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Results of the analysis of non-coding regions of the chloroplast genome in Italian population of deciduous oaks (subgenus Quercus) and holm oak (subgenus Scleropyllodris) are reported. Deciduous oak revealed the occurrence of six chloroplast haplotypes, differently distributed in the single geographic areas (northern, central, and southern Italy, and major islands). Moreover, most of the present Italian oak populations seems to derive from two major refugia, located in Sicily and in the Balkans, respectively. The most likely migration dynamics from the refugia towards the central and northern part of the peninsula are discussed. Migration pathways resulted to have been different in the various geographic areas. The presence of an endemic haplotype in Sardinia and Corsica was considered of particular interest. In Italian holm oak populations eight haplotypes were detected, six of them in Sicily. Five out of six Sicilian haplotypes resulted to be endemic. The Italian peninsula was colonized by two major haplotypes, one of them originating from Sicily. Results on deciduous oaks and holm oak in Italy highlight the important role played by the populations from the south and from the major islands in the colonization the Italian peninsula after the last ice age.

Background and Aims: Assessing adaptive genetic variation and its spatial distribution is crucial to conserve forest genetic resources and manage species' adaptive potential. Macro-environmental gradients commonly exert divergent selective pressures that enhance adaptive genetic divergence among populations. Steep micro-environmental variation might also result in adaptive divergence at finer spatial scales, even under high gene flow, but it is unclear how often this is the case. Here, we assess genetic variation in early fitness traits among distant and nearby maritime pine (Pinus pinaster Ait.) populations, to investigate climatic factors associated with trait divergence, and to examine trait integration during seedling establishment., Methods: Open pollinated seeds were collected from seven population pairs across the European species distribution, with paired populations spatially close (between <1 km up to 21 km) but environmentally divergent. Seeds were sown in semi-natural conditions at three environmentally contrasting sites, where we monitored seedling emergence, growth and survival., Key Results: At large spatial scales, we found significant genetic divergence among populations in all studied traits, with certain traits exhibiting association with temperature and precipitation gradients. Significant trait divergence was also detected between pairs of nearby populations. Besides, we found consistent trait correlations across experimental sites, notably heavier seeds and earlier seedling emergence were both associated with higher seedling survival and fitness over two years in all experimental conditions., Conclusions: We identified mean annual temperature and precipitation seasonality as potential drivers of P. pinaster population divergence in the studied early-life traits. Populations genetically diverge also at local spatial scales, potentially suggesting that divergent natural selection can override gene flow along local-scale ecological gradients. These results suggest the species exhibits substantial adaptive potential that has allowed it to survive and evolve under contrasting environmental conditions., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Annals of Botany Company.)

The effect of past environmental changes on the demography and genetic diversity of natural populations remains a contentious issue and has rarely been investigated across multiple, phylogenetically distant species. Here, we perform comparative population genomic analyses and demographic inferences for seven widely distributed and ecologically contrasting European forest tree species based on concerted sampling of 164 populations across their natural ranges. For all seven species, the effective population size, N e , increased or remained stable over many glacial cycles and up to 15 million years in the most extreme cases. Surprisingly, the drastic environmental changes associated with the Pleistocene glacial cycles have had little impact on the level of genetic diversity of dominant forest tree species, despite major shifts in their geographic ranges. Based on their trajectories of N e over time, the seven tree species can be divided into three major groups, highlighting the importance of life history and range size in determining synchronous variation in genetic diversity over time. Altogether, our results indicate that forest trees have been able to retain their evolutionary potential over very long periods of time despite strong environmental changes., (© 2024. The Author(s).)

Most tree species underwent cycles of contraction and expansion during the Quaternary. These cycles led to an ancient and complex genetic structure that has since been affected by extensive gene flow and by strong local adaptation. The extent to which hybridization played a role in this multi-layered genetic structure is important to be investigated. To study the effect of hybridization on the joint population genetic structure of two dominant species of the Eurasian boreal forest, Picea abies and P. obovata, we used targeted resequencing and obtained around 480 K nuclear SNPs and 87 chloroplast SNPs in 542 individuals sampled across most of their distribution ranges. Despite extensive gene flow and a clear pattern of Isolation-by-Distance, distinct genetic clusters emerged, indicating the presence of barriers and corridors to migration. Two cryptic refugia located in the large hybrid zone between the two species played a critical role in shaping their current distributions. The two species repeatedly hybridized during the Pleistocene and the direction of introgression depended on latitude. Our study suggests that hybridization helped both species to overcome main shifts in their distribution ranges during glacial cycles and highlights the importance of considering whole species complex instead of separate entities to retrieve complex demographic histories., (© 2024 The Author(s). Molecular Ecology published by John Wiley & Sons Ltd.)

