Biology subjects

Fady, B.

Publications and source records attributed to Fady, B..

12 recordsLinked to original sources

bioRxiv2026

Multiscale intraspecific variation and coordination of hydraulic traits in silver fir

O_LIIntraspecific variability in hydraulic and morphological traits may alter projections of forest vulnerability to climate change. Recognizing multiscale nature is essential, as trait relationships within populations may not reflect those across the species range. C_LIO_LIWe assessed variability in 11 traits in 10 natural populations of Abies alba across environmental and phylogeographic gradients to evaluate potential impacts on drought vulnerability. We quantified trait variation within and among populations, tested effects of climate, phylogeny and local factors, and evaluated trait coordination across scales. C_LIO_LIHydraulic safety traits and wood density showed low variability, indicating strong constraints. In contrast, water-use and efficiency traits were highly variable. Aridity influenced several traits, but reduced variance was detected only for leaf residual conductance and succulence consisted with stabilising selection. Trait coordination was weak within populations than among populations. C_LIO_LIOverall, A. alba combines constrained hydraulic safety traits with variable water use traits. This may buffer drought impacts but limits shifts in hydraulic safety margins, potentially increasing risks of hydraulic failure, especially in humid environments where populations lack the capacity to tolerate prolonged dry periods. Thus, our findings highlight the need to account for scale-dependent trait variability, coordination, and their underlying drivers when predicting species adaptive capacity to drought. C_LI

plant biology↗

bioRxiv2025

Near-infrared spectroscopy-based models correctly classify Abies alba seed origin and predict germination properties

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{degrees}C, 20{degrees}C, and 25{degrees}C after stratification treatments at 4{degrees}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.

ecology↗

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

PDG-Arena: An ecophysiological model for characterizing tree-tree interactions in heterogeneous stands

In the context of the ongoing climate and biodiversity crises, mixed forest stands are increasingly considered as a sustainable management alternative to monocultures. We developed a new individual-based and process-based forest growth model, PDG-Arena, to simulate mixed forest functioning and test ecophysiological interactions among trees in mixed stands. The model builds upon the validated ecophysiological stand-scale model CASTANEA and integrates tree competition for light and water. We evaluated the performance of PDG-Arena by comparing the simulated growth with annual dendrochronological growth data from 37 common beech and silver fir monospecific and mixed plots in the French Alps. PDG-Arena showed a slightly better performance than CASTANEA when simulating even-age and monospecific forests (r2 of 32.1 versus 29.5%). When using structure-diverse and species-diverse inventories, PDG-Arena performed better than CASTANEA in pure beech (38.3 versus 22.9%) and mixed stands (40.5 versus 36.3%), but not in pure fir stands (39.8 versus 42.0%). The new model also showed a significant positive effect of species mixing on gross primary production (+5.5%), canopy absorbance (+11.1%) and transpiration (+15.8%). Our results thus show that tree-level process-based models such as PDG-Arena, formally simulating interspecific interactions, can serve as a valuable tool to understand and simulate the carbon, light and water dynamics of mixed stands.

ecology↗

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

Fine-scale spatial genetic structure across the species range reflects recent colonization of high elevation habitats in silver fir (Abies alba Mill.)

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, 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 FGSG across populations. These results may 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 complementary information about demographic history and could be used for defining conservation priorities.

evolutionary biology↗

bioRxiv2019

Patterns of phenotypic plasticity among populations of three Mediterranean pine species and implications for evolutionary responses to climate change

