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URPP Evolution in Action: From Genomes to Ecosystems

“UZH is a leader in evolutionary biology research”

How do organisms and pathogens evolve and adapt to the environment? This was the question that the URPP Evolution in Action sought to address. The program allowed UZH to put its considerable research competence in evolutionary biology to excellent use, says the initiator and former co-director Beat Keller.
Interview: Stefan Stöcklin, Translation: Astrid Freuler
Kentaro Shimizu points to the plant Cardamine amara, a precursor of the newly discovered species Cardamine insueta. In the URPP Evolution in Action, the researchers were able to show genetic processes of speciation. (Picture: Hiroto Kawabata)

The URPP Evolution in Action: From Genomes to Ecosystems explores one of the most exiting but also complex subjects in all of biology – how do new species come into existence and evolve, and how do they adapt to their environment? Evolution is a cross-departmental topic that encompasses many scientific disciplines. From molecular genetics, microbial and organismic biology at one end of the spectrum, trough to bioinformatics and other scientific disciplines at the other end. "We decided to take a broad approach right from the start and researched the subject of evolution far beyond biology and medicine," says Beat Keller. Genome analyses are an important catalyst and a central element of the URPP. They have revolutionized this field of research and allow us insights into the molecular-genetic mechanisms that underlie many evolutionary processes. Correspondingly, the program placed an emphasis on bioinformatics and recruited several specialists in that field to support all of the research groups. "The genome analyses acted as a link and brought the different approaches to research in evolutionary biology closer together. This collaboration is an important reason for the success of the URPP," adds Beat Keller.

Beat Keller, in your opinion, what are the key outcomes of the URPP Evolution in Action: From Genomes to Ecosystems? 

Beat Keller:  A great many publications were produced over the course of the past 12 years and there are numerous highlights. One is the work of Kentaro Shimizu and his group, on the bitter cress Cardamine insueta found in the Urnerboden area. The group was able to demonstrate how this young species, first recorded as recently as 1972, originated from two different parent groups through hybridization. Another highlight is the work of Chiara Barbieri on the evolution of languages. Her work shows that, to a certain extent, the evolutionary development of humans and their languages run in parallel. Projects on language and evolution laid the basis for the National Center of Competence in Research (NCCR) Evolving Language. The third subject I’d like to highlight is the subject of paleogenetics, specifically the work of Verena Schünemann and her group on historic DNA samples of pathogens such as leprosy, influenza and syphilis. In all of these examples, we were able to describe and explain short-term evolutionary processes, in other words evolution in action.

Several projects related to pathogens, the prime example for fast evolutive changes, as we’ve known since the coronavirus pandemic. Did these projects meet the expectations?

Beat Keller: Certainly. The group around Urs Greber, for instance, deciphered the resistance mechanisms of cold viruses against medication. These demonstrate the rapid evolutionary adaptation processes of viruses in an exemplary way. Our project examined the powdery mildew fungus on triticale, a cereal crop that was developed by crossing rye with wheat. We were able to clarify on a molecular level how an existing pathogen expanded its host range. This is fundamental research work that provides the basis for new applications in medicine and agriculture. 

beat keller

We made a timely decision to use genome analysis to undertake evolutionary biology research.

Beat Keller
Professor for Plant Biology

Has the URPP improved our understanding of evolution?

Beat Keller: With regard to short-term, fast occurring evolutionary events, yes, it has. Thanks to the URPP, we now have very detailed knowledge of countless molecular mechanisms. We also have a better understanding of how some species evolve and how that can affect ecosystems. On the conceptual level, researchers involved with the URPP have developed new concepts and theories on how evolutionary processes function. One of the issues we explored, for instance, was epigenetic variation and its role in the adaptation of organisms. As I’ve already mentioned, it’s an enormous field. We were able to open a few windows into it and catch new glimpses. 

What societal relevance does the URPP Evolution in Action have? How did the general public benefit from it?

Beat Keller: Our findings on the evolution of pathogens and the development of pathogen resistance will help to better prepare for existing and new epidemics. But I would say that the success of the URPP mainly lies in the knowledge gain, as opposed to any specific applications. As someone engaged in pure research, I see the newly obtained knowledge on evolution and the training of junior researchers as the principle aim. And I think as researchers and teaching staff working at a university, that is our main task. We also introduced the subject of evolution to a broader spectrum of the public. For instance, we have the "evolution happens!" touring exhibition, which is mainly aimed at teenagers and has been on tour for several years. The exhibition uses practical examples such as antibiotic resistance to demonstrate evolutionary processes. 

Researchers from the research focus at a retreat in Grindelwald in 2019. (Picture used with permission)

How much value is placed on evolution research at UZH? How do the research groups position themselves in relation to other universities?

Beat Keller: The University of Zurich has some exceptional research groups and it certainly offers the widest overall palette of evolutionary biology research in Switzerland. The URPP promoted interdisciplinary information exchange among the groups, which are spread across more than ten institutes. That is our great strength and sets UZH apart. Exchange and networking are an integral part of fundamental research and, correspondingly, we have strong connections and are well established both nationally and internationally.

What distinguished the approach of this URPP? In what respect is it unique?

Beat Keller: I’d like to highlight the linking element of genome analyses. We decided on this methodology very early on, and gathered and exchanged knowledge across the different research groups and institutes. That really paid off, as we now see in retrospect. 

Was there a result that surprised you? What was your personal highlight?

Beat Keller: As a senior researcher who has worked in research for many years, the greatest satisfaction for me was to watch inquisitive young people grow into extremely capable scientists who also overtook me in many aspects.

Taking stock in three sentences – what were the benefits of the URPP Evolution in Action: From Genomes to Ecosystems?

Beat Keller: We made a timely decision to use genome analysis to undertake evolutionary biology research. We took an interdisciplinary approach to the subject, which allowed us to gain new insights. And we were able to train excellent junior researchers, some of which are now continuing this work in a wide range of locations, thereby strengthening our research network. 

What’s next now that the program has drawn to an end?

Beat Keller: A comprehensive follow-up project in the sense of a related program isn’t being planned. Thanks to the URPP, evolution research at UZH has continued to forge internal links. Lasting collaborations were set up and research and teaching in the field of bioinformatics was boosted. Another part of the program is being continued in the NCCR Evolving Language. The extensive network of researchers will certainly continue to explore issues in evolutionary biology and use the latest sequencing technology and methods of bioinformatic analysis.