Biology subjects

Bagnoli, F.

Publications and source records attributed to Bagnoli, F..

12 recordsLinked to original sources

bioRxiv2026

Rapid evolutionary responses to climate change in maritime pine (Pinus pinaster Ait.) despite widespread adaptive lag

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.

genomics↗

bioRxiv2026

Haplotype-resolved chromosome-level genome assembly of four European white oak species

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.

genomics↗

bioRxiv2026

Development of the 4TREE SNP array, a forest multispecies array to enhance European Breeding and conservation programs in pine, poplar and ash.

Within the framework of the European Adaptive BREEDING for Better FORESTs project (B4EST, https://b4est.eu/), we have developed genotyping tools for Poplar, Ash, and Pine forest tree species. SNP arrays are attractive genotyping tools because of the user-friendly genotype calling system and the robust transferability among laboratories. Here we describe the development of an Axiom SNP array for Pinus pinaster (13,407 SNPs), Pinus pinea (5,671 SNPs), Poplar spp. (13,408 SNPs), and Fraxinus spp. (13,407 SNPs) based on a two-step process. We first assembled a high-density (>100,000 SNPs/species) screening array that served to test a large panel of candidate SNPs on a diversity panel involving at least 120 individual trees per species or species group. In the second step, we selected and combined the most informative SNPs to build the final 50,000 SNP 4TREE array. This approach resulted in high genotyping success rates, including for species lacking previously validated high-quality SNP resources. The 4TREE SNP array provides a valuable and transferable genomic tool to support genomic prediction, breeding, and adaptive management of forest tree species.

genomics↗

bioRxiv2025

Evaluation of Klebsiella pneumoniae antigen MrkA reveals expression-limited therapeutic potential

Klebsiella pneumoniae (KP) poses a major global health concern, particularly as hospital-acquired strains become increasingly antibiotic resistant. MrkA, the major type 3 fimbrial (T3F) subunit, is a recognised prospective vaccine and monoclonal antibody (mAb) target. We assessed T3F structural (mrkABCDF) and regulatory (mrkHIJ) gene prevalence and allelic variation across 1649 KP genomes, using 100 diverse isolates for detailed phenotypic characterisation. Despite high conservation MrkA expression itself is variable with genotype failing to predict phenotype. We constructed isogenic KP T3F mutants with absent and supraphysiological MrkA expression to investigate functional consequences and therapeutic responses during infection. In a severe pneumonia model blood dissemination inversely correlated with T3F expression. In vivo antigen profiling revealed only [~]20% of wild-type lung bacteria express MrkA, dropping to [~]5% in blood, with low MrkA expression defining bacteraemic KP irrespective of infection route. Critically, anti-MrkA mAb efficacy was contingent on antigen abundance, with therapeutic benefit restricted to supraphysiological MrkA expression. These findings reveal substantial in vivo MrkA expression variability with critical onward implications for vaccine and mAb development.

microbiology↗

bioRxiv2025

The FORGENIUS genomic resources: new genotyping tools and genomic data for 23 forest tree species and their Genetic Conservation Units

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 {square}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.

genomics↗

bioRxiv2025

Genomic signatures of climate-driven (mal)adaptation in an iconic conifer, the English yew (Taxus baccata L.)

