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.

• Coşgun S, Gauthier J, …, Schwörer C, Sperisen C, van Vugt L, Alvarez N, Conedera M, Gugerli F, Tinner W 2025. Exploring the connection between climatic conditions and genetic properties of Abies alba, including warm and summer-dry Mediterranean environments. Science of the Total Environment. 964: 78559. DOI 10.1016/j.scitotenv.2025.178559.
• Coşgun S, Gauthier J, …, Schwörer C, Sperisen C, Alvarez N, Gugerli F, Tinner W 2025. Genetic differentiation of Abies alba outside its main range under warm meso- and sub-Mediterranean conditions in Italy and Switzerland. Ecology and Evolution 15: e70909. DOI 10.1002/ece3.e70909
• Rogivue A, Leempoel K, Guillaume A, Choudhury RR, Felber F, Kasser M, Joost S, Parisod C, Gugerli F 2025. Locally specific genome-wide signatures of adaptation to environmental variation at high resolution in an alpine plant. Molecular Ecology 34: 17646. DOI 10.1111/mec.17646
• Guillaume AS, Rogivue A, Leempoel K, Gugerli F, Parisod C, Joost S 2024. Integrating very high resolution environmental proxies in genome-environment association studies. Evolutionary Applications 17: e13737. DOI 10.1111/eva.13737.
• Milesi P, Kastally C, Dauphin B, Cervantes S, …, GenTree Consortium, Lascoux M, Pyhäjärvi T 2024. Resilience of genetic diversity in forest trees over the Quaternary. Nature Communications 15: 8538. DOI 10.1038/s41467-024-52612-y
• Pearman PB, Broennimann O, …, Guisan A, Bruford M 2024. Conserving genetic diversity during climate change: Niche marginality and discrepant monitoring effort in Europe. Nature Ecology & Evolution 8: 267–281.
• Sonnenwyl V, Dauphin B, Fragnière Y, …, Parisod C, Kozlowski G, Gugerli F 2024. Genetic underpinning of failed afforestation with allochthonous Pinus cembra in the northwestern Swiss Alps. Alpine Botany 134: 1–13. DOI 10.1007/s00035-023-00304-6
• Dauphin B, Rellstab C, Wüest RO, Karger DN, Holderegger R, Gugerli F, Manel S 2023. Re-thinking the environment in landscape genomics. Trends in Ecology & Evolution. 38: 261–274
• Gugerli F, Brodbeck S, Lendvay B, Dauphin B, …, Morales-Molino C, Schwörer C 2023. A range-wide postglacial history of Swiss stone pine based on molecular markers and palaeoecological evidence. Journal of Biogeography 50: 1049–1062.
• Kersten B, Rellstab C, Schroeder H, Brodbeck S, Fladung M, Krutovsky KV, Gugerli F 2022. The mitochondrial genome sequence of Abies alba Mill. reveals a high structural and combinatorial variation. BMC Genomics 23: 776. DOI 10.1186/s12864-022-08993-9.
• Schwörer C, Leunda M, Alvarez N, Gugerli F, Sperisen C 2022. The untapped potential of macrofossils in plant aDNA research. New Phytologist 235: 391–401.
• Wötzel S, Andrello M, Albani MC, Koch MA, Coupland G, Gugerli F (2022). Arabis alpina: a perennial model plant for ecological genomics and life-history evolution. Molecular Ecology Resources 22: 468–486.
• Dauphin B, Rellstab C, Schmid M, Zoller S, Karger DN, Brodbeck S, Guillaume F, Gugerli F 2021. Genomic vulnerability to rapid climate warming in a tree species with a long generation time. Global Change Biology 27: 1181–1195.
• Dauphin B, Wüest RO, Brodbeck S, Zoller S, Fischer MC, Holderegger R, Gugerli F, Rellstab C 2020. Disentangling the effects of geographic peripherality and habitat suitability on neutral and adaptive genetic variation in Swiss stone pine. Molecular Ecology 29: 1972–1989.
• Rellstab C, Zoller S, Sailer C, Tedder A, Gugerli F, Shimizu KK, Holderegger R, Widmer A, Fischer MC 2020. Genomic signatures of convergent adaptation to Alpine environments in three Brassicaceae species. Molecular Ecology 29: 4350–4365.
• Mosca E, Cruz F, Gómez Garrido J, Bianco L, Rellstab C, Brodbeck S, …, Gugerli F, Heinze B, Höhn M, Troggio M, Neale DB 2019. The Abies alba genome project: a new genomic resource for a sensitive species. G3—Genes, Genomes, Genetics 9: 7, 2039–2049.
• Rellstab C, Dauphin B, Zoller S, Brodbeck S, Gugerli F 2019. Using transcriptome sequencing and pooled exome capture to study local adaptation in the giga-genome of Pinus cembra. Molecular Ecology Resources 19: 536–551.
• Rogivue A, Choudhury RR, Zoller S, Joost S, Felber F, Kasser M, Parisod C, Gugerli F 2019. Genome-wide variation in nucleotides and retrotransposons in alpine populations of Arabis alpina (Brassicaceae). Molecular Ecology Resources 19: 773–787.
• Rogivue A, Graf R, Parisod C, Holderegger R, Gugerli F 2018. The phylogeographic structure of Arabis alpina in the Alps shows consistent patterns across different types of molecular markers and of geographic scales. Alpine Botany 128: 35–45.
• Sailer C, Babst-Kostecka A, Fischer MC, Zoller S, Widmer A, Vollenweider P, Gugerli F, Rellstab C 2018. Transmembrane transport and stress response genes play an important role in adaptation of Arabidopsis halleri to metalliferous soils. Scientific Reports 8 16085.