, and other noncoding RNA elements, several of which are predicted to regulate key biological pathways that likely contribute to the tiger{\textquoteright}s apex predatory traits. We identify signatures of positive selection in the tiger genome that are consistent with the Panthera lineage. Our high-quality genome will enable use of noninvasive samples for comprehensive assessment of genetic diversity, thus supporting effective conservation and management of wild tiger populations.

}, doi = {10.1093/gigascience/giac112.}, author = {Shukla, H and Suryamohan, K and Khan, A and Mohan, K and Perumal, RC and Mathew, OK and Menon, R and Dixon, MD and Muraleedharan, M and Kuriakose, B and Michael, S and Krishnankutty, SP and Zachariah, A and Seshagiri, S and Ramakrishnan, U} } @article {78173, title = {Are shed hair genomes the most effective noninvasive resource for estimating relationships in the wild?}, journal = {Ecol Evol}, volume = {10}, year = {2020}, month = {05/2020}, pages = {4583-4594}, abstract = {

Knowledge of relationships in wild populations is critical for better understanding mating systems and inbreeding scenarios to inform conservation strategies for endangered species. To delineate pedigrees in wild populations, study genetic connectivity, study genotype-phenotype associations, trace individuals, or track wildlife trade, many identified individuals need to be genotyped at thousands of loci, mostly from noninvasive samples. This requires us to (a) identify the most common noninvasive sample available from identified individuals, (b) assess the ability to acquire genome-wide data from such samples, and (c) evaluate the quality of such genome-wide data, and its ability to reconstruct relationships between animals within a population.We followed identified individuals from a wild endangered tiger population and found that shed hair samples were the most common compared to scat samples, opportunistically found carcasses, and opportunistic invasive samples. We extracted DNA from these samples, prepared whole genome sequencing libraries, and sequenced genomes from these.Whole genome sequencing methods resulted in between 25\%-98\% of the genome sequenced for five such samples. Exploratory population genetic analyses revealed that these data were free of holistic biases and could recover expected population structure and relatedness. Mitochondrial genomes recovered matrilineages in accordance with long-term monitoring data. Even with just five samples, we were able to uncover the matrilineage for three individuals with unknown ancestry.In summary, we demonstrated that noninvasive shed hair samples yield adequate quality and quantity of DNA in conjunction with sensitive library preparation methods, and provide reliable data from hundreds of thousands of SNPs across the genome. This makes shed hair an ideal noninvasive resource for studying individual-based genetics of elusive endangered species in the wild.Knowledge of relationships in wild populations is critical for better understanding mating systems and inbreeding scenarios to inform conservation strategies for endangered species. To delineate pedigrees in wild populations, study genetic connectivity, study genotype-phenotype associations, trace individuals, or track wildlife trade, many identified individuals need to be genotyped at thousands of loci, mostly from noninvasive samples. This requires us to (a) identify the most common noninvasive sample available from identified individuals, (b) assess the ability to acquire genome-wide data from such samples, and (c) evaluate the quality of such genome-wide data, and its ability to reconstruct relationships between animals within a population.We followed identified individuals from a wild endangered tiger population and found that shed hair samples were the most common compared to scat samples, opportunistically found carcasses, and opportunistic invasive samples. We extracted DNA from these samples, prepared whole genome sequencing libraries, and sequenced genomes from these.Whole genome sequencing methods resulted in between 25\%-98\% of the genome sequenced for five such samples. Exploratory population genetic analyses revealed that these data were free of holistic biases and could recover expected population structure and relatedness. Mitochondrial genomes recovered matrilineages in accordance with long-term monitoring data. Even with just five samples, we were able to uncover the matrilineage for three individuals with unknown ancestry.In summary, we demonstrated that noninvasive shed hair samples yield adequate quality and quantity of DNA in conjunction with sensitive library preparation methods, and provide reliable data from hundreds of thousands of SNPs across the genome. This makes shed hair an ideal noninvasive resource for studying individual-based genetics of elusive endangered species in the wild.

}, doi = {10.1002/ece3.6157}, author = {Khan, A and Patel, K and Bhattacharjee, S and Sharma, S and Chugani, AN and Sivaraman, K and Hosawad, V and Sahu,YK and Reddy, GV and Ramakrishnan, U} } @article {77440, title = {Human footprint differentially impacts genetic connectivity of four wide-ranging mammals in a fragmented landscape}, journal = {DIVERSITY AND DISTRIBUTIONS}, volume = {26}, year = {2020}, month = {03/2020}, pages = {299-314}, abstract = {

Aim: Maintaining connectivity is critical for long-term persistence of wild carnivores in landscapes fragmented due to anthropogenic activity. We examined spatial genetic structure and the impact of landscape features on genetic structure in four widespread species-jungle cat (Felis chaus), leopard (Panthera pardus), sloth bear (Melursus ursinus) and tiger (Panthera tigris).

