Summary: Despite the large body of research devoted to understanding the role of Quaternary glacial cycles in the genetic divergence of European trees, the differential contribution of geographic isolation and/or environmental adaptation in creating population genetic divergence remains unexplored. In this study, we used a long‐lived tree (Taxus baccata) as a model species to investigate the impact of Quaternary climatic changes on genetic diversity via neutral (isolation‐by‐distance) and selective (isolation‐by‐adaptation) processes. We applied approximate Bayesian computation to genetic data to infer its demographic history, and combined this information with past and present climatic data to assess the role of environment and geography in the observed patterns of genetic structure. We found evidence that yew colonized Europe from the East, and that European samples diverged into two groups (Western, Eastern) at the beginning of the Quaternary glaciations, c. 2.2 Myr before present. Apart from the expected effects of geographical isolation during glacials, we discovered a significant role of environmental adaptation during interglacials at the origin of genetic divergence between both groups. This process may be common in other organisms, providing new research lines to explore the effect of Quaternary climatic factors on present‐day patterns of genetic diversity.

The complex of beech taxa in western Eurasia (Fagus sylvatica L. s.l.) represents one of the most widespread broad-leaved trees in the temperate forests of the northern hemisphere. Two subspecies are generally recognized, F. sylvatica ssp. sylvatica in Europe and F. sylvatica ssp. orientalis in southwestern Asia, but several strongly differentiated regional populations were identified within this complex. To reveal geographical and genomic patterns of hybridization and introgression, genetic variation at 6789 single-nucleotide polymorphisms (SNP) resulting from ddRAD sequencing was studied in 288 specimens representing 207 populations distributed across the whole range. Two clusters resulting from a Bayesian analysis of population Structure well coincided with the subspecies, while increasing the number of clusters allowed to distinguish divergent lineages within subspecies. Two zones of potential hybridization between such lineages were analyzed: western Balkans at the contact of both subspecies and the Alpine area at the contact of populations coming from different glacial refugia. Geographical distribution of hybrid indices in the Balkan hybrid zone indicates asymmetric gene flow preferentially directed from F. orientalis to F. sylvatica. Eight SNPs showed a significant shift of genomic cline centers, seven of them toward excess F. orientalis ancestry, suggesting that introgression irregularly affects different regions of the beech genome. On the other hand, no genomic cline outliers were found in the Alpine hybrid zone. Implications for assisted gene flow are shortly discussed.

European beech is an ecologically and commercially important species, which is expected to decline in several regions because of heat and drought stress associated with climate change. Knowledge of the genetic basis of the adaptation to climate is needed to guide assisted migration. Genetic variation at 1704 single-nucleotide polymorphisms (SNPs) resulting from ddRAD sequencing, primarily located in gene exons, was studied in 181 specimens representing 123 populations distributed over most of the whole range. Bayesian analysis of population structure yielded two clusters exhibiting a clear longitudinal cline and correlated with indicators of low temperatures and temperature fluctuation. Five SNPs were significantly associated with climatic variables related primarily to heat and temperature ranges. Two alternative explanations are offered for the observed response patterns: (i) differential sensitivity to heat and (ii) response mediated by vegetative phenology.