sDiv Newsletter 2024

For a long time, I had no intention of making a career out of it. I just wanted to do research and work in the profession I chose to study. There are no other scientists in my family, so I was not naturally prepared for the academic system. I graduated from Johannes Gutenberg University at the age of 28 after a 4-year research stay in China. During my doctoral thesis, I encountered epigenetics for the first time and studied its mechanisms in the fruit fly. Epigenetics was still a very young field of research in the early 2000s. I really enjoyed working in molecular laboratories, but writing my doctoral thesis and my first publications in English was rather difficult for me at the time. After my doctorate, I did my first postdoc in Germany. I spent a total of 18 years as a postdoc, eight of which I financed myself by successfully applying for third-party funding applications. With the help of these applications for third-party funding, I was able to bypass the German Academic Fixed-Term Act, which only permits a 9-year time limit for internal institute funding. The projects were fun because they allowed me to work on my own ideas. However, as they were limited in time, there was pressure to succeed, so that the next projects had a chance of being funded and I could continue my scientific work.

Good project management is essential for the success of these projects, which I taught myself with the support of coaching sessions. This includes planning and managing finances, establishing methods in the lab and for data analysis, supervising students, expanding a network, regularly stepping in if something doesn’t work and constantly solving problems. It was an exciting, challenging and long journey. In principle, these project applications and continuous coaching were my strategic career planning. Neither proposal writing nor third-party funding providers were covered during my studies; so I also attended events, familiarized myself with the subject and spoke to my colleagues. Particularly in early scientific careers, it is important to select funding sources with a high success rate, as well as co-applicants who have good publication record and are also supportive when writing.

When I saw the call for individual synthesis postdocs, which offered considerable research freedom and had a comparably light application process, I applied. In this call, sDiv funded three postdocs out of 32 applications and I was one of those successful ones. One of the decision-making criteria for my project was (next to the general quality, of course) that epigenetics hadn’t been addressed in any previously funded synthesis projects and that I found a very enthusiastic iDiv collaborator (Dr. Walter Durka). My 2-year sDiv synthesis project on interspecies epigenetics at iDiv gave me the opportunity to expand my knowledge to a cross-species analysis, to work with new cooperation partners and to expand my network. Together with Dr. Walter Durka, Prof. Christina Richards (University of South Florida, Tampa) and Dr. Marc Schmid, we are currently working on the revisions of a paper in which we are suggesting a strategy on how to combine genetics with epigenetics to study the adaptive potential. Together with my French collaborator Prof. Christoph Grunau, we wrote a book chapter on „Epigenetics in Evolution“ in a book for undergraduate students entitled „Explique-moi Epigénétique“.

Besides the project, sDiv enabled me to finish my manuscript on „Epigenetic signatures of social status in wild female spotted hyenas (Crocuta crocuta) “. I was part of the enthusiastic folks of EvoDiv meetings and contributed to the EvoDiv conference. Ever since, I am collaborating with Prof. Anja Widdig (iDiv and Uni Leipzig) on a newly funded project on crested macaques (FlexPool). Furthermore, I travelled to conferences and collaboration partners, presented my work in several scientific talks, attended a workshop on methylation analysis, took part in 3 writing retreats and expanded my skills within several coaching’s. All this would not have been possible without the flexible and always friendly support of iDiv/sDiv by Marten Winter, Caro Kögler and Isabella Maasberg.

The funding allowed me to bridge the time between a third-party funded project and a permanent position at my previous employer (IZW) and thus ultimately to continue my scientific work without risking being potentially unemployed. At the Leibniz Institute for Zoo and Wildlife Research in Berlin, Germany (IZW), I am now leading the Wildlife Epigenetics group within the Department of Evolutionary genetics, where we focus on epigenetic analysis on wild species in response to environmental conditions.

During my time at iDiv, together with three female iDiv colleagues (Sreetama Bhadra (sDiv), Daniela Hoss (sDiv), Gabriella de Faria Oliveira Damasceno Ribeiro (MLU)), we founded an initiative for women in science (iDiv female scientists), which was supported by the iDiv Female Scientist Career Fund, and now has more than 120 members. The open, highly international and scientific environment in my group at sDiv and generally at iDiv was a very enriching experience. A lot of work, a good sense of humor, perseverance and a good dose of luck were necessary on my path to succeed in science, especially as a woman.

