Studying ancient genes to protect current biodiversity

Uma Ramakrishnan received the 2023 Molecular Ecology Prize for bringing molecular genetics to conservation practice, policy, and the public. She spoke to Nature India from the National Centre for Biological Sciences in Bengaluru, where she uses genetic data and molecular methods to understand ecology in India.

Nature India: How is the new field of molecular ecology evolving, especially in helping further biodiversity conservation goals in India?

Uma Ramakrishnan: The field of molecular ecology has been revolutionised by recent advances in sequencing technology to better study natural systems. All organisms have genetic material that hold the story of their past. Sampling and reading their DNA allows us to understand more about species, and their interactions. Importantly, the recent Convention on Biological Diversity explicitly uses genetic variation to understand and conserve biodiversity. Molecular ecology can be used for biodiversity surveys, species discovery, understanding more about the impacts of habitat fragmentation on rare and endangered species, the impacts of inbreeding in isolated populations and in genetically identifying individuals involved in negative interactions with humans. All these issues are crucial to understanding biodiversity and minimizing species extinction, especially in India.

We will see more use of molecular tools to determine founder individuals for rewilding and to monitor re-introduction of species; environmental DNA, metabarcoding and sequencing approaches for rapid survey, successful restoration, understanding of animal ecology and ecosystem monitoring. I am sure there will be several other unknown new directions. That’s the fun part of science.

NI: What are the biggest hurdles in generating genetic data on tigers? How do you address those hurdles?

UR: The biggest hurdle is getting the samples. This requires permission and while, luckily, I have never been denied permissions, it often takes a very long time. Also, there are many permits to get: institutional biosafety, state forest department, Ministry of Environment, Forest and Climate Change, in case of tissue/blood samples; and the National Tiger Conservation Authority in case of tigers, and lots of follow-up. As a scientist, sometimes I resent this. It's part and parcel of working on tigers, but it is difficult.

The fieldwork itself is challenging. We work in remote places and with teams of up to five or six people. Students in the field have to ensure everyone is healthy, happy and fed, and also coordinate logistics like sampling routes in protected areas.

Many of our reagents come from outside India, and sometimes take up to three months to arrive. Raising funds is also a challenge and fieldwork, lab work and genomics and computational analyses are very expensive.

We tackle the hurdles by engaging, contacting anyone who might be able to help and by working very hard, I am so proud of all the early career researchers in my team for taking all this in their stride, making it happen at pace, and learning along the way.

NI: What drew you to paleogenetics and what exactly do you look for in ancient DNA?

UR: I did paleogenetics in my post-doctorate, and a little bit of museum skin work in 2010-2013. I am hoping to start a large project now again on the genetics of tiger trophies from India. What is not to love about going back in time? The idea is so fascinating, and we can do genetic time travel with these trophies. When did the inbreeding in Ranthambore start? How did the isolation of Similipal Tiger Reserve play out over the last hundred years? What did we lose when we lost all of Haryana’s tigers?

Again, technologies to work with these poor-quality DNA samples have revolutionised recently. Also, many of the people who know about trophies and hunting are old now, and unless we gain their insights and sample these trophies soon, we will lose this information forever.

NI: Can you share a specific experience with sample collection from the Western Ghats that was particularly daunting?

UR: It was very special to work on the sky island birds with V.V. Robin, who was then an NCBS campus fellow with my lab. We also teamed up with Prasenjeet Yadav, a National Geographic photographer. On one field trip, we mist-netted high elevation grassland birds, specifically the endemic Nilgiri pipit. The habitat was special, handling the birds (so calm compared to feistier mammals), and the team was amazing. This bird is now on Schedule 1 of the recently amended Wildlife Protection Act, in part due to Robin's work.

NI: How do you blend molecular ecology with other disciplines to develop conservation tools, including predictive modeling?

UR: My PhD student, Prachi Thatte, used genetic data from tiger samples collected from across central India to understand connectivity and land use (e.g. high traffic roads, agriculture or forest). She then modelled future scenarios for connectivity and tiger extinction. This work showed that if National Highway 7, the highway between Kanha and Pench tiger reserves, becomes a barrier, the extinction probability of tigers will increase substantially.

Such inferences are easy for policy-makers to understand. This and an earlier generation of Prachi’s work was used in court to get a ruling favouring wildlife, and for an underpass. In the court case filed by citizens, we helped with science and evidence. We hope that decisions are based on evidence and not just opinion.

NI: What does your future work entail?

UR: We are working on Dhole population dynamics in the Southern-Central Western Ghats, and multi-species carnivore connectivity in Central India and the Terai. I am hoping to initiate a programme on unknown pathogens in northeast India, with many collaborators from across the country.

I will continue to study inbreeding and its consequences in big cats, through the genetics of trophies (and which genetic variants we have lost), inbreeding in zoos, and functionally testing specific mutations in big cat cell lines. I am hoping to continue studying the two isolated populations of tigers in Ranthambore and Similipal for as long as possible.