@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 {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 {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 {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 {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 {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} }