Vullioud, C., Benhaiem, S., Meneghini, D., Szyf, M., Shao, Y., Hofer, H., East, M. L., Fickel, J., Weyrich, A.: Epigenetic signatures of social status in wild female spotted hyenas (Crocuta crocuta). Commun Biol7, 313 (2024). https://doi.org/10.1038/s42003-024-05926-y

Microbes are diverse, ubiquitous, and central to the functioning of all ecosystems. This knowledge is owed to the past three decades of advancements in sequencing technologies, which have allowed scientists to study microbes impossible to isolate or observe directly. However, the high cost of sequencing and the computational equipment needed to process sequence data have slowed the documentation, analysis, and reanalysis of microbes in underrepresented regions. Our goal with sIBTEDs is to ‘close the data loop’ by providing data producers with a real opportunity to benefit from the archived data through training in data reuse.

The sIBTEDs project idea was conceived during the first Datathon event, a three-day initiative designed to train researchers in sequence data archiving, inspire them to reuse existing data, and form collaborative networks to execute these projects. This event was held in Uruguay and Argentina in 2022 and was facilitated by an iDiv internal Flexpool project, with funding from the Uruguayan Agencia Nacional de Investigacion e Innovacion. Since then, Datathons have been held yearly, targeting Latin America in 2023, Africa in 2024, and South Asia in 2025. The iDiv internal Flexpool Support Fund provides iDiv members up to 10k€ in consumables for research activities and project ideas that lack funding. It’s a fantastic opportunity to work on smaller research activities and to push projects (e.g., via student helpers and funding extended visits of external collaborators).

The 2022 Datathon resulted in the formation of a collaborative network led by Dr. Garaycochea, Dr. Figuerola, and Dr. Jurburg, to develop the sDiv sIBTEDs project as a full synthesis project proposal for sDiv. The primary aim and key outcome of the project was to focus on capacity building among researchers in Latin America. sIBTEDs draws from the participant pools of the 2022 and 2023 Datathons, which now include over 300 microbial ecologists. The program advertises training and exchange opportunities in a monthly newsletter. It is supported by a student helper and available funds, which are used to send trainers to Latin America and bring Latin American researchers to iDiv, where they receive support in finalizing complex synthesis projects.

We submitted the project proposal to the 11th sDiv call and, out of 28 applications, we were successfully funded as a SynFlex project. sIBTEDS is a rather unique sDiv project, because it includes 2-year funding for a student helper who supports organizing Datathons in Latin America, and travel support for iDiv researchers visiting Latin America, as well as for Latin American researchers visiting iDiv. Additionally, we advertised the possibility of applying for a sIBTEDs-associated sDiv synthesis postdoc project. In this specific synthesis postdoc call, sDiv offered all active sDiv synthesis projects to apply for additional postdoc support. The successful joint application from Dr. Clara Arboleda Baena and the sIBTEDS PIs resulted in her joining the project to perform major syntheses of the data collected during the Datathons, and to coordinate the synthesis working groups formed during the Datathons.

The Microbial Community Database (MiCoDa, https://micoda.idiv.de), created together with Anahita Kazem and Birgitta Koenig-Ries from the iDiv Biodiversity Informatics Unit is key to lowering the barriers to data reuse. The database allows participants to reuse data from a pre-curated and pre-processed database containing more than 30,000 microbiome samples from around the world. As Datathons reduce biodiversity blindspots in microbial ecology, the archived data will be integrated into MiCoDa, facilitating data reuse by researchers regardless of their access to computational facilities.

The sIBTEDs project started in early 2024, with Dr. Clara Arboleda-Baena as an associated postdoc and Santiago Castillo Rivadeneira as our student helper, community organizer and data curator. The project is already very successful. Since the beginning of 2024, sIBTEDs has been creating monthly newsletters that allow Latin American researchers to exchange opportunities and news, strengthening local research networks. Since September, sIBTEDs began offering monthly training events in various formats, including virtual lectures and in-person training by Latin American and German researchers.

Together, the first two Datathons have consolidated approximately 7,000 samples from Latin American metabarcoding projects and resulted in 6 virtual working groups focusing on different synthesis questions that emerged during the Datathon’s brainstorming sessions. In 2025, members of these working groups will be welcomed at iDiv to finalize their synthesis projects with support from iDiv researchers.

This journey began sometime in 2020 after way too many difficult months of being locked down due to COVID-19 in our apartment with my pregnant wife and my (then 2 year old, and thankfully now diagnosed and much happier) autistic son. The pandemic was an extremely tough time for us as a family, and we had zero space or energy for creative thinking, but as the doom slowly started to lift and we began to experience something resembling a normal existence again, discussions with my wife (also an evolutionary biologist and nature lover) began to scratch at some long-standing questions that were in my head. As late summer turned into a cold and dark Leipzig winter, my ideas slowly grew alongside my wife’s belly, ultimately crystallising as the ‘Life on the edge’ proposal which was funded in 2021 by sDiv as a three year individual postdoc grant.