Location: Our study was carried out in the central Indian landscape, a stronghold in terms of distribution and abundance of large mammals. The landscape comprises fragmented forests embedded in a heterogeneous matrix of multiple land use types.

Methods: Microsatellite data from non-invasively sampled individuals (90 jungle cats, 82 leopards, 104 sloth bears and 117 tigers) were used to investigate genetic differentiation. Impact of landscape features on genetic structure was inferred using a multimodel landscape resistance optimization approach.

Results: All four study species revealed significant isolation by distance (IBD). The correlation between genetic and geographic distance was significant only over a short distance for jungle cat, followed by longer distances for sloth bear, leopard and tiger. Overall, human footprint had a high negative impact on gene flow in tigers, followed by leopards, sloth bears and the least on jungle cats. Individual landscape variables-land use, human population density, density of linear features and roads-impacted the study species differently. Although land use was found to be an important variable explaining genetic structure for all four species, the amount of variation explained, and the optimum spatial resolution and the resistance values of different land use classes varied.

Main conclusions: As expected from theory, but rarely demonstrated using empirical data, the pattern of spatial autocorrelation of genetic variation scaled with dispersal ability and density of the study species. Landscape genetic analyses revealed species-specific impact of landscape features and provided insights into interactions between species biology and landscape structure. Our results emphasize the need for incorporating functional connectivity data from multiple species for landscape-level conservation planning.

}, doi = {10.1111/ddi.13022}, author = {Thatte, P and Chandramouli, A and Tyagi, A and Patel, K and Baro, P and Chhattani, H and Ramakrishnan, U} } @article {53170, title = {Evidence of filovirus and henipavirus in bats and bat harvesters, India}, journal = {International Journal of Infectious Diseases}, volume = {79}, year = {2019}, month = {02/2019}, pages = {60}, doi = {10.1016/j.ijid.2018.11.156}, author = {Br, A and Dovih, P and Ramakrishnan, U and Liang, E and Mendenhall, I and Wen Hong, D L and Smith, J G D} } @article {71094, title = {Human footprint differentially impacts genetic connectivity of four wide-ranging mammals in a fragmented landscape}, journal = {Diversity and Distribution}, year = {2019}, month = {12/2019}, abstract = {

Aim

Maintaining connectivity is critical for long-term persistence of wild carnivores in landscapes fragmented due to anthropogenic activity. We examined spatial genetic structure and the impact of landscape features on genetic structure in four widespread species{\textemdash}jungle cat (Felis chaus), leopard (Panthera pardus), sloth bear (Melursus ursinus) and tiger (Panthera tigris).

Location

Our study was carried out in the central Indian landscape, a stronghold in terms of distribution and abundance of large mammals. The landscape comprises fragmented forests embedded in a heterogeneous matrix of multiple land use types.

Methods

Microsatellite data from non-invasively sampled individuals (90 jungle cats, 82 leopards, 104 sloth bears and 117 tigers) were used to investigate genetic differentiation. Impact of landscape features on genetic structure was inferred using a multimodel landscape resistance optimization approach.

Results

All four study species revealed significant isolation by distance (IBD). The correlation between genetic and geographic distance was significant only over a short distance for jungle cat, followed by longer distances for sloth bear, leopard and tiger. Overall, human footprint had a high negative impact on gene flow in tigers, followed by leopards, sloth bears and the least on jungle cats. Individual landscape variables{\textemdash}land use, human population density, density of linear features and roads{\textemdash}impacted the study species differently. Although land use was found to be an important variable explaining genetic structure for all four species, the amount of variation explained, and the optimum spatial resolution and the resistance values of different land use classes varied.

Main conclusions

As expected from theory, but rarely demonstrated using empirical data, the pattern of spatial autocorrelation of genetic variation scaled with dispersal ability and density of the study species. Landscape genetic analyses revealed species-specific impact of landscape features and provided insights into interactions between species biology and landscape structure. Our results emphasize the need for incorporating functional connectivity data from multiple species for landscape-level conservation planning.