AimUnder rapid environmental change, phenotypic plasticity, if adaptive, could increase the odds for organisms to persist. Environmental variation over time is an important source of phenotypic plasticity. Likewise, phenotypic plasticity can vary with age in many organisms. However, little is known on phenotypic plasticity variation across species ranges. Our aims are: (i) to assess whether populations phenotypic plasticity is related to the inter-annual climate variation under which populations have evolved during the last century; (ii) to compare phenotypic plasticity among developmental classes; and (iii) to predict phenotypic plasticity across species ranges.\n\nLocationEurope and North-Africa.\n\nTime period1901-2014.\n\nMajor taxa studiedPinus nigra, P. pinaster and P. pinea.\n\nMethodsWe used 372 646 individual tree height measurements at three developmental classes from a wide network of 38 common gardens in Europe and North Africa with provenances covering the distribution range of the species. With this data, we: i) build linear mixed-effect models of tree height as a function of tree age, population and climate; ii) estimate populations reaction norms from the fitted models; iii) calculate populations phenotypic plasticity indexes; iv) build models of populations phenotypic plasticity indexes as a function of inter-annual climate variation during the last century.\n\nResultsWe found that i) most populations that have evolved under high inter-annual climate variation, in either maximum or minimum values in temperature or precipitation, exhibited high values of plasticity in tree height; ii) phenotypic plasticity for tree height was higher in young trees than in older ones, iii) phenotypic plasticity did not follow any particular geographical pattern across species ranges.\n\nMain conclusionsPhenotypic plasticity across the three Mediterranean pines ranges is related with the climate variation experienced over time and calls into question whether this plasticity could be adaptive and hence beneficial to cope with climate change in the short-term.

ecology↗

bioRxiv2019

Adaptation to drought is coupled with slow growth in marginal silver fir (Abies alba Mill.) populations

Drought is increasingly considered as the most important selection pressure for forest trees in the context of climate change. We studied adaptation to drought in marginal populations of silver fir (Abies alba Mill.) from the French Mediterranean Alps. Drought tolerance was assessed using proxies both from seedlings and adult trees. We measured water stress response, growth and bud break of seedlings originating from 16 populations in a greenhouse common garden experiment (N=8199) and water use efficiency via{delta} 13C of adult trees of the source populations in-situ (N=315). Further, 357 single nucleotide polymorphisms (SNPs) were used to uncover the demographic history of the populations. Demographic distances between populations were used to generate a null expectation for trait divergence, thereby detect the signature of natural selection. We found evidence for adaptive population divergence in drought tolerance across life stages. Seedlings originating from source populations with low soil water capacity resisted better to water stress in the greenhouse, and additionally, adult trees from these populations had a higher water use efficiency. Seedling growth showed an evolutionary trade-off with drought tolerance: seedlings with fast growth and high stature came from populations that had lower drought tolerance. In contrast, population divergence in bud break showed only a weak signal of adaptation, which was independent of that in drought tolerance. Variation in phenology between populations was associated with variance in temperature and drought frequency and severity at the source populations. Our results highlight the adaptive value of marginal populations, advance our understanding of the different processes that have allowed silver fir to cope with drought stress under a warming climate, and contribute to our knowledge to advise assisted migration programs.

evolutionary biology↗

bioRxiv2019

The genetic structure of the European black pine (Pinus nigra Arnold) is shaped by its recent Holocene demographic history.

Fragmentation acting over geological times confers wide, biogeographical scale, genetic diversity patterns to species, through demographic and natural selection processes. To test the effects of historical fragmentation on the genetic diversity and differentiation of a major European forest tree and to resolve its demographic history, we describe and model its spatial genetic structure and gene genealogy. We then test which Pleistocene event, whether recent or ancient, could explain its widespread but patchy geographic distribution using population genetic data, environmental data and realistic demographic timed scenarios. The taxon of interest is a conifer forest tree, Pinus nigra (Arnold), the European black pine, whose populations are located in the mountains of southern Europe and North Africa, most frequently at mid-elevation. We used a set of different genetic markers, both neutral and potentially adaptive, and either bi-parentally or paternally inherited, and we sampled natural populations across the entire range of the species. We analysed the data using frequentist population genetic methods as well as Bayesian inference methods to calibrate realistic, demographic timed scenarios. Species with geographically fragmented distribution areas are expected to display strong among-population genetic differentiation and low within-population genetic diversity. Contrary to these expectations, we show that the current diversity of Pinus nigra and its weak genetic spatial structure are best explained as resulting from late Pleistocene or early Holocene fragmentation of one ancestral population into seven genetic lineages, which we found to be the main biogeographical contributors of the natural black pine forests of today. Gene flow among the different lineages is strong across forests and many current populations are admixed between lineages. We propose to modify the currently accepted international nomenclature made of five subspecies and name these seven lineages using regionally accepted subspecies-level names. HighlightsO_LIThe European black pine, Pinus nigra (Arnold), has a weak spatial genetic structure. C_LIO_LIGene flow among populations is frequent and populations are often of admixed origin. Current genealogies result from recent, late Pleistocene or Holocene events. C_LIO_LISeven modern genetic lineages emerged from divergence and demographic contractions. C_LIO_LIThese seven lineages warrant a revision of subspecies taxonomic nomenclature. C_LI

ecology↗

bioRxiv2019

Inferring phenotypic plasticity and local adaptation to climate across tree species ranges using forest inventory data