We investigated the dendroclimatic response of a Pinus heldreichii metapopulation distributed over a wide elevation interval (from 882 to 2143 m a.s.l.), spanning from low mountain to upper subalpine vegetation belts in the southern Italian Apennines. The tested hypothesis is that wood growth along an elevational gradient is non-linearly related to air temperature. During three years of fieldwork (2012-2015) at 24 sites, we collected wood cores from a total of 214 pine trees with diameter at breast height from 19 to 180 cm (average 82.7 ± 32.9 cm). We used a combination of tree-ring and genetic methods to reveal factors involved in growth acclimation using a space-for-time approach. Scores from canonical correspondence analysis were used to combine individual tree-ring series into four composite chronologies related to air temperature along the elevation gradient. Overall, the June dendroclimatic response followed a bell-shaped thermal niche curve, increasing until a peak around 13-14 °C. A similarly bell-shaped response was found with previous autumn air temperature, and both dendroclimatic signals interacted with stem size and growth rates, generating a divergent growth response between the top and the bottom of the elevation gradient. Increased tree growth in the upper subalpine belt was consistent with the consequences of increasing air temperature under no drought stress. A positive link was uncovered between pine growth at all elevations and April mean temperature, with trees growing at the lowest elevations showing the strongest growth response. No elevational genetic differences were found, hence long-lived tree species with small geographical ranges may reverse their climatic response between the lower and upper bioclimatic zones of their environmental niche. Our study revealed a high resistance and acclimation capability of Mediterranean forest stands, and such low vulnerability to changing climatic conditions highlights the potential to store carbon in these ecosystems for the coming decades., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

Microgeographical adaptation occurs when the effects of directional selection persist despite gene flow. Traits and genetic loci under selection can then show adaptive divergence, against the backdrop of little differentiation at other traits or loci. How common such events are and how strong the selection is that underlies them remain open questions. Here, we discovered and analysed microgeographical patterns of genomic divergence in four European and Mediterranean conifers with widely differing life-history traits and ecological requirements (Abies alba MIll., Cedrus atlantica [Endl.] Manetti, Pinus halepensis Mill. and Pinus pinaster Aiton) by screening pairs from geographically close forest stands sampled along steep ecological gradients. We inferred patterns of genomic divergence by applying a combination of divergence outlier detection methods, demographic modelling, Approximate Bayesian Computation inferences and genomic annotation to genomic data. Surprisingly for such small geographical scales, we showed that selection is strong in all species but generally affects different loci in each. A clear signature of selection was systematically detected on a fraction of the genome, of the order of 0.1%-1% of the loci depending on the species. The novel modelling method we designed for estimating selection coefficients showed that the microgeographical selection coefficient scaled by population size (Ns) was 2-30. Our results convincingly suggest that selection maintains within-population diversity at microgeographical scales in spatially heterogeneous environments. Such genetic diversity is likely to be a major reservoir of adaptive potential, helping populations to adapt under fluctuating environmental conditions., (© 2022 John Wiley & Sons Ltd.)

A decade of genetic association studies in multiple organisms suggests that most complex traits are polygenic; that is, they have a genetic architecture determined by numerous loci, each with small effect-size. Thus, determining the degree of polygenicity and its variation across traits, environments and time is crucial to understand the genetic basis of phenotypic variation. We applied multilocus approaches to estimate the degree of polygenicity of fitness-related traits in a long-lived plant (Pinus pinaster Ait., maritime pine) and to analyse this variation across environments and years. We evaluated five categories of fitness-related traits (survival, height, phenology, functional, and biotic-stress response) in a clonal common-garden network planted in contrasted environments (over 20,500 trees). Most of the analysed traits showed evidence of local adaptation based on Q st -F st comparisons. We further observed a remarkably stable degree of polygenicity, averaging 6% (range of 0%-27%), across traits, environments and years. We detected evidence of negative selection, which could explain, at least partially, the high degree of polygenicity. Because polygenic adaptation can occur rapidly, our results suggest that current predictions on the capacity of natural forest tree populations to adapt to new environments should be revised, especially in the current context of climate change., (© 2022 John Wiley & Sons Ltd.)

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 1,368 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 (F CT = 0.148) was an order of magnitude greater than between elevations within sites (F SC = 0.031), nevertheless high elevation populations consistently exhibited a stronger FSGS. Structural equation modelling 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., (© 2021 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.)

