Alpine rockcress (Arabis alpina) has become a model species of ecological genetics, facilitated by the release of a high-quality reference genome. In the southwestern Swiss Alps, re-sequencing of individuals and very high-resolution environmental characterization of microhabitats derived from remote sensing data (LiDAR) allowed for environmental association analyses at the individual level. (photo: F. Gugerli)
Landscape barriers (indicated by arrows) coinciding with interpolated levels of genetic differentiation among groups of roe deer individuals in the wildlife corridor Suret (canton of Aargau). Dark shading indicates high level of genetic differentiation, A1 and T5 refer to fenced freeways, SBB marks a four-track railway line, Aare represents a wide river with concrete embarkments. (Hepenstrick et al. 2012)
Swiss stone pine (Pinus cembra) is a keystone species of the Alpine timberline ecotone, vulnerable to climate warming owing to increased competition. Exome capture of adult and juvenile cohorts in association with interpolated climate data (historic, present, future) indicate whether genotypes adapted to future environmental conditions are currently colonizing areas above the species current range. (photo: F. Gugerli)
Predicted change in local site water balance (open circles) and estimated risk (closed circles ±SE), based on required allele frequency change, to cope with expected environmental change by 2070. (Rellstab et al. 2016)
Landscape Genomics of Forest Trees and Alpine Plants
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.
- 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
- Reproductive ecology