Evolutionary Genomics

Our group is fascinated by the diversity and evolution of living organisms, populations and ecological systems. Our primary goal is to understand the basic principles underlying both macro- and microevolutionary changes using plants as model organisms. In particular, our interest extends over several fields of plant biology, including ecology, population genomics, molecular evolution, evo-devo, systematics and comparative genomics with special attention to basal groups of land plants. We combine field-based ecological and lab-based molecular/reverse genetic approaches including computationally intensive modeling and genome analysis to understand evolutionary processes both at the macro- and microevolutionary scales.

• The evolution of life cycle transitions in plants
• The evolution of the land plant sporophyte
• The effect of ploidy on evolutionary processes
• Sex chromosome evolution and sex determination in haploid dioecy
• The genetics and epigenetics of inbreeding and outbreeding depression
• Genomic imprinting in plants lacking endosperm

► Google Scholar: https://scholar.google.ch/citations?hl=de&user=slEELEoAAAAJ

• An optimized transformation protocol for Anthoceros agrestis and three more hornwort species
  M Waller, E Frangedakis, AO Marron, S Sauret‐Güeto, J Rever, ...
  The Plant Journal 114 (3), 699-718  2023
• What can hornworts teach us?
  E Frangedakis, AO Marron, M Waller, A Neubauer, SW Tse, Y Yue, ...
  Frontiers in Plant Science 14, 621,  2023
• Comparative genomics elucidates the origin of a supergene controlling floral heteromorphism
  G Potente, É Léveillé-Bourret, N Yousefi, RR Choudhury, B Keller, SI Diop, ...
  Molecular Biology and Evolution 39 (2), msac035  2022
• Different molecular changes underlie the same phenotypic transition: Origins and consequences of independent shifts to homostyly within species
  Mora-Carrera, Emiliano; Stubbs, Rebecca L.; Keller, Barbara; Leveille-Bourret, Etienne; Vos, Jurriaan M.; Szoevenyi, Peter; Conti, Elena
  Molecular Ecology 10.1111/mec.16270  NOV 2021
• Extensive Genome-Wide Phylogenetic Discordance Is Due to Incomplete Lineage Sorting and Not Ongoing Introgression in a Rapidly Radiated Bryophyte Genus
  Meleshko, Olena; Martin, Michael D.; Korneliussen, Thorfinn Sand; Schroeck, Christian; Lamkowski, Paul; et al.
  Molecular Biology And Evolution 10.1093/molbev/msab063  JUL 2021
• An Agrobacterium-mediated stable transformation technique for the hornwort model Anthoceros agrestis
  Frangedakis, Eftychios; Waller, Manuel; Nishiyama, Tomoaki; Tsukaya, Hirokazu; Xu, Xia; et al.
  New Phytologist 10.1111/nph.17524  NOV 2021
• Lipid exchanges drove the evolution of mutualism during plant terrestrialization
  Rich, Melanie K.; Vigneron, Nicolas; Libourel, Cyril; Keller, Jean; Xue, Li; et al.
  Science 10.1126/science.abg0929  MAY 21 2021
• Charting the genomic landscape of seed-free plants
  Szovenyi, Peter; Gunadi, Andika; Li, Fay-Wei
  Nature Plants  10.1038/s41477-021-00888-z  Early Access: APR 2021
• The hornworts: morphology, evolution and development
  Frangedakis, Eftychios; Shimamura, Masaki; Villarreal, Juan Carlos; Li, Fay-Wei; Tomaselli, Marta; et al.
  New Phytologist  DOI: 10.1111/nph.16874 SEP 2020
• Evolutionary History of the Marchantia polymorpha Complex
  Linde, Anna-Malin; Sawangproh, Weerachon; Cronberg, Nils; Szoevenyi, Peter; Lagercrantz, Ulf
  Frontiers In Plant Science  DOI: 10.3389/fpls.2020.00829  JUN 26 2020
• Transcriptional Landscapes of Divergent Sporophyte Development in Two Mosses, Physcomitrium (Physcomitrella) patens and Funaria hygrometrica
  Kirbis, Alexander; Waller, Manuel; Ricca, Mariana; Bont, Zoe; Neubauer, Anna; et al.
  Frontiers In Plant Science  DOI: 10.3389/fpls.2020.00747 JUN 10 2020
• A pseudomolecule-scale genome assembly of the liverwort Marchantia polymorpha
  Diop, Seydina I.; Subotic, Oliver; Giraldo-Fonseca, Alejandro; Waller, Manuel; Kirbis, Alexander; et al.
  Plant Journal  DOI: 10.1111/tpj.14602  Published: MAR 2020
• Development and characterization of novel SSR markers in the endangered endemic species Ferula sadleriana
  Malkocs, Tamas; Laczko, Levente; Bereczki, Judit; Meglecz, Emese; Szoevenyi, Peter; et al.
  Applications In Plant Sciences 8(2) Special Issue, DOI: 10.1002/aps3.11321 FEB 2020
• Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts
  Fay-Wei Li, Tomoaki Nishiyama, Manuel Waller, Eftychios Frangedakis, Jean Keller, Zheng Li, Noe Fernandez-Pozo, Michael S. Barker, Tom Bennett, Miguel A. Blázquez, Shifeng Cheng, Andrew C. Cuming, Jan de Vries, Sophie de Vries, Pierre-Marc Delaux, Issa S. Diop, C. Jill Harrison, Duncan Hauser, Jorge Hernández-García, Alexander Kirbis, John C. Meeks, Isabel Monte, Sumanth K. Mutte, Anna Neubauer, Dietmar Quandt, Tanner Robison, Masaki Shimamura, Stefan A. Rensing, Juan Carlos Villarreal, Dolf Weijers, Susann Wicke, Gane K.-S. Wong, Keiko Sakakibara & Péter Szövényi
  Nature Plants. March 13, 2020. DOI: 10.1038/s41477-020-0618-2
• Towards a plant model for enigmatic U-to-C RNA editing: the organelle genomes, transcriptomes, editomes and candidate RNA editing factors in the hornwort Anthoceros agrestis
  Gerke, Philipp; Szovenyi, Peter; Neubauer, Anna; Lenz, Henning; Gutmann, Bernard; et al.
  New Phytologist, 10.1111/nph.16297  2019
• Organellomic data sets confirm a cryptic consensus on (unrooted) land-plant relationships and provide new insights into bryophyte molecular evolution
  Bell, David; Lin, Qianshi; Gerelle, Weslery K.; Joya, Steve; Chang, Ying; et al.
  American Journal Of Botany,  DOI: 10.1002/ajb2.1397 2019
• One thousand plant transcriptomes and the phylogenomics of green plants
  Leebens-Mack, James H.; Barker, Michael S.; Carpenter, Eric J.; Deyholos, Michael K.; Gitzendanner, Matthew A.; et al.
  Nature DOI: 10.1038/s41586-019-1693-2  2019
• …

• Comparative evolutionary developmental biology
• Evolutionary genomics
• Adaptation to changing climate
• Evolutionary transcriptomics
• Breeding system evolution