AimTo test whether adaptive and plastic trait responses to climate across species distribution ranges can be untangled using field observations, under the rationale that, in natural forest tree populations, long-term climate shapes local adaptation while recent climate change drives phenotypic plasticity. LocationEurope. Time period1901-2014. TaxaSilver fir (Abies alba Mill.) and sessile oak (Quercus petraea (Matt.) Liebl.). MethodsWe estimated the variation of individual tree height as a function of long-term and short-term climates to tease apart local adaptation, plasticity and their interaction, using mixed-effect models calibrated with National Forest Inventory data (in-situ models). To validate our approach, we tested the ability of in-situ models to predict independently tree height observations in common gardens where local adaptation to climate of populations and their plasticity can be measured and separated. In-situ model predictions of tree height variation among provenances (populations of different geographical origin) and among planting sites were compared to observations in common gardens and to predictions from a similar model calibrated using common garden data (ex-situ model). ResultsIn Q. petraea, we found high correlations between in-situ and ex-situ model predictions of provenance and plasticity effects and their interaction on tree height (r > 0.80). We showed that the in-situ models significantly predicted tree height variation among provenances and sites for Abies alba and Quercus petraea. Spatial predictions of phenotypic plasticity across species distribution ranges indicate decreasing tree height in populations of warmer climates in response to recent anthropogenic climate warming. Main conclusionsOur modelling approach using National Forest Inventory observations provides a new perspective for understanding patterns of intraspecific trait variation across species ranges. Its application is particularly interesting for species for which common garden experiments do not exist or do not cover the entire climatic range of the species.

ecology↗

bioRxiv2018

Distribution maps of twenty-four Mediterranean and European ecologically and economically important forest tree species compiled from historical data collections

Background Background Methods Access to data and... Technical validation Reuse potential and limits Contribution of the co-authors Funding References Information on species geographic distribution is a strategic scientific resource for many research, innovation and development purposes, such as: biodiversity assessment, habitat and species management, restoration and conservation as well as for predicting the effects of global environmental change on ecosystems, species and populations and their genetic resources (Fady et al. 2016; Franklin 2009; Noce et al. 2016; Sinclair et al. 2010).\n\nMaps are one of the ways information on geographic distribution can best be summarized and used ( ...

ecology↗

bioRxiv2017

Linking Dendroecology And Association Genetics: Stress Responses Archived In Tree Rings Associate With SNP Genotypes In Abies alba (Mill.)

O_LIGenetic association studies in forest tress would greatly benefit from information on tree response to environmental stressors over time. Dendroecology can close this gap by providing such time series measurements. Here, we jointly analyzed dendroecological and genetic data to explore the genetic basis of resistance, recovery and resilience to episodic stress in silver fir.\nC_LIO_LIWe used individual level tree-ring data to characterize the growth patterns of surviving silver fir (Abies alba) during the forest dieback in the 1970s and 1980s in Central Europe and associated them with SNPs in candidate genes.\nC_LIO_LIMost trees at our study sites in the Bavarian Forest experienced severe growth decline from 1974 until the mid-1980s, which peaked during the drought year of 1976. Using the machine learning algorithm random forest, we identified 15 candidate genes that were associated with the variance in resistance, resilience and recovery among trees in this period.\nC_LIO_LIWith our study we show that the unique possibility of phenotypic time series archived in tree-rings are a powerful resource in genetic association studies. We call for a closer collaboration of dendroceologists and forest geneticists to focus on integrating individual tree level signals in genetic association studies in long lived trees.\nC_LI

ecology↗