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Genetic variation and signatures of natural selection in populations of European beech (Fagus sylvatica L.) along precipitation gradients


European beech (Fagus sylvatica L.) is one of the most important forest tree species in Europe, and its genetic adaptation potential to climate change is of great interest. Saplings and adults from 12 European beech populations were sampled along two steep precipitation gradients in Switzerland. All individuals were genotyped at 13 microsatellite or simple sequence repeat (SSR) markers and 70 single nucleotide polymorphisms (SNPs) in 24 candidate genes potentially involved in stress response and phenology. Both SSR and SNP markers revealed high genetic diversity in the studied populations and low but statistically significant population differentiation. The SNPs were searched for FST outliers using three different methods implemented in LOSITAN, Arlequin, and BayeScan, respectively. Additionally, associations of the SNPs with environmental variables were tested by two methods implemented in Bayenv2 and Samβada, respectively. There were 14 (20%) SNPs in 12 (50%) candidate genes in the saplings and 9 (12.8%) SNPs in 7 (29.2%) candidate genes in the adults consistently identified by at least two of the five methods used, indicating that they are very likely under selection. Genes with SNPs showing signatures of selection are involved in a wide range of molecular functions, such as oxidoreductases (IDH), hydrolases (CysPro), transferases (XTH), transporters (KT2), chaperones (CP10), and transcription factors (DAG, NAC transcription factor). The obtained data will help us better understand the genetic variation underlying adaptation to environmentally changing conditions in European beech, which is of great importance for the development of scientific guidelines for the sustainable management and conservation of this important species.

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We thank Florian Schreyer and Jhon Rivera-Monroy for their help in the fieldwork, and Alexandra Dolynska for her assistance in the laboratory. We also thank Hadrien Lalagüe for providing the SNP positions and haplotype sequences from his study to select the haplotype tag SNPs. We also thank COLFUTURO and the Administrative Department of Science, Technology and Innovation COLCIENCIAS for supporting Laura Cuervo-Alarcon during this study. We appreciate very much two anonymous reviewers for their thorough reviews that greatly helped us improve the manuscript.


This study was financially supported by the Swiss Federal Office for the Environment FOEN and the Swiss Federal Institute for Forest, Snow and Landscape Research WSL.

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Authors and Affiliations



LCA collected the samples, generated and analyzed the data, and wrote the manuscript. MA helped with the sample collection; MA, CS, KVK, and RF conceived and designed the study, developed the experimental plan, coordinated the research, and participated in the drafting of the manuscript. MM helped with data analysis, interpretation, and manuscript editing. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Konstantin V. Krutovsky.

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Conflict of interest

The authors declare that they have no conflicts of interest.

Data archiving statement

Genotype data corresponding to SSR and SNP markers were submitted to the TreeGenes Database (; accession number: TGDR073).

Additional information

Communicated by F. Gugerli

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Cuervo-Alarcon, L., Arend, M., Müller, M. et al. Genetic variation and signatures of natural selection in populations of European beech (Fagus sylvatica L.) along precipitation gradients. Tree Genetics & Genomes 14, 84 (2018).

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  • Adaptation
  • Climate change
  • Environmental association analysis
  • Microsatellite
  • Outlier analysis
  • SNP