December 11, 2018, by Lexi Earl

Meet the Beacon: Associate Prof Levi Yant

Levi Yant is an Associate Professor in Life Sciences and a member of the Future Food Beacon of Excellence. His research is focused on wild plant populations to understand how evolution finds solutions to significant environment and physiological challenges. Dr Yant uses innovative population genomic approaches to identify changes specific to adapted populations. This reveals candidate genes and process mediating adaption. Dr Yant completed his PhD at the Max Planck Institute for Developmental Biology, pioneering the application of genome-scale technologies to plants, in order to understand the molecular control of flowering time. While a postdoc at Harvard, Dr Yant focused on evolution and population genomics to understand the molecular basis of adaption. Dr Yant joins the Future Food Beacon from the John Innes Centre in Norwich.

In this interview, Levi talks to Lexi Earl about his research, plans for the future, and life as a scientist. 

What do you do?

I use genomics to study the evolution of plant and animal populations to understand how they overcome environmental hazards. By working on quantifiable adaptations, we can understand the ways replicate populations adapt and determine if there are common factors; if, in fact, evolution can be predictable. Many of these systems can also have clear impacts on the rational design of future plants, for example.

 

How did you get into this kind of work?

I’ve always studied evolution. I started in HIV vaccine development and that was really exciting, because we were able to use quick and highly reductionist systems to track viral evolution inside infected hosts. It was important work, but a rather difficult thing to do in the long term – a very territorial field – so I was drawn to Arabidopsis because it is also quite fast and offers many interesting questions, especially the wild outcrossing relatives of Arabidopsis thaliana. It is one of the fastest plant systems where we can see evolution happening almost in real time. That is how I got into plants, but it has always been evolutionary genetics.

 

Can you tell me a little bit about your history?

I started university in Wisconsin. I began graduate school studying HIV virus evolution, switching systems halfway through my PhD to Arabidopsis, at the Max Planck Institute for Developmental Biology in Tübingen, Germany. I finished my PhD there and then I did a postdoc at Harvard, working on the evolution of development (Evo-Devo) in non-model systems with Professor Elena Kramer, who was a fabulous mentor. I then came over to the UK to join the John Innes Centre, thanks in part of an ERC Starting Grant from the European Union.

What is your aim while you are with the Future Food Beacon?

I want to develop meaningful collaborations between the Beacon and both East African and Chinese partners with the goal of making new impactful and interesting work possible on underutilised systems. This is in addition to growing my research programme working on the adaptation of natural systems to environmental stressors, as well as genome evolution. In other words, I’d like to do a lot while I am with the Beacon!

One way I like to think about scientists follows what has been written about other thinkers: there are hedgehogs and there are foxes. Hedgehogs know one great thing, and they obsess on that thing. They focus on that one thing with laser intensity. On the other hand, there are foxes: they love to do many things, get involved in different problems, and collaborate a lot, working on diverse systems. One can be a bit fox and a bit hedgehog, but I see myself pretty solidly in the fox camp. My science has always been highly collaborative, and I’ve always worked on multiple systems, both in terms of the biological context, and species. When the Future Food Beacon opportunity came up, I thought that was an even more powerful way to use my natural traits better, to collaborate broadly, to work on diverse systems. I’d like for it to be relevant to food security but also for us to have a strong fundamental science focus.

 

How do you think you balance that?

It’s crucial to pick the right study systems to have the best shot at both important fundamental science and applied impact of the science. On the one hand many amazing people have been working on the major systems, for example, wheat and maize; so I want to contribute to new systems instead, where possible. I’d particularly like to focus on underutilised, ‘orphan’ crops. I know there are a number of people at Nottingham who are also interested in that, and that was an attraction as well, developing links in Asia and East Africa with groups that want to do excellent science on indigenous crops. It will be an adventure to see where we can take this!

 

Was it that diversity and collaborative opportunities of the Beacon that attracted you to the post?

Yes, definitely. And the strong, progressive, forward-thinking leadership was a real attraction. The people at the Beacon are very good at identifying where new opportunities are, and have links all over the world which is hugely important.

 

How do you explain your research to an ordinary person?

We try to understand how evolution works, at a fundamental level. We are happy to work on different, diverse, and strange adaptations that we find in the wild. By looking at repeated evolution in different organisms to the same stressors, this gives some fundamental idea of whether evolution is constrained, whether the same changes happen each time or whether evolution can meander down different paths. The beautiful side benefit of that is you can learn a lot of different and useful biology doing that.

 

How did you first become interested and involved in science research?

I was really interested in some pretty far out science fiction and what people are trying in terms of life extension while I was in college. I thought that was really progressive and forward thinking – different ways to extend life spans (and, crucially, extension of health and high-quality life span) in different organisms. So, when I finished my undergraduate degree I called up a scientist on the other side of the country doing that work, who had just had a fancy paper in Science – I think it was one of the first microarray studies in a vertebrate – looking at the global gene expression impact of caloric restriction. I offered to work in his lab, to experience what ‘doing science’ was like, because I did not have that experience as an undergraduate. I was a technician in his lab for a few years and I learned I really liked it. Oddly, though, I am not a bench scientist at all now, but that was a natural development towards computational work for which I am better suited and excites me more.

Do you have a greatest career moment?

Hmm… I just had one that felt pretty special that I’m riding high on: a few days ago we had a paper really well reviewed at a top journal. It’s not just that it was well-received, it’s how it came about: the thing that made me most excited about it is that the paper is an equal partnership of three shared first authors which is a bit uncommon, even in genomics. And they all absolutely poured themselves into it, with absolutely no territorialism: they worked so well as a team that as senior author I really felt I was just watching the beautiful process unfold as they put together something somewhat special. They drafted and redrafted it all together over the course of six months in an intense way. It is a very carefully honed manuscript and by the time I got it, needed very little input; it was deep and beautiful. The paper is really important for the three first authors, and it was a really great moment for me, as a lab leader. As a young group leader it is very difficult to know how much to micromanage. I am still learning that, progressing in that skill, and this was a happy example for me of how things can work very well with a light touch.

 

Do you have any advice for young scientists?

Yes! Please do not worry too much about things! That sounds horrible from someone who has a long-term job he loves now, but earlier in my career I worried all the time and it only made me less productive. And of course, it is a miserable way to live. Just do you best and push at what captures your passion, and be selfish to that. If you love it, keep doing it, and work hard. But also play hard! Do intense non-science activities that absolutely reset and refresh. For me, that’s trail running, sailing and rock climbing. I am pretty mardy and miserable if I miss out on any of these for a few days, even when the science is going really well.

 

Will your research impact on ordinary people’s lives?

We are bridging the gap between interesting fundamental science and increasingly urgent practical issues such as environmental degradation and climate change. In particular, recent studies published by my group have increasingly focused on how certain amazing plant populations have evolved to thrive on highly degraded, saline, or heavy metal-contaminated soils. This work contributes to a knowledge-base that we can use to design crops resilient to climate volatility and environmental hazards. Complementary to this, we are starting to work on dramatically understudied orphan crops that constitute key components of people’s diets and livelihoods in developing nations. This work can have a rapid impact on ordinary people as we characterise and develop crops already adapted to highly challenging local conditions. Going forward, I am optimistic that this work can aid both developed and developing nations as we struggle to cope together with climate change.

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