Ecological Genetics

To study adaptive processes in plant populations, we apply molecular-genetic and genomic tools to describe patterns of genetic diversity and to search for allele or genotype frequencies that co-vary with environmental variation. Such environmental associations allow us to infer putatively adaptive genes or gene networks, and to infer their possible roles in adaptive responses to future climate. We focus on forest trees, which are key structural species in forest ecosystems, and alpine plants that will likely face limits to upward shifts of their range to track global warming.

In rare species with often small population sizes, connectivity among habitat fragments is crucial for maintaining genetic diversity, a pre-requisite for adaptive processes in a changing world. We analyze effects of landscape elements on dispersal and, hence, connectivity of organisms and their populations or how land use affects rare species of plants and animals of conservation concern. Our findings serve for deducing implementation strategies and formulating guidelines to support decision making in the planning of connectivity measures, also allowing for the evaluation of their effectiveness.

• Developing a monitoring program of genetic diversity: what do stakeholders say?
  Parli, Rea; Lieberherr, Eva; Holderegger, Rolf; Gugerli, Felix; Widmer, Alex; et al.
  Conservation Genetics  10.1007/s10592-021-01379-6  OCT 2021
• Genomic signatures of convergent adaptation to Alpine environments in three Brassicaceae species
  Rellstab, Christian; Zoller, Stefan; Sailer, Christian; Tedder, Andrew; Gugerli, Felix; Shimizu, Kentaro K; Holderegger, Rolf; Widmer, Alex; Fischer, Martin C
  Molecular Ecology 10.1111/mec.15648 NOV 2020
• Adaptation to local climate in multi-trait space: evidence from silver fir (Abies alba Mill.) populations across a heterogeneous environment
  Csillery, Katalin; Ovaskainen, Otso; Sperisen, Christoph; Buchmann, Nina; Widmer, Alex; Gugerli, F
  Heredity, 10.1038/s41437-019-0240-0, JAN 2020
• A Reference Genome Sequence for the European Silver Fir (Abies alba Mill.): A Community-Generated Genomic Resource
  Mosca, E; Cruz, F; Gomez-Garrido, J; Bianco, L; Rellstab, C; Brodbeck, S; Csillery, K; Fady, B; Fladung, M; Fussi, B; Gomory, D; Gonzalez-Martinez, SC; Grivet, D; Gut, M; Hansen, OK; Heer, K; Kaya, Z; Krutovsky, KV; Kersten, B; Liepelt, S; Opgenoorth, L; Sperisen, C; Ullrich, KK; Vendramin, GG; Westergren, M; Ziegenhagen, B; Alioto, T; Gugerli, F; Heinze, B; Hohn, M; Troggio, M; Neale, DB
  G3-GENES GENOMES GENETICS, 9 (7):2039-2049; 10.1534/g3.119.400083 JUL 2019
• 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
• Using transcriptome sequencing and pooled exome capture to study local adaptation in the giga-genome of Pinus cembra
  Rellstab, Christian; Dauphin, Benjamin; Zoller, Stefan; Brodbeck S; Gugerli F.
  MOLECULAR ECOLOGY RESOURCES   Volume: 19   Issue: 2   Pages: 536-551  10.1111/1755-0998.12986 MAR 2019
• Transmembrane transport and stress response genes play an important role in adaptation of Arabidopsis halleri to metalliferous soils
  Sailer, Christian; Babst-Kostecka, Alicja; Fischer, Martin C.; et al.
  Scientific Reports Volume: 8 Published: OCT 31 2018, DOI: 10.1038/s41598-018-33938-2
• No distinct barrier effects of highways and a wide river on the genetic structure of the Alpine newt (Ichthyosaura alpestris) in densely settled landscapes
  Luqman, Hirzi; Muller, Roxane; Vaupel, Andrea; et al.
  Conservation Genetics Volume: 19 Issue: 3 Pages: 673-685 Published: JUN 2018,  DOI: 10.1007/s10592-018-1046-y
• Biotic interactions and seed deposition rather than abiotic factors determine recruitment at elevational range limits of an alpine tree
  Neuschulz, Eike Lena; Merges, Dominik; Bollmann, Kurt; et al.
  Journal of Ecology Volume: 106 Issue: 3 Pages: 948-959 Published: MAY 2018, DOI: 10.1111/1365-2745.12818
• The phylogeographic structure of Arabis alpina in the Alps shows consistent patterns across different types of molecular markers and geographic scales
  Rogivue, Aude; Graf, Rene; Parisod, Christian; et al.
  Alpine Botany Volume: 128 Issue: 1 Pages: 35-45 Published: APR 2018, DOI: 10.1007/s00035-017-0196-8
• Improved recovery of ancient DNA from subfossil wood - application to the world's oldest Late Glacial pine forest
  Lendvay, Bertalan; Hartmann, Martin; Brodbeck, Sabine; et al.
  New Phytologist Volume: 217 Issue: 4 Pages: 1737-1748 Published: MAR 2018, DOI: 10.1111/nph.14935
• Preserving genetic connectivity in the European Alps protected area network
  Schoville, Sean D.; Dalongeville, Alicia; Viennois, Gaelle; et al.
  Biological Conservation Volume: 218 Pages: 99-109 Published: FEB 2018, DOI: 10.1016/j.biocon.2017.12.017

• Local adaptation to changing environment
• Patterns of genetic diversity in alpine plants
• Conservation genetics
• Landscape genetics
• Hybridization and introgression

• Environmental characterization through remote sensing
• Bioinformatics
• Reproductive ecology
• Demography