Camilla Avanzi

Climate change is profoundly affecting species worldwide and poses a major threat to their long-term persistence. Although trees may have the potential for rapid adaptation to changing climates, empirical evidence remains limited, and whether these long-lived organisms can adapt quickly enough to keep pace with ongoing climate change is still an open question. To investigate real-time responses to contemporary climate change, we combined genomic data from 82 range-wide populations of the widespread tree Pinus pinaster Ait. with intensive sampling of two successive cohorts from two natural populations. Using an original genotype-environment association (GEA) approach to quantify climate (mal)adaptation, we found that most individuals from both target populations showed evidence of an adaptive lag to current climatic conditions, and are predicted to face substantial risk of maladaptation under future climates. Importantly, changes in genomic composition at climate-associated loci between cohorts were consistent with rapid evolutionary responses to ongoing climate change and could not be explained by neutral demographic processes alone, as supported by forward-time genetic simulations. We also observed a lower realised genetic load in the younger cohort, suggesting that the dynamics of deleterious mutations may change with climatic pressure. Our work provides evidence suggesting genetic responses to contemporary climate change within a single generation, including signals of rapid evolutionary changes in genomic composition at climate-associated loci and signatures of purifying selection, despite widespread adaptive lag to current climates. These findings challenge the view that trees only respond slowly to environmental change and highlight the need to integrate evolutionary dynamics into predictive models of species persistence under future climates.

Aim of study: We performed a fine scale characterization of two European black poplar (Populus nigra) in situ conservation units, using a large sample of individuals and a comprehensive set of genetic markers. This information is pivotal to understand the population dynamics of the units for implementing conservation and management plans. Area of study: We studied two populations with distinct environments and management practices in Spain and Austria. Material and methods: We genotyped 500 adults and 250 juveniles within each population using 13K single nucleotide polymorphism (SNP) markers. The populations were characterized in terms of fine scale genetic structure and clonality, while controlling for genotyping errors. Main results: The genomic data, with a low error rate, allowed the identification of groups of clones. The proportion of clonal individuals was 21.7% in Austria and 12.9% in Spain, despite efforts to avoid sampling obvious clonal copies. Some ramets within clonal groups were found more than 60 m apart at both sites. The genetic population structure of black poplar is complex in the two investigated sites, resulting from both clonal and sexual relationships among the individuals. Research highlights: A large number of SNP markers reveals novel information about within-population relationships in black poplar. We found substantial clonal reproduction, together with a high number of distinct genotypes resulting from sexual reproduction and/or migration. This structure allows natural selection to operate at two levels. We should take into consideration this complex genetic structure in conservation management to preserve the adaptive potential of the species under future climate conditions.

Key message: This dataset reports translocation experiments on 15,774 seeds from 43 populations of Abies alba Mill., Acer pseudoplatanus L., Fagus sylvatica L., Quercus petraea (Matt.) Liebl., Quercus pubescens Willd., and Quercus suber L. It informs ecological and evolutionary processes in early tree stages. Dataset access at https://doi.org/10.5281/zenodo.22043408 and metadata accessible at https://metadata-afs.nancy.inra.fr/geonetwork/srv/fre/catalog.search#/metadata/15a31f1d-6658-4264-abed-67b5664b9c12 .

European white oaks (Quercus section Quercus) are ecologically and economically important forest trees characterized by extensive shared genetic variation and a history of interspecific gene flow. Genomic resources remain uneven across species, limiting comparative analyses and pangenome development. Here, we present haplotype-resolved chromosome-scale genome assemblies and genome annotations for four European white oak species: Quercus robur, Q. petraea, Q. pubescens, and Q. frainetto. The assemblies were generated from PacBio HiFi sequencing data and include both phased haplotypes for each species. Genome sizes range from 779 to 817 Mb and all assemblies are organized into 12 chromosome-scale pseudomolecules with high completeness and contiguity. We additionally provide species-specific repeat annotations, structurally and functionally annotated protein-coding gene sets, and complete organellar genomes. The dataset includes the first reference genomes for Q. pubescens and Q. frainetto, together with newly generated assemblies for Q. robur and Q. petraea produced using a consistent sequencing and analysis workflow. These resources provide a standardized framework for comparative genomics, pangenome construction, genome evolution studies, and investigations of adaptation and introgression across European white oaks.

Genetic diversity is a critical but often overlooked component of biological diversity. The European H2020 FORGENIUS project is precisely aimed at increasing the quality and quantity of genetic data to start monitoring the European network of forest Genetic Conservation Units (GCUs). A first step in this direction was developing standardized genomic resources for 23 forest tree species, spanning from rare and scattered (e.g., Abies nebrodensis and Torminalis glaberrima ) to widespread, economically relevant ones (e.g., Fagus sylvatica, Picea abies and Pinus sylvestris ). Here, we describe the development and application of targeted genotyping tools, primarily based on Single Primer Enrichment Technology (SPET), along with existing SNP arrays for the selected species. The SPET panels developed in FORGENIUS were designed to capture □10,000 loci per species, balancing species-specific and randomly distributed regions to ensure broad genome coverage and minimize ascertainment bias. Across 7,192 genotyped trees, we identified over 1.8 million single nucleotide polymorphisms (SNPs) covering approximately 50 Mb of DNA sequence. SPET panels demonstrated high genotyping efficiency and cross-species transferability, especially within genera such as Quercus and Abies . They represent a cost-effective, flexible, and scalable solution for population-level genetic assessments across diverse taxa, enabling standardized, genome-wide characterization of the GCU network. These resources not only promote the establishment of genetic monitoring, support genetically informed conservation strategies and improve our understanding of adaptive responses in European forests, but also enhance species delimitation and hybrid detection, and enable the characterization of phylogenetically related but previously underexplored species.

