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Biography
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 to an ERC Starting Grant from the European Union.
Expertise Summary
Evolution, genomics, plant adaptation, polyploidy, gene flow, genomics, genome, biology, structural variation, long reads, bioinformatics, data analysis, salinity, edaphic
Teaching Summary
2019 Taught 'AfriPlantSci2019' (Kilifi, Kenya). Gave interactive seminars on developing your scientific questions and proposal writing.
2018 Taught 'Innovations in Agriculture and Food for Healthy Societies' (Shanghai, China). Lead workshops on challenge-based interdisciplinary thinking in an international context to deliver ethical and equitable solutions to global challenges and mentored Chinese and European students.
2014-2015 Developed a new course in the Molecules, Cells, and Organisms graduate program (Harvard University), "Next Generation Sequencing 101: Massively parallel RNA and DNA sequencing". This course covered de novo genome assembly, resequencing and scanning for signatures of selection in non-model systems.
2013-2015 International Masters Program Mentor (Harvard University, MEME)
-Genomics laboratory mentoring of two graduate students, focusing on obtaining genomic information in non-model systems by a variety of next generation approaches
2011-2014 Senior Honors Thesis Co-mentor (Harvard University)
-Investigated the effects of climate change on developmental timing in diverse wild plant species and initiated development of several as potential model laboratory systems
-Performed genome-wide transcriptional profiling of a temperature tracking species, along with phenological profiling of species' responses to climate change
2011-2015 High School Student Mentor (Cambridge Rindge & Latin School and Harvard University)
-Involved high school and Harvard students in bioinformatic analyses of genome-scale variation
-Exposed students to the diversity of bioscience possibilities in bioinformatics and wet lab research
2011-2012 Head Teaching Fellow, Organismic and Evolutionary Biology 57: Animal Behavior (Harvard University)
-Developed curricula, coordinated, and taught sections of a class of 146 students
-Coordinated and oversaw the efforts of 7 teaching fellows
-Awarded excellent reviews by students (4.5/5.0)
Research Summary
I focus on wild populations to understand how evolution finds clever solutions to significant environmental and physiological challenges. Among these are the internal struggle in the nucleus… read more
Selected Publications
MARBURGER, SARAH, MONNAHAN, PATRICK, SEEAR, PAUL J., MARTIN, SIMON H., KOCH, JORDAN, PAAJANEN, PIRITA, BOHUTINSKA, MAGDALENA, HIGGINS, JAMES D., SCHMICKL, ROSWITHA and YANT, LEVI, 2019. Interspecific introgression mediates adaptation to whole genome duplication NATURE COMMUNICATIONS. 10, BUSOMS, SILVIA, PAAJANEN, PIRITA, MARBURGER, SARAH, BRAY, SIAN, HUANG, XIN-YUAN, POSCHENRIEDER, CHARLOTTE, YANT, LEVI and SALT, DAVID E., 2018. Fluctuating selection on migrant adaptive sodium transporter alleles in coastal Arabidopsis thaliana PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 115(52), E12443-E12452 BADUEL, PIERRE, BRAY, SIAN, VALLEJO-MARIN, MARIO, KOLAR, FILIP and YANT, LEVI, 2018. The "Polyploid Hop": Shifting Challenges and Opportunities Over the Evolutionary Lifespan of Genome Duplications FRONTIERS IN ECOLOGY AND EVOLUTION. 6, MONNAHAN P, KOLÁŘ F, BADUEL P, SAILER C, KOCH J, HORVATH R, LAENEN B, SCHMICKL R, PAAJANEN P, ŠRÁMKOVÁ G, BOHUTÍNSKÁ M, ARNOLD B, WEISMAN CM, MARHOLD K, SLOTTE T, BOMBLIES K and YANT L, 2019. Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa. Nature ecology & evolution. 3(3), 457-468
Current Research
I focus on wild populations to understand how evolution finds clever solutions to significant environmental and physiological challenges. Among these are the internal struggle in the nucleus following whole genome duplication (polyploidy), as well as adaptations to extreme elemental conditions such as those that occur in toxic mine adapted extremophile plants. My lab develops large-scale population genomic approaches to identify genomic changes specific to adapted populations, revealing candidate alleles and process mediating adaptations, as well as adaptive gene flow. A major goal is our work is to understand the fundamental rules that determine whether evolutionary change must be constrained and thus predictable, in contrast to changes that may meander along diverse paths.
Running throughout this research is an interest in understanding the population-level processes that influence how populations of plants or animals evolve in response to extreme conditions. We pick systems that not only promise important fundamental scientific population-level insights (such as understanding adaptive gene flow or how other demographic phenomena influence adaptation), but also may provide molecular mechanistic understanding of adaptations that are of consequence for the social good. For example, how is it that certain terrestrial plant populations can grow in pure seawater, while closely related populations of the same species are intolerant to salinity? Such systems provide powerful stories of evolutionary change and also will inform rational crop design in the face of landscape degradation and climate change.
Current work in my lab is evenly split between an ERC funded population genomic programme assessing hotspots of repeated evolution and my role in the Future Foods Beacon of Excellence, which is beginning work on orphan, underutilized crops, especially in Africa.