Biology subjects

Archambeau, J.

Publications and source records attributed to Archambeau, J..

14 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

An overexpression platform reveals the functional diversity of human KRAB-Zinc Finger Proteins in maintaining cellular homeostasis

Kruppel associated box zinc finger proteins (KZFPs) form the largest family of transcriptional regulators in mammals, yet most remain uncharacterized. Here we established a scalable framework to probe KZFP function. An arrayed inducible overexpression screen of 366 human KZFPs in K562 cells identified factors that alter cellular proliferation, enabling functional prioritization. Integrative transcriptomic, chromatin and proteomic analyses revealed diverse mechanisms, including transposable element-linked repression (ZNF43), promoter proximal regulation (ZNF257), and SCAN domain dependent transcriptional activation (ZNF498/ZSCAN25 and ZNF18). These results highlight the functional diversity of KZFPs and provide a strategy for their annotation.

genetics↗

bioRxiv2026

Demographic history shapes forest tree vulnerability to climate change

Demographic history is expected to play a central role in shaping population vulnerability to climate change through its lasting effects on effective population sizes and genetic connectivity. However, existing studies report contrasting outcomes, and the consequences of alternative demographic histories have seldom been assessed concurrently across multiple taxa. Here, we analysed population genomic data from six of the major European forest tree species to address this gap. Across species, genetic isolation reduced adaptive potential, as reflected in lower standing genetic diversity. Greater genetic differentiation was also associated with increased maladaptation to climate, whereas the purge or accumulation of deleterious mutations depended on the severity of past demographic events. Finally, the beneficial effects of gene flow were evidenced across the six species by more optimal climate adaptation in highly connected populations. Altogether, our results provide valuable insights into how genetic differentiation, reflecting the combined effects of genetic drift and limited historical gene flow, influences current vulnerability of forest tree populations to climate change.

evolutionary biology↗

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

The genetic consequences of population marginality: a case study in maritime pine

AimMarginal 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 populations 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. LocationSouthwestern Europe and North Africa. MethodsUsing 10,185 SNPs across 82 populations of maritime pine (Pinus pinaster Ait.), a widespread and economically important 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 all SNPs and two kind of outlier loci), 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 random factor) and range-wide spatial scales. ResultsWe showed a trend towards decreasing overall genetic diversity (albeit not necessarily for genetic diversity estimates based on outlier loci) and increasing differentiation with geographic marginality, supporting the centre-periphery hypothesis (CPH). Moreover, 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) and ecologically marginal populations had a higher genomic offset, suggesting higher maladaptation to future climate. Main conclusionsOverall, our results indicate that marginal populations could be at higher risk of maladaptation to climate change than core populations, despite reduced levels of genetic load, a risk that is exacerbated by typically small effective population sizes and increasing human impact.

genetics↗

bioRxiv2023

Characterizing the microbial metagenome of calcareous stromatolite formations in the San Felipe Creek in Anza Borrego Desert

Here we describe the metagenome composition, community functional annotation, and diversity of prokaryotic microbial species derived from calcareous stromatolite formations discovered in the dry stream bed of the open-canopy, ephemeral San Felipe Creek in the Anza Borrego Desert. In this environment, resident microbes must be able to adapt to the harsh conditions of extreme heat, high UV light, desiccation and fluctuating solubilization/precipitation and hydration/evaporation. Metagenomic analysis revealed a community capable of carrying out complete nitrogen fixation and assimilatory nitrate reduction, forming biofilms and quorum sensing, and potentially forming thick-walled akinetes as desiccation-resistant stages. Nitrogen cycling is likely to play a fundamental role in mediating both the structure of the stromatolite microbial community and the mineral precipitation/dissolution. The viruses present in the stromatolites, particularly Nodularia and Mycobacterium phages are also likely to impact community population dynamics and activity. Stromatolite community members possess different morphological and physiological strategies to cope with desiccation stress. Metagenomic signatures were found for scytonemin, carotenoids, synthesis of potential microsporine-like amino acids; genes involved in microalgal desiccation tolerance, including those encoding aquaporins, chaperones, antioxidants; and enzymes responsible for the synthesis of trehalose, sucrose, and polyamines. The stromatolite ecosystem provides a diverse array of microniches where different functional guilds can develop complex metabolite exchange with the substrate supporting their life in extreme conditions. Metagenome analyses revealed several genes that might enable a specialized and unique group of endolithic cyanobacteria including Chroococcidiopsis, Hyella, Myxosarcina, and Pleurocapsa to derive metals and important nutrients from rocks, being potentially destructive for the calcareous formations. Our study revealed environmental adaptations of freshwater microbial communities in desert stream stromatolites which may provide valuable insights into Precambrian paleoenvironments, which are little known.

genomics↗

bioRxiv2021

Extreme climatic events but not environmental heterogeneity shape within-population genetic variation in maritime pine

