Research summary
In the past several decades, biodiversity loss, global change and interactions between them have pushed ecosystems on earth towards tipping points. Humans are critically dependent on nature, and functional ecosystems for well-being. This is especially true in bio-diverse, habitat-rich, and crowded India. Uma's research is based on a passion for India's biodiversity and a deep internalization of these facts. She aims to understand the distribution of biodiversity, and direct and indirect human impacts on populations and ecological communities. Some of the research directions that have yielded significant biological insights from her work are highlighted below.

How does tiger genetics inform conservation?
Like large carnivore species worldwide, tiger populations have declined historically, and now retain only 5% of its historical range. About 65% of the world's remaining 5,000 or so wild tigers inhabit the Indian subcontinent, making it an important region for attention to its conservation. In order to understand the effects of past population changes on tiger genetic variation, Uma's group sampled individuals across the Indian subcontinent for mitochondrial and nuclear genetic variation. Her analyses revealed that Indian tigers retain more than half of the extant genetic diversity in the species. This diversity is retained despite a precipitous, likely human-induced population crash ~200 years ago in India (Mondol et al., 2009). Work with historic tiger skins primarily from the London Museum of Natural History allowed Uma's group to compare past population genetic variation (100–200 years ago) to modern tigers. Results suggest that existing tigers have lost substantial mitochondrial genetic variation, and tiger populations have become more fragmented in the last 200 or so years (Mondol et al., 2013). Recent genome-wide studies (10,000 SNPs) of tiger population structure from her group identified isolated and genetically impoverished populations (e.g. Ranthambore), and connected landscapes with high genetic variation (e.g. Central India, Natesh et al., 2017). Such analyses allow prioritization of populations of conservation concern, like Ranthambore. Novel network-based coalescent models help understand structuring of genetic variation in India, and the 'genetic value' of connections and populations (Alcala et al., 2019). Ongoing work with whole genomes re-iterates high genetic variation of Indian tigers, but highlights ongoing effects of fragmentation on the genome (Armstrong et al., 2021).
Gene flow between populations is important, and tigers have already lost connectivity in the last 200 years (Mondol et al., 2013). But what determines geneflow and connectivity in current populations? Uma's group used landscape genetics approaches to investigate correlations between genetic data (collected from Central India) and resistance to movement offered by landscape features (human settlements, forest cover, roads). They showed that human footprints on the landscape (such as high traffic roads, urban settlements) significantly impact recent movement of tigers across this landscape (Joshi et al., 2013, Thatte et al., 2018). Recent work reveals that roads and human footprint impact the varied species in this landscape (jungle cat, leopard, tiger, sloth bear) differentially, with smaller species being least impacted (Thatte et al., 2019).
Given this understanding of how tiger population size and connectivity between populations has changed over the last 200 years, Uma's group used simulations to explore how best to sustain tiger connectivity in the future within the Central Indian landscape (Thatte et al., 2018). Uma's results reveal that securing corridors, with new protected sites within them is the way ahead. While the attention of conservation biologists and governments has largely been directed at the national population size of the tigers, Uma's group unequivocally establishes that connectivity between populations that make up these national numbers is critical for sustaining tigers and their diversity.
Recently, Uma and her team identified the genetic basis of an unusual tiger phenotype (pseudo-melanism), and inferred that its high frequency in one protected area is most probably because of founding events and genetic drift (Sagar et al., 2021). We have sequenced tiger genomes to reveal that one isolated population (identified in Natesh et al., 2017) is inbred, and individuals here harbour fewer but closer-to-fixation loss of function mutations, suggesting the possibility of impending inbreeding depression (Khan et al., 2021).

What drives biodiversity and speciation in the Indian subcontinent?
Uma has investigated biodiversity and speciation in the Western Ghats, and Peninsular India.
In the Western Ghats, Uma has shown (Robin et al., 2010) that deep valleys or gaps in this mountain chain drive speciation and biodiversity. Genetic data from 23 montane bird species across nine locations revealed the nested effect of valleys, with several species (10 of 23) demonstrating the oldest divergence associated with the widest and deepest valley in the mountain range, the Palghat Gap. Further, a subset of these ten species revealed younger divergences across shallower, narrower valleys. Studying the entire community revealed a range of species' responses, some generalizable and others with unpredicted patterns (Robin et al., 2015).
Peninsular India has relatively poorer biodiversity and as a result fewer studies on diversification and speciation have been conducted. A dated phylogeny from Uma's group on dry-zone lizards (Ophisops) revealed that diversification in this group increased by 8-fold during the time of global C4 grassland expansion. Ophisops is a dramatic example of an endemic radiation on the Indian plate, and overlooked cryptic diversity outside forests (Agarwal & Ramakrishnan, 2017).
Through these biogeographic explorations Uma's group has identified new genera and species of birds (Robin et al., 2017), upgraded subspecies to species for small mammals in the Himalaya (Dahal et al., 2017) and identified new species of lizards in Central India (Agarwal et al., 2018).

What are the ecological and evolutionary drivers of zoonoses?
Human interface with biodiversity and fragmentation of habitat profoundly impact ecological communities. Such interfaces and community transitions are fascinating, especially in the context of disease ecology and zoonotic disease spillover. The bat harvest in Nagaland is a century-old tradition where individuals of the Bomrr tribe harvest thousands of cave roosting bats over a two-day period provided a unique opportunity to investigate a high-risk human bat interface. In collaboration with researchers at Duke-NUS, Uma and her team investigated the diversity of RNA virus and bacterial diversity co-occurring with the two bat species in the cave, and investigated serology for known filoviruses in both bats and the Bomrr. They found shared antibody response to several known filoviruses in both bats and people. These studies indicate the presence of a filovirus, which has elicited a similar immune response in both bats and people, suggestive of past spillover (Dovih et al., 2019). Uma and team investigated the prevalence of Bartonella in small mammals in a mixed-use landscape in the Western ghats, and our research here reveals that Bartonella is very common and genetically diverse in abundant and 'generalist' species of rodents in this landscape (Ansil et al., 2021). Ongoing research compares communities in mixed-used landscapes to those in undisturbed landscapes, and reveals that Bartonella prevalence is lower among small mammals in undisturbed landscapes.