I conceived the Life on the edge project because I’m committed to combining predictive spatial modelling and genomics to contribute to conservation efforts. Although there are lots of really cool climate change vulnerability assessment tools available that can predict which species are likely to be at risk from climate and anthropogenic changes, these lack information about what happens within species (i.e. using populations as early warning signals). The decreasing cost of high throughput sequencing naturally led many people to begin thinking of interesting ways to plug this knowledge gap using population genomic data, but this was always system or species-specific and we lack a generalized framework to do this on any species.

Together with my iDiv and external collaborators, I developed a new informatic toolbox which makes it possible to predict population vulnerability by integrating spatial modelling and population genomics approaches. Harnessing the recommendations from the IPCC’s fourth and fifth assessments, we built a tool that can comparatively and objectively quantify biodiversity related metrics across populations using ecological and evolutionary principles. Life on the edge integrates ecological, environmental and genomic data and analyses (environmental dissimilarity, species distribution models, landscape connectivity, neutral and adaptive genetic diversity, genotype-environment associations and genomic offset) to estimate population vulnerability, which can be compared across populations to see which may need conservation interventions. Within the toolbox, functions and data structures are coded in a transparent and standardised way so that it is applicable to any species or geographic region where appropriate data are available.

To demonstrate its applicability, we applied Life on the edge to three georeferenced genomic datasets for co-occurring East African spiny reed frogs (Afrixalus fornasini, A. delicatus and A. sylvaticus) to predict their population vulnerability, as well as demonstrating that range loss projections based on adaptive variation can be accurately reproduced from a previous study using data for two European bat species (Myotis escalerai and M. crypticus). Life on the edge sets the stage for large scale, multi-species genomic datasets to be leveraged in a novel climate change vulnerability framework to quantify intraspecific differences in genetic diversity, local adaptation, range shifts and population vulnerability based on exposure, sensitivity and landscape barriers. This is one of the major projects that I continue to work on, and several related manuscripts are either published or forthcoming.

Barratt, C. D., Onstein, R. E., Pinsky, M. L., Steinfartz, S., Kühl, H. S., Forester, B. R., & Razgour, O. (2024). Life on the edge: A new toolbox for population-level climate change vulnerability assessments. Methods in Ecology and Evolution, 00, 1–21. https://doi.org/10.1111/2041-210X.14429

Just like for biodiversity, the study of human evolution gathers rare, discrete and punctual data that researchers must reconcile with global and dynamic theories. Similarly, it also mobilises distant disciplines varying from evolutionary biology to atomic physics, from ethnography to remote sensing technologies. However, in this research field the concept of research synthesis is not widespread and platforms for collaborative integrations are scarce, probably because until recently archaeological and anthropological data were essentially qualitative, and the structuration of “schools” limited circulation of ideas. In the absence of a collaborative platform for synthesis, the mobilization of relevant volume of data and knowledge is impossible without being biased. It is based on this gap that the researchers of ICArEHB (Interdisciplinary Center for Archaeology and Evolution of Human Behaviour) settled in Faro, Southern Portugal, have decided to establish HEIRS – the hub for Human Evolution Research Synthesis, the new place to elaborate synthesis on human evolution questions such as: Did Neanderthals have different ethno-cultures? Was fire an adaptation against cold during the paleolithic? Did crop farming change our foot morphology? What is a “fast expansion” out of Africa?

HEIRS is inspired by the model of the synthesis centres in biodiversity research and especially by sDiv. Indeed, when I was the former coordinator of iDiv’s graduate school yDiv during 2016, I also appreciated the power of sDiv, both in terms of knowledge production and as a tool for researcher. Since my move to Faro, the project of establishing a synthesis centre there has always been on my mind. I was in constant contact with sDiv head Marten Winter (now in the scientific advisory board of HEIRS) and his team. HEIRS, just like sDiv, keeps the main elements of a synthesis centre (collaborative working groups, data platforms, sabbaticals) but incorporates also a strong policy-making component and trainings dedicated to their community. Besides learning how to establish scientific and administrative structures and process to start a synthesis centre from the scratch, the community at iDiv, the larger research centre sDiv is part of, already proved instrumental: iDiv researchers and experienced statistic teachers Christian Ristok and Stephan Kambach (Martin-Luther University Halle-Wittenberg) visited ICArEHB in December 23 to teach a course on Systematic synthesis for prehistoric data and literature. More trainings will be scheduled, but for now the next big event of HEIRS is its Opening Symposium, that will happen on the 28-29 January 2025 in Faro.

There are many ways human evolution is linked to biodiversity questions. If you are interested in Human Evolution and would like to participate or propose a project, visit HEIRS website https://heirs.icarehb.com.