Aim: Knowing a species’ response to historical climate shifts helps understanding its perspectives under global warming. We infer the hitherto unresolved postglacial history of Pinus cembra. Using independent evidence from genetic structure and demographic inference of extant populations, and from palaeoecological findings, we derive putative refugia and re-colonisation routes. Location: European Alps and Carpathians. Taxa: Pinus cembra. Methods: We genotyped nuclear and chloroplast microsatellite markers in nearly 3,000 individuals from 147 locations across the entire natural range of P. cembra. Spatial genetic structure (Bayesian modelling) and demographic history (Approximate Bayesian Computation) were combined with palaeobotanical records (pollen, macrofossils) to infer putative refugial areas during the Last Glacial Maximum (LGM) and re-colonisation of the current range. Results: We found distinct spatial genetic structure, despite low genetic differentiation even between the two disjunct mountain ranges. Nuclear markers revealed five genetic clusters aligned East–West across the range, while chloroplast haplotype distribution suggested nine clusters. Spatially congruent separation at both marker types highlighted two main genetic lineages in the East and West of the range. Demographic inference supported early separation of these lineages dating back to a previous interstadial or interglacial c. 210,000 years ago. Differentiation into five biologically meaningful genetic clusters likely established during post-glacial re-colonisation. Main conclusions: Combining genetic and palaeoecological evidence suggests that P. cembra primarily survived the LGM in “cold period” refugia south of the Central European Alps and near the Carpathians, from where it expanded during the Late Glacial into its current Holocene “warm period” refugia. This colonisation history has led to the distinct East–West structure of five genetic clusters. The two main genetic lineages likely derived from ancient divergence during an interglacial or interstadial. The respective contact zone (Brenner line) matches a main biogeographic break in the European Alps also found in herbaceous alpine plant species.

Variation in genetic diversity across species ranges has long been recognized as highly informative for assessing populations’ resilience and adaptive potential. The spatial distribution of genetic diversity within populations, referred to as fine-scale spatial genetic structure (FSGS), also carries information about recent demographic changes, yet it has rarely been connected to range scale processes. We studied eight silver fir (Abies alba Mill.) population pairs (sites), growing at high and low elevations, representative of the main genetic lineages of the species. A total of 1368 adult trees and 540 seedlings were genotyped using 137 and 116 single nucleotide polymorphisms (SNPs), respectively. Sites revealed a clear east-west isolation-by-distance pattern consistent with the post-glacial colonization history of the species. Genetic differentiation among sites (FCT=0.148) was an order of magnitude greater than between elevations within sites (FSC=0.031), nevertheless high elevation populations consistently exhibited a stronger FSGS. Structural equation modeling revealed that elevation and, to a lesser extent, post-glacial colonization history, but not climatic and habitat variables, were the best predictors of FSGS across populations. These results suggest that high elevation habitats have been colonized more recently across the species range. Additionally, paternity analysis revealed a high reproductive skew among adults and a stronger FSGS in seedlings than in adults, suggesting that FSGS may conserve the signature of demographic changes for several generations. Our results emphasize that spatial patterns of genetic diversity within populations provide information about demographic history complementary to non-spatial statistics, and could be used for genetic diversity monitoring, especially in forest trees.

Wildfire is a major ecological driver of plant evolution. Understanding the genetic basis of plant adaptation to wildfire is crucial, because impending climate change will involve fire regime changes worldwide. We studied the molecular genetic basis of serotiny, a fire-related trait, in Mediterranean maritime pine using association genetics. A single nucleotide polymorphism (SNP) set was used to identify genotype : phenotype associations in situ in an unstructured natural population of maritime pine (eastern Iberian Peninsula) under a mixed-effects model framework. RR-BLUP was used to build predictive models for serotiny in this region. Model prediction power outside the focal region was tested using independent range-wide serotiny data. Seventeen SNPs were potentially associated with serotiny, explaining approximately 29% of the trait phenotypic variation in the eastern Iberian Peninsula. Similar prediction power was found for nearby geographical regions from the same maternal lineage, but not for other genetic lineages. Association genetics for ecologically relevant traits evaluated in situ is an attractive approach for forest trees provided that traits are under strong genetic control and populations are unstructured, with large phenotypic variability. This will help to extend the research focus to ecological keystone non-model species in their natural environments, where polymorphisms acquired their adaptive value.

Taxanes are defensive metabolites produced by Taxus species (yews) and used in anticancer therapies. Despite their medical interest, patterns of natural diversity in taxane related genes are unknown. We examined variation at five main taxol-related genes of T. baccata in the Iberian Peninsula, a region where unique yew genetic resources are endangered. We looked at several gene features and applied complementary neutrality tests, including diversity/divergence tests, tests solely based on site-frequency spectrum and Zeng’s compound tests. To account for specific demography, microsatellite data were used to infer historical changes in population size based on an Approximate Bayesian Computation (ABC) approach. Polymorphism-divergence tests pointed to positive selection for genes TBT and TAT, and balancing selection for DBAT. In addition, neutrality tests based on site-frequency spectrum found that while a recent reduction in population size may explain most of statistics’ values, selection may still be in action in genes TBT and DBAT, at least in some populations. Molecular signatures on taxol genes suggest the action of frequent selective waves with different direction or intensity, possibly related to varying adaptive pressures produced by the host-enemy co-evolution on defense-related genes. Such natural selection processes may have produced taxane variants still undiscovered.

The study of dispersal capability of a species can provide essential information for the management and conservation of its genetic variability. Comparison of gene flow rates among populations characterized by different management and evolutionary histories allows one to decipher the role of factors such as isolation and tree density on gene movements. We used two paternity analysis approaches and different strategies to handle possible presence of genotyping errors to obtain robust estimates of pollen flow in four beech (Fagus sylvatica L.) populations from Austria and France. In each country one of the two plots is located in an unmanaged forest, the other plots are managed with a shelterwood system and inside a colonization area (in Austria and France, respectively). The two paternity analysis approaches provided almost identical estimates of gene flow. We found high pollen immigration (~75% of pollen from outside), with the exception of the plot from a highly isolated forest remnant (~50%). In the unmanaged plots the average within-population pollen dispersal distances (from 80 to 184 m) were higher than previously estimated for beech. From the comparison between the Austrian managed and unmanaged plots, that are only 500 m apart, we found no evidence that either gene flow or reproductive success distributions were significantly altered by forest management. Shelterwood seems to have an effect on the distribution of within-population pollen dispersal distances. In the managed plot, pollen dispersal distances were shorter, possibly because adult tree density is threefold (163 vs. 57 trees/ha) with respect to the unmanaged one.