Plant Genome Evolution and Diversification

Despite evidence pointing to gene duplication, transposition and epigenetic changes going along with plant diversification, the evolutionary significance of such genome dynamics remains elusive. Our work thus integrates evolutionary ecology and genomics to better understand speciation and adaptive radiation under changing environments.

Our projects often (but not only) use polyploid speciation as a model process integrating genomic and ecological changes. They combine high-throughput genomic technologies with experimental and empirical field studies to untangle the genetic and ecological drivers of diversification in alpine and Mediterranean plant populations.

• Genome-wide variation in nucleotides and retrotransposons in alpine populations of Arabis alpina (Brassicaceae)
  Rogivue A; Choudhury RR; Zoller S; Joost S; Felber F; Kasser M; Parisod C; Gugerli F
  MOLECULAR ECOLOGY RESOURCES, 19 (3):773-787;  https://doi.org/10.1111/1755-0998.12991 MAY 2019
• Impact of polymorphic transposable elements on linkage disequilibrium along chromosomes
  Choudhury, RR; Rogivue, A; Gugerli, F; Parisod, C
  MOLECULAR ECOLOGY, 28 (6):1550-1562; SI  https://doi.org/10.1111/mec.15014 MAR 2019
• Lateral transfers of large DNA fragments spread functional genes among grasses
  Dunning, LT; Olofsson, JK; Parisod, C; Choudhury, RR; Moreno-Villena, JJ; Yang, Y; Dionora, J; Quick, WP; Park, M; Bennetzen, JL; Besnard, G; Nosil, P; Osborne, CP; Christin, PA
  PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 116 (10):4416-4425; 10.1073/pnas.1810031116 MAR 5 2019
• Parental transposable element loads influence their dynamics in young Nicotiana hybrids and allotetraploids
  Mhiri, C; Parisod, C; Daniel, J; Petit, M; Lim, KY; de Borne, FD; Kovarik, A; Leitch, AR; Grandbastien, MA
  NEW PHYTOLOGIST, 221 (3):1619-1633; 10.1111/nph.15484 FEB 2019
• The phylogeographic structure of Arabis alpina in the Alps shows consistent patterns across different types of molecular markers and geographic scales
  Rogivue, Aude; Graf, René; Parisod, Christian; Holderegger, Rolf; Gugerli, Felix (2018)
  Alpine Botany, 128(1):35-45. Springer https://doi.org/10.1007/s00035-017-0196-8 2018
• Multiscale landscape genomic models to detect signatures of selection in the alpine plant Biscutella laevigata 
  Leempoel, Kevin; Parisod, Christian; Geiser, Celine; et al. 
  ECOLOGY AND EVOLUTION, 8 (3): 1794-1806; https://doi.org/10.1002/ece3.3778 FEB 2018
• Jumping genes: Genomic ballast or powerhouse of biological diversification 
  Choudhury, Rimjhim Roy; Parisod, Christian 
  MOLECULAR ECOLOGY, 26 (18): 4587-4590, https://doi.org/10.1111/mec.14247 SEP 2017
• Phylogeography of the moonwort fern Botrychium lunaria (Ophioglossaceae) based on chloroplast DNA in the Central-European Mountain System 
  Maccagni, Alessio; Parisod, Christian; Grant, Jason R. 
  ALPINE BOTANY, 127 (2): 185-196; https://doi.org/10.1007/s00035-017-0188-8 OCT 2017
• Resolving fine-grained dynamics of retrotransposons: comparative analysis of inferential methods and genomic resources 
  Choudhury, Rimjhim Roy; Neuhaus, Jean-Marc; Parisod, Christian 
  PLANT JOURNAL, 90 (5): 979-993; http://dx.doi.org/10.1111/tpj.13524 JUN 2017
• Benefits from living together? Clades whose species use similar habitats may persist as a result of eco-evolutionary feedbacks 
  Prinzing, Andreas; Ozinga, Wim A.; Brandle, Martin; et al. 
  NEW PHYTOLOGIST, 213 (1): 66-82, http://dx.doi.org/10.1111/nph.14341 JAN 2017

• Mechanisms of reproductive isolation and speciation
• Polyploidy (hybridization and whole genome duplication)
• Transposable elements and genome dynamics
• Landscape genetics and adaptation to environmental heterogeneity
• Alpine botany

• Integration of genetic variation with environmental heterogeneity at high resolution
• Characterization of genetic resources in wild relatives of crop species
• Genetic diversity for the monitoring of rare endemics or ill-defined species