}, doi = {10.1111/ddi.13022}, author = {Thatte, P and Chandramouli, A and Tyagi, A and Patel, K and Baro, B and Chhattani, H and Ramakrishnan, U} } @article {66849, title = {Protected areas and biodiversity conservation in India}, journal = {BIOLOGICAL CONSERVATION}, volume = {237}, year = {2019}, month = {09/2019}, pages = {114-124}, abstract = {

Three well-supported generalizations in conservation biology are that developing tropical countries will experience the greatest biodiversity declines in the near future, they are some of the least studied areas in the world, and in these regions especially, protection requires local community support. We assess these generalizations in an evaluation of protected areas in India. The 5\% of India officially protected covers most ecoregions and protected areas have been an important reason why India has suffered no documented species extinctions in the past 70 years. India has strong legislation favouring conservation, government investment focused on 50 Tiger Reserves, and government compensation schemes that facilitate local support, all of which brighten future prospects. However, many protected areas are too small to maintain a full complement of species, making connectivity and species use of buffer zones a crucial issue. Conservation success and challenges vary across regions according to their development status. In less developed areas, notably the biodiverse northeast Himalaya, protected areas maintaining the highest biodiversity result from locally-focused efforts by dedicated individuals. Across India, we demonstrate considerable opportunities to increase local income through ecotourism. Our evaluation confirms a lack of data, increasing threats, and the importance of local support. Research on biodiversity in buffer zones, development of long-term monitoring schemes, and assessment of cash and conservation benefits from tourism are in particular need. For policy makers, two main goals should be the development of monitoring plans for {\textquoteleft}eco-sensitive zones{\textquoteright} around protected areas, and a strong emphasis on preserving established protected areas.

}, doi = {10.1016/j.biocon.2019.06.024}, author = {Ghosh-Harihar, M and An, R and Athrey, R and Borthakur, U and Chanchani, P and Chetry, D and Datta, A and Harihar, A and Karanth, KK and Mariyam, D and Mohan, D and Onial, M and Ramakrishnan, U and Robin, VV and Saxena, A and Shahabuddin, G and Thatte, P and Vijay, V and Wacker, K and Mathur, VB and Pimm, SL and Price, TD} } @article {36664, title = {Two new species of the Ophisops microlepis (Squamata: Lacertidae) complex from northwestern India with a key to Indian Ophisops }, journal = {JOURNAL OF NATURAL HISTORY }, volume = {52}, year = {2018}, month = {2018}, pages = {819-847 }, doi = {10.1080/00222933.2018.1436203 }, author = {Agarwal, I and Khandekar, A and Ramakrishnan, U and Vyas, R and Giri, VB} } @article {14060, title = {Serological Evidence of Lyssavirus Infection among Bats in Nagaland, a North-Eastern State in India.}, journal = {Epidemiol Infect}, year = {2017}, month = {2017 Feb 23}, pages = {1-7}, abstract = {

Bats are known to be reservoirs of several medically important viruses including lyssaviruses. However, no systematic surveillance for bat rabies has been carried out in India, a canine rabies endemic country with a high burden of human rabies. Surveillance for rabies virus (RABV) infection in bats was therefore carried out in Nagaland, a north-eastern state in India at sites with intense human-bat interfaces during traditional bat harvests. Brain tissues and sera from bats were tested for evidence of infection due to RABV. Brain tissues were subjected to the fluorescent antibody test for detection of viral antigen and real-time reverse transcriptase PCR for presence of viral RNA. Bat sera were tested for the presence of rabies neutralizing antibodies by the rapid fluorescent focus inhibition test. None of the bat brains tested (n = 164) were positive for viral antigen or viral RNA. However, rabies neutralizing antibodies were detected in 4/78 (5{\textperiodcentered}1\%) bat sera tested, suggesting prior exposure to RABV or related lyssaviruses. The serological evidence of lyssaviral infection in Indian bats may have important implications in disease transmission and rabies control measures, and warrant extensive bat surveillance to better define the prevalence of lyssaviral infection in bats.

