One million of the world’s estimated 8 million species are currently at risk of extinction. Changes to our climate and ecosystems are driving this devastating loss of global biodiversity. One way conservation and biodiversity researchers are addressing these challenges is by using genomic science. To find out more about how genomics can support conservation, we spoke to EMBL alumna and winner of the academics Young Scientist of the Year award, Lara Urban.  

In her early career, Urban focused on ecological research and computational biology. She completed a joint PhD at EMBL-EBI and the University of Cambridge working on statistical genomics in human cancer. She then applied these computational and genomics skills to her work on nature conservation and biodiversity, supporting the conservation management of critically endangered species such as the kākāpō. 

Urban now works as a principal investigator at Helmholtz AI and the Helmholtz Pioneer Campus at Helmholtz Munich, and at the Technical University of Munich. She and her team are broadening their conservation and biodiversity research by using new genomics and artificial intelligence approaches to better understand One Health – a unified approach to optimise the health of all people, animals, and ecosystems. 

Can you tell us about your current research into planetary health?

Our current research focuses on using real-time genomic approaches to better understand One Health. To do so, we conduct research that focuses on biodiversity monitoring, such as non-invasively monitoring different species in New Zealand, Brazil, and across Europe. We have other research projects on environmental monitoring, specifically freshwater and air monitoring, and looking at these in relation to human health.

For example, a postdoc in my group studies avian influenza, a big threat for wild and captive bird populations. For this work, we are using air, water, and faecal samples to non-invasively monitor the transmission and evolution of the virus, and its risk of becoming a zoonotic disease by being transmitted to humans. 

Can you tell us a bit more about your time at EMBL?

I honestly have to say that my time at EMBL contributed immensely to making me the scientist I am today. My PhD made me realise how much work and stamina a research project requires. You have to stick to it and work through the failures. The environment and atmosphere at EMBL were always very supportive and my colleagues were open-minded. I felt like I was able to talk to senior researchers and go to them for advice.

In terms of computational biology skills, I learned a lot during my time at EMBL-EBI, and I’ve been able to apply these skills to my current conservation and One Health research. During my PhD, my supervisor, Oliver Stegle, moved to EMBL Heidelberg, which provided an opportunity to work with other groups from whom I picked up many computational biology methods. 

How did your time at EMBL influence your career path?

I had some fantastic mentors during my time at EMBL. Not just my supervisor but also many of the other group leaders and scientists were open to discussing ideas. Ewan Birney, the EMBL-EBI Director, was always very supportive of my work with endangered species such as the kākāpō, and he still is to this day. I see both EMBL and the University of Cambridge as my scientific homes.

How can genomics support conservation efforts? 

Genomics can support conservation efforts on many different levels – starting from understanding the biodiversity of an ecosystem, to enabling researchers to monitor different species in the long term using non-invasive genomic methods.

You can also look at the genomic underpinnings of fitness in the species themselves, especially in critically endangered species. Often what we see on the surface of how populations exist doesn’t necessarily tell us about how endangered they are. Genomic sequencing allows us to estimate the genomic fitness of a species and understand what would help that species to adapt to changes in the environment, such as climate change. 

Looking at a species’ genomic information also helps us to protect it from infectious diseases. On the one hand, we can analyse something called genomic load – the decrease in fitness of a population due to mutations accumulating in the species’ genome. A good example of this comes from the work we have done with the kākāpō in New Zealand and the pink pigeon in Mauritius. Despite these populations having increased in size, they still have an increased genomic load which can make them susceptible to infectious diseases. We can also use genomics to help us monitor the spread of infectious diseases themselves, and thereby help protect critically endangered species. 

How are new technologies enabling your work in conservation and climate change?

We are mainly using nanopore sequencing because the machines are portable and we can use them at the point of care. We can also get results very quickly; the moment that the DNA is sequenced, we can immediately begin analysis, and this saves us a lot of time.

We are also using AI to develop approaches that make understanding the genomic data we collect straightforward and fast. We are integrating our data into models to broaden what we can predict about the species or environment we’re working with. 

Finally,  we’re exploring the use of machine learning methods to help us filter out unwanted noise from nanopore sequencing data. For this, we’re analysing the information from the electrical current that represents genomic information – the output of the nanopore sequencer. Using only this raw data, we try to predict, for example, if a pathogen we are detecting is living and therefore virulent, or dead. 

What is the benefit of open data sharing for these fields of research?

Having reference genomes for different species is a vital first step for biodiversity research. Researchers need these to inform their genomic conservation studies. Creating high-quality, standardised reference genomes for this work is difficult and I think the answer lies in the global, centralised efforts that are currently taking place to create these reference genomes, like the Earth BioGenome Project and its affiliated networks. 

Creating platforms that allow open access to reference genomes through publicly-available data portals will help inform many downstream conservation and biodiversity efforts. It is, however, also important to think about what we are going to do with these data. Scientists should work with conservationists directly. There is still a lot of work to be done in this regard but it has an enormous amount of untapped potential.  

I think that it’s generally important that the biodiversity data collected is made publicly available so that everyone around the world can leverage it. Having said that, it’s also essential to take into account the interests and beliefs of the people from the areas where you are collecting the data. For example, I have experience working with Māori iwi – or tribes – in New Zealand, and they preferred some of the data we collected not to be made public because of cultural beliefs and their past experience with colonialism. We as scientists need to accept this. 

What role do life scientists play in shaping biodiversity policy?

It’s important for scientists to engage with policymakers and take responsibility for the societal consequences of their research. We can provide the data and analyses that are necessary to push policies to change. Biodiversity loss and climate change are the best examples here.

It’s also really important for scientists to communicate their work to the public not just through the media but through public engagement events and activities. This can have such a big impact on society and shaping the future of science. That said, the current academic system doesn’t always support public engagement well, and so this also needs to change to encourage and support scientists. 

What needs to change to allow genomics to benefit biodiversity and climate change initiatives? 

Genomic approaches need to be more accessible. The types of conservation studies we’re doing still require a lot of skill and computational ability. Automating genomics approaches both with respect to the practical steps, such as DNA extraction and sequencing, but then also with respect to the computational analysis, will help make these approaches available to more conservationists in the field.  

What are you most excited about in your field?

Ever since I was young, I wanted to increase awareness of nature conservation, biodiversity, and animal welfare. The One Health research field gives us an amazing anchor to talk about biodiversity, while also taking into account human health and the welfare of our society. It shows people that there is a real link between human health and our environment. There is so much more we need to explore, so this is an exciting time for the research community.  

Find out more about Lara Urban and her research on genomics and AI in the context of One Health. 

Find out more about the biodiversity research and initiatives that EMBL are involved in and how this work sits within the Planetary Biology transversal theme introduced in EMBL’s ‘Molecules to Ecosystems’ Programme.

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