The risk of climate maladaptation is increasing for numerous species, including trees. Developing robust methods to assess population maladaptation remains a critical challenge. Genomic offset approaches aim to predict climate maladaptation by characterising the genomic changes required for populations to maintain their fitness under changing climates. In this study, we assessed the risk of climate maladaptation in European populations of English yew (Taxus baccata), a long-lived tree with a patchy distribution across Europe, the Atlas Mountains, and the Near East, where many populations are small or threatened. We found evidence suggesting local climate adaptation by analysing 8,616 SNPs in 475 trees from 29 European T. baccata populations, with climate explaining 18.1% of genetic variance and 100 unlinked climate-associated loci identified via genotype- environment association (GEA). Then, we evaluated the deviation of populations from the overall gene-climate association to assess variability in local adaptation or different adaptation trajectories across populations and found the highest deviations in low latitude populations. Moreover, we predicted genomic offsets and successfully validated these predictions using fitness proxies assessed in plants from 26 populations grown in a comparative experiment. Finally, we integrated information from current local adaptation, genomic offset, historical genetic differentiation and effective migration rates to show that Mediterranean and high-elevation T. baccata populations face higher vulnerability to climate change than low-elevation Atlantic and continental populations. Our study demonstrates the practical use of the genomic offset framework in conservation genetics, offers insights for its further development, and highlights the need for a population-centred approach that incorporates additional statistics and data sources to credibly assess climate vulnerability in wild plant populations.

genomics↗

bioRxiv2024

Evaluating genomic offset predictions in a forest tree with high population genetic structure

Predicting how tree populations will respond to climate change is an urgent societal concern. An increasingly popular way to make such predictions is the genomic offset (GO) approach, which aims to use genomic and climate data to identify populations that may experience climate maladaptation in the near future. More precisely, GO tries to represent the change in allele frequencies required to maintain the current gene-climate relationships under climate change. However, the GO approach has major limitations and, despite promising validation of its predictions using height data from common gardens, it still lacks broad empirical testing. In the present study, we evaluated the consistency and empirical validity of GO predictions in maritime pine (Pinus pinaster Ait.), a tree species from southwestern Europe and North Africa with a marked population genetic structure. First, gene-climate relationships were estimated using 9,817 SNPs genotyped in 454 trees from 34 populations; and candidate SNPs potentially involved in climate adaptation were identified. Second, GO was predicted using four methods, namely Gradient Forest (GF), Redundancy Analysis (RDA), latent factor mixed model (LFMM) and Generalised Dissimilarity Modeling (GDM), two sets of SNPs (candidate and control SNPs) and five climate general circulation models (GCMs) to account for uncertainty in future climate predictions. Last, the empirical validity of GO predictions was evaluated within a Bayesian framework by estimating the associations between GO predictions and two independent data sources: mortality data from National Forest Inventories (NFI), and mortality and height data from five common gardens in contrasting environments. We found high variability in GO predictions across methods, SNP sets and GCMs. Regarding validation, GO predictions with GDM and GF (and to a lesser extent RDA) based on the candidate SNPs showed the strongest and most consistent associations with mortality rates in common gardens and NFI plots. We found almost no association between GO predictions and tree height in common gardens, most likely due to the overwhelming effect of population genetic structure on tree height in this species. Our study demonstrates the imperative to validate GO predictions with a range of independent data sources before they can be used as informative and reliable metrics in conservation or management strategies.

evolutionary biology↗

bioRxiv2023

Spatial conservation prioritisation for intraspecific genetic diversity of three forest tree species with a fragmented distribution in Italy

The Kunming-Montreal Global Biodiversity Framework recognised the urgency of taking action to conserve intraspecific genetic diversity (IGD) as an insurance against habitat degradation and environmental change. Recent work suggests that 90-99% of IGD should be conserved to safeguard viability of future generations. Here, we addressed such a conservation issue in three forest tree species in Italy: silver fir (Abies alba Mill.), Heldreichs pine (Pinus heldreichii H. Christ), and pedunculate oak (Quercus robur L.). We used microsatellite markers to measure IGD of 36 (A. alba), 15 (P. heldreichii) and 25 (Q. robur) natural sites, including several putative glacial refugia. We developed a spatial conservation planning (SCP) analysis to quantify the genetic irreplaceability of each site and identify the minimum set coverage ensuring IGD protection. Finally, we compared SCP results with the contributions to allelic diversity within and between sites, total allelic diversity and private allelic richness. We found that between 44% and 73% of sites were required to conserve 90-99% of the alleles, and that this conservation effort held even when targeting lower percentages of alleles to protect (50-75%). Glacial refugia were often included in the minimum set coverage, confirming theoretical and biogeographical expectations. Finally, sites with high genetic irreplaceability were found to have higher private allelic richness on average. These results are discussed in the light of the biogeographic history of the species studied and the current policies for the conservation of forest genetic resources.