Forestry industry requires high-quantity and quality seeds for afforestation and assisted migration programs. Finding reliable non-destructive methods to characterize seeds would significantly enhance efforts to identify climate-adapted populations. This study presents near-infrared (NIR) spectroscopy models to classify seed origin and predict germination characteristics at different temperatures non-destructively. We focus on Abies alba Mill., a key European forest tree with genetic variation along climatic gradients and seeds with shallow physiological dormancy. Seeds from six populations were analyzed using NIR spectroscopy, and germination was tested at 15°C, 20°C, and 25°C after stratification treatments at 4°C (0 or 3 weeks). Population classification accuracy using Partial Least Squares Discriminant Analysis was 69%, with significant NIR peaks at 1712, 1929, and 2111 nm, linked to moisture content and storage compounds. NIR spectra explained 51% and 65% of the variation in germination probability and timing using Partial Least Squares Regression, with significant peaks at 1712, 1929, 2111, 1632, and 2073 nm. General Linear Mixed-Effects Models showed that a NIR predictor contributed to 39% of the germination probability variance explained by fixed-effects, and the stratification treatment was the most important driver explaining germination time. Our results proved the utility of NIR-based tools to effectively classify bulked seeds and predict germination, opening new perspectives to nursery and forestry sectors and populations’ adaptation and adjustments to warming climate. This study will facilitate further investigations on the physiological processes that occur during dormancy, a critical process for forest regeneration given the expected impact of shorter and warmer winters on seed behavior.

Aim: Marginal tree populations, either those located at the edges of the species' range or in suboptimal environments, are often a valuable genetic resource for biological conservation. However, there is a lack of knowledge about the genetic consequences of population marginality, estimated across entire species' ranges. Our study addresses this gap by providing information about several genetic indicators and their variability in marginal and core populations identified using quantitative marginality indices.Location: Southwestern Europe and North Africa.Methods: Using 10,185 SNPs across 82 populations of maritime pine (Pinus pinaster Ait.), a widespread conifer characterised by a fragmented range, we modelled the relationship of seven genetic indicators potentially related to population evolutionary resilience, namely genetic diversity (based on both all SNPs and outlier SNPs), inbreeding, genetic differentiation, recessive genetic load and genomic offset, with population geographical, demo‐historical and ecological marginality (as estimated by nine quantitative indices). Models were constructed for both regional (introducing gene pool as a random factor) and range‐wide spatial scales.Results: We showed a trend towards decreasing overall genetic diversity and increasing differentiation with geographic marginality, supporting the centre‐periphery hypothesis (CPH). However, we found no correlation between population inbreeding and marginality, while geographically marginal populations had a lower recessive genetic load (only models without the gene pool effect). Ecologically marginal populations had a higher genomic offset, suggesting higher maladaptation to future climate, albeit some of these populations also had high genetic diversity for climate outliers.Main Conclusions: Overall genetic diversity (but not outlier‐based estimates) and differentiation patterns support the CPH. Ecologically marginal populations and those at the southern edge could be more vulnerable to climate change due to higher climate maladaptation, as predicted by genomic offsets, and/or lower potentially adaptive genetic diversity. This risk is exacerbated by typically small effective population sizes and increasing human impact in marginal populations.

Context: Habitat fragmentation is expected to erode genetic diversity, which instead needs to be preserved for promoting species adaptation to a changing climate. As this expectation has found mixed support in forest trees, consistent results on the genetic consequences of fragmentation requires adequately replicated experimental designs, as well as an explicit assessment of which landscape features, if any, could mitigate its detrimental effects. Objective: Evaluating the role of several landscape attributes in buffering the detrimental effects of fragmentation in two metapopulations of silver fir. Methods: We genotyped 904 silver fir (Abies alba Mill.) trees from 18 local populations forming two metapopulations comparable for size and extension in the Apennines, a Mediterranean mountain range. We identified the signatures left by the fragmentation process on the genetic features of silver fir local populations. After removing potentially confounding effects due to different evolutionary histories, we used a multivariate approach for testing the relative effect of demographic, geographic, environmental and topographic factors on genetic features of both metapopulations. Results: We found comparable signals of the habitat fragmentation impact on the genetic diversity and structure of both investigated metapopulations. Fragmentation effects were less pronounced in the largest local populations (but not the least isolated), located on gentler slopes with higher soil water availability and lower heat exposure. Conclusions: Our results suggest the existence of a set of demographic and environmental factors that could have coherently buffered the detrimental genetic effects of fragmentation in both metapopulations. These findings could be useful to plan landscape restoration for the evolutionary rescue of mixed forests that once characterized Mediterranean mountain ecosystems.