High genetic variation and extensive gene flow may help forest trees with adapting to ongoing climate change, yet the genetic bases underlying their adaptive potential remain largely unknown. We investigated range-wide patterns of potentially adaptive genetic variation in 64 populations of European beech (Fagus sylvatica L.) using 270 SNPs from 139 candidate genes involved either in phenology or in stress responses. We inferred neutral genetic structure and processes (drift and gene flow) and performed differentiation outlier analyses and gene-environment association (GEA) analyses to detect signatures of divergent selection. Beech range-wide genetic structure was consistent with the species' previously identified postglacial expansion scenario and recolonization routes. Populations showed high diversity and low differentiation along the major expansion routes. A total of 52 loci were found to be putatively under selection and 15 of them turned up in multiple GEA analyses. Temperature and precipitation related variables were equally represented in significant genotype-climate associations. Signatures of divergent selection were detected in the same proportion for stress response and phenology-related genes. The range-wide adaptive genetic structure of beech appears highly integrated, suggesting a balanced contribution of phenology and stress-related genes to local adaptation, and of temperature and precipitation regimes to genetic clines. Our results imply a best-case scenario for the maintenance of high genetic diversity during range shifts in beech (and putatively other forest trees) with a combination of gene flow maintaining within-population neutral diversity and selection maintaining between-population adaptive differentiation., (© 2021 John Wiley & Sons Ltd.)

Key Message: Complementary gene-resequencing and transcriptomic approaches reveal contrasted evolutionary histories in a species complex. Pinus halepensis and Pinus brutia are closely related species that can intercross, but occupy different geographical ranges and bioclimates. To study the evolution of this species complex and to provide genomic resources for further research, we produce and analyze two new complementary sets of genetic resources: (i) a set of 172 re-sequenced genomic target loci analyzed in 45 individuals, and (ii) a set of 11 transcriptome assemblies. These two datasets provide insights congruent with previous studies: P. brutia displays high level of genetic diversity and no genetic sub-structure, while P. halepensis shows three main genetic clusters, the western Mediterranean and North African clusters displaying much lower genetic diversity than the eastern Mediterranean cluster, the latter cluster having similar genetic diversity to P. brutia. In addition, these datasets provide new insights on the timing of the species-complex history: the two species would have split at the end of the tertiary, and the changing climatic conditions of the Mediterranean region at the end of the Tertiary-beginning of the Quaternary, together with the distinct species tolerance to harsh climatic conditions would have resulted in different geographic distributions, demographic histories and genetic patterns of the two pines. The multiple glacial-interglacial cycles during the Quaternary would have led to the expansion of P. brutia in the Middle East, while P. halepensis would have been through bottlenecks. The last glaciations, from 0.6 Mya on, would have affected further the Western genetic pool of P. halepensis., (© 2021. The Author(s), under exclusive licence to Springer Nature B.V.)

Knowledge of the molecular mechanisms underlying the stress response in plants is essential to understand evolutionary processes that result in long-term persistence of populations. Populations inhabiting marginal ecological conditions at the distribution range periphery may have preserved imprints of natural selection that have shaped functional genetic variation of the species. Our aim was to evaluate the extent of selection processes in the extremely fragmented, peripheral and isolated populations of Scots pine in central-eastern Europe. Autochthonous populations of the Carpathian Mts. and the Pannonian Basin were sampled and drought stress-related candidate genes were re-sequenced. Neutrality tests and outlier detection approaches were applied to infer the effect and direction of selection. Populations retained high genetic diversity by preserving a high number of alleles and haplotypes, many of them being population specific. Neutrality tests and outlier detection highlighted nucleotide positions that are under divergent selection and may be involved in local adaptation. The detected genetic pattern confirms that natural selection has played an important role in shaping modern-day genetic variation in marginal Scots pine populations, allowing for the long-term persistence of populations. Selection detected at functional regions possibly acts to maintain diversity and counteract the effect of genetic erosion., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Trees play a key role in the structure and function of many ecosystems worldwide. In the Mediterranean Basin, forests cover approximately 22% of the total land area hosting a large number of endemics (46 species). Despite its particularities and vulnerability, the biodiversity of Mediterranean trees is not well known at the taxonomic, spatial, functional, and genetic levels required for conservation applications. The WOODIV database fills this gap by providing reliable occurrences, four functional traits (plant height, seed mass, wood density, and specific leaf area), and sequences from three DNA-regions (rbcL, matK, and trnH-psbA), together with modelled occurrences and a phylogeny for all 210 Euro-Mediterranean tree species. We compiled, homogenized, and verified occurrence data from sparse datasets and collated them on an INSPIRE-compliant 10 × 10 km grid. We also gathered functional trait and genetic data, filling existing gaps where possible. The WOODIV database can benefit macroecological studies in the fields of conservation, biogeography, and community ecology.