evolutionary biology↗

bioRxiv2023

The latitudinal trend in genetic diversity and distinctiveness of Quercus robur rear edge forest remnants calls for new conservation priorities

Knowledge of the spatial distribution of intraspecific genetic variation is essential for planning conservation actions, designing networks of protected areas, and informing possible assisted migration strategies. Although the Italian peninsula harbours unique genetic variation as a legacy of Quaternary migrations, only sporadic genetic information is available for forest tree species. Here, we present the first geographically comprehensive genetic characterisation of Quercus robur, an iconic broadleaved species of European floodplain forests, in an area which acted as a primary glacial refugium for the species. 745 individuals from 25 populations were sampled and genotyped with 16 microsatellite markers. Their genetic structure was assessed through various metrics of diversity and distinctiveness, as well as by Bayesian clustering and multivariate methods. The demographic history of inferred gene pools was evaluated through Approximate Bayesian Computation analysis. Genetic distinctiveness showed a decline with increasing latitude, while allelic richness reached its peak in central Italy. A south-to-north trend in the complexity of the genetic structure was observed, with peninsular Italy being characterised by intermingled gene pools in contrast to the relative homogeneity exhibited by northern populations. Demographic inference indicated that the southern gene pool has been genetically isolated since the penultimate interglacial, whereas populations from central Italy persisted locally in a mosaic of small refugia during the last glaciation. Our results brought out the complexity of the genetic structure of forest trees populations in southern Europe. At least three Q. robur refugia contributed to the genetic layout of extant populations after the last glacial period, but refugial areas were probably even more numerous in central Italy. Such a detailed characterization sheds new light on the priorities to be established for the conservation of highly fragmented Q. robur populations in an area rich in diversified genetic lineages.

genetics↗

bioRxiv2023

Synchronous effective population size changes and genetic stability of forest trees through glacial cycles

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 performed comparative population genomic analyses and demographic inferences for seven widely distributed and ecologically contrasted European forest tree species based on concerted sampling of 164 populations across their natural ranges. For all seven species, the effective population size, Ne, increased or remained stable over many glacial cycles and up to 15 million years in the most extreme cases. Hence, 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 Ne 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 were able to retain their evolutionary potential over very long periods of time despite strong environmental changes. One-Sentence SummaryPopulation genomic analyses reveal that forest trees retained their evolutionary potential over the Quaternary.

evolutionary biology↗

bioRxiv2021

Genetic signatures of divergent selection in European beech (Fagus sylvatica L.) are associated with the variation in temperature and precipitation across its distribution range

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.

evolutionary biology↗

bioRxiv2020

Staphylococcal protein A inhibits complement activation by interfering with IgG hexamer formation

IgG molecules are essential players in the human immune response against bacterial infections. An important effector of IgG-dependent immunity is the induction of complement activation, a reaction that triggers a variety of responses that help to kill bacteria. Antibody-dependent complement activation is promoted by the organization of target-bound IgGs into hexamers that are held together via noncovalent Fc-Fc interactions. Here we show that Staphylococcal protein A (SpA), an important virulence factor and vaccine candidate of Staphylococcus aureus, effectively blocks IgG hexamerization and subsequent complement activation. Using native mass spectrometry and high-speed atomic force microscopy, we demonstrate that SpA blocks IgG hexamerization through competitive binding to the Fc-Fc interaction interface on IgG monomers. In concordance, we show that SpA interferes with the formation of (IgG)6:C1q complexes and prevents downstream complement activation on the surface of S. aureus. Lastly, we demonstrate that IgG3 antibodies against S. aureus can potently induce complement activation even in the presence of SpA. Altogether, this study identifies SpA as an immune evasion protein that specifically blocks IgG hexamerization.

microbiology↗