}, issn = {1469-4409}, doi = {10.1017/S0950268817000310}, author = {Mani, R S and Dovih, D P and Ashwini, M A and Chattopadhyay, B and Harsha, P K and Garg, K M and Sudarshan, S and Puttaswamaiah, R and Ramakrishnan, U and Madhusudana, S N} } @article {910, title = {Commensalism facilitates gene flow in mountains: a comparison between two Rattus species.}, journal = {Heredity (Edinb)}, volume = {115}, year = {2015}, month = {2015 Sep}, pages = {253-61}, abstract = {

Small mammal dispersal is strongly affected by geographical barriers. However, commensal small mammals may be passively transported over large distances and strong barriers by humans (often with agricultural products). This pattern should be especially apparent in topographically complex landscapes, such as mountain ranges, where valleys and/or peaks can limit dispersal of less vagile species. We predict that commensal species would have lower genetic differentiation and higher migration rates than related non-commensals in such landscapes. We contrasted population genetic differentiation in two sympatric Rattus species (R. satarae and R. rattus) in the Western Ghats mountains in southern India. We sampled rats from villages and adjacent forests in seven locations (20-640 km apart). Capture-based statistics confirmed that R. rattus is abundant in human settlements in this region, whereas R. satarae is non-commensal and found mostly in forests. Population structure analyses using ~970-bp mitochondrial control region and 17 microsatellite loci revealed higher differentiation for the non-commensal species (R. satarae F-statistics=0.420, 0.065, R. rattus F-statistics=0.195, 0.034; mitochondrial DNA, microsatellites, respectively). Genetic clustering analyses confirm that clusters in R. satarae are more distinct and less admixed than those in R. rattus. R. satarae shows higher slope for isolation-by-distance compared with R. rattus. Although mode of migration estimates do not strongly suggest higher rates in R. rattus than in R. satarae, they indicate that migration over long distances could still be higher in R. rattus. We suggest that association with humans could drive the observed pattern of differentiation in the commensal R. rattus, consequently impacting not only their dispersal abilities, but also their evolutionary trajectories.

}, keywords = {Animal Distribution, Animals, Cluster Analysis, DNA, Mitochondrial, Ecosystem, Gene Flow, Genetic Variation, Genetics, Population, Geography, India, Microsatellite Repeats, Molecular Sequence Data, Rats, Sequence Analysis, DNA, Sympatry}, issn = {1365-2540}, doi = {10.1038/hdy.2015.34}, author = {Varudkar, A and Ramakrishnan, U} } @article {893, title = {Cryptic diversity and habitat partitioning in an economically important aphid species complex.}, journal = {Infect Genet Evol}, volume = {30}, year = {2015}, month = {2015 Mar}, pages = {230-7}, abstract = {

Cardamom Bushy Dwarf Virus (CBDV) is an aphid-borne nanovirus which infects large cardamom, Amomum subulatum (Zingiberaceae family), in the Himalayan foothills of Northeast India, Nepal and Bhutan. Two aphid species have been reported to transmit CBDV, including Pentalonia nigronervosa and Micromyzus kalimpongensis (also described as Pentalonia kalimpongensis). However, P. nigronervosa was recently split into two species which exhibit different host plant affiliations. Whilst P. nigronervosa primarily feeds on banana plants, Pentaloniacaladii (previously considered a {\textquoteright}form{\textquoteright} of P. nigronervosa) typically feeds on plants belonging to the Araceae, Heliconiaceae and Zingiberaceae families. This raises the possibility that CBDV vectors that were originally described as P. nigronervosa correspond to P. caladii. Accurate identification of vector species is important for understanding disease dynamics and for implementing management strategies. However, closely related species can be difficult to distinguish based on morphological characteristics. In this study, we used molecular markers (two mitochondrial loci and one nuclear locus) and Bayesian phylogenetic analyses to identify aphid specimens collected from 148 CBDV infected plants at a range of locations and elevations throughout Sikkim and the Darjeeling district of West Bengal (Northeast India). Our results revealed the presence of a diversity of lineages, comprising up to six distinct species in at least two related genera. These included the three species mentioned above, an unidentified Pentalonia species and two lineages belonging to an unknown genus. Surprisingly, P. caladii was only detected on a single infected plant, indicating that this species may not play an important role in CBDV transmission dynamics. Distinct elevation distributions were observed for the different species, demonstrating that the community composition of aphids which feed on large cardamom plants changes across an elevation gradient. This has implications for understanding how competent vector species could influence spatial and temporal transmission patterns of CBDV.

}, keywords = {Animals, Aphids, Babuvirus, Ecosystem, Elettaria, India, Insect Vectors, Musa, Phylogeny, Plant Diseases}, issn = {1567-7257}, doi = {10.1016/j.meegid.2014.12.020}, author = {Savory, F R and Ramakrishnan, U} }