How evolutionary forces interact to maintain quantitative genetic variation within populations has been a matter of extensive theoretical debates. While mutation and migration increase genetic variation, natural selection and genetic drift are expected to deplete it. To date, levels of genetic variation observed in natural populations are hard to predict without accounting for other processes, such as balancing selection in heterogeneous environments. We aimed to empirically test three hypotheses: (i) admixed populations have higher quantitative genetic variation due to introgression from other gene pools, (ii) quantitative genetic variation is lower in populations from harsher environments (i.e. experiencing stronger selection), and (iii) quantitative genetic variation is higher in populations from spatially heterogeneous environments. We used phenotypic measurements of five growth, phenological and functional traits from three clonal common gardens, consisting of 523 clones from 33 populations of maritime pine (Pinus pinaster Aiton). Populations from harsher climates (mainly colder areas) showed lower genetic variation for height in the three common gardens. Surprisingly, we did not find any association between within-population genetic variation and environmental heterogeneity or population admixture for any trait. Our results suggest a predominant role of natural selection in driving within-population genetic variation, and therefore indirectly their adaptive potential.

evolutionary biology↗

bioRxiv2020

Combining climatic and genomic data improves range-wide tree height growth prediction in a forest tree

Population response functions based on climatic and phenotypic data from common gardens have long been the gold standard for predicting quantitative trait variation in new environments. However, prediction accuracy might be enhanced by incorporating genomic information that captures the neutral and adaptive processes behind intra-population genetic variation. We used five clonal common gardens containing 34 provenances (523 genotypes) of maritime pine (Pinus pinaster Aiton) to determine whether models combining climatic and genomic data capture the underlying drivers of height-growth variation, and thus improve predictions at large geographical scales. The plastic component explained most of the height-growth variation, probably resulting from population responses to multiple environmental factors. The genetic component stemmed mainly from climate adaptation, and the distinct demographic and selective histories of the different maritime pine gene pools. Models combining climate-of-origin and gene pool of the provenances, and positive-effect height-associated alleles (PEAs) captured most of the genetic component of height-growth and better predicted new provenances compared to the climate-based population response functions. Regionally-selected PEAs were better predictors than globally-selected PEAs, showing high predictive ability in some environments, even when included alone in the models. These results are therefore promising for the future use of genome-based prediction of quantitative traits.

genetics↗

bioRxiv2020

Occurrence but not intensity of mortality rises towards the climatic trailing edge of tree species ranges in European forests.

AimTree mortality is increasing worldwide, leading to changes in forest composition and altering global biodiversity. Yet, due to the multi-faceted stochastic nature of tree mortality, large-scale spatial patterns of mortality across species ranges and their underlying drivers remain difficult to understand. Our main goal is to describe the geographical patterns and drivers of the occurrence and intensity of tree mortality in Europe. We hypothesize that the occurrence of mortality represents background mortality and is higher in the margin than the core populations, whereas the intensity of mortality could have a more even distribution according to the spatial and temporal stochasticity of die-off events. LocationEurope (Spain, France, Germany, Belgium, Sweden and Finland) Time period1981 to 2014. Major taxa studiedMore than 1.5 million trees belonging to 20 major forest tree species MethodsWe develop hurdle models to tease apart the occurrence and intensity of tree mortality in National Forest Inventory plots at range-wide scale. The occurrence of mortality indicates that at least one tree has died in the plot and the intensity of mortality refers to the number of trees dead per plot. ResultsThe highest mortality occurrence was found in peripheral regions and the climatic trailing edge linked with drought, whereas the intensity of mortality was driven by competition, drought and high temperatures and was uniformly scattered across species ranges. Main conclusionsOur findings provide a new perspective in our understanding of tree mortality across species ranges. We show that tree background mortality but not die-off is generally higher in the trailing edge populations, but whether other demographic traits such as growth, reproduction and regeneration would also decrease at the trailing edge of European tree populations needs to be explored.

ecology↗

bioRxiv2019

Similar patterns of background mortality across Europe are mostly driven by drought in European beech and a combination of drought and competition in Scots pine.

AimBackground tree mortality is a complex demographic process that affects forest structure and long-term dynamics. We aimed to test how drought intensity interacts with interspecific and intraspecific competition (or facilitation) in shaping individual mortality patterns across tree species ranges. LocationEuropean latitudinal gradient (Spain to Finland). Time period1985 - 2014. Major taxa studiedScots pine (Pinus sylvestris L.) and European beech (Fagus sylvatica L.). MethodsWe performed logistic regression models based on individual tree mortality recorded in five European National Forest Inventories. We computed the relative importance of climatic drought intensity, basal area of conspecific and heterospecific trees (proxy of indirect intra- and interspecific competition or facilitation) and the effects of their interactions on mortality along the latitudinal gradient of both species range. ResultsIncrease in drought intensity over the study period was associated with higher mortality rates in both species. Drought was the most important driver of beech mortality at almost all latitudes while Scots pine mortality was mainly driven by basal area. High conspecific basal area was associated with high mortality rates in both species while high heterospecific basal area was correlated with mortality rates that were high in Scots pine but low in beech. Main conclusionsBeech mortality was directly affected by drought while Scots pine mortality was indirectly affected by drought through interactions with basal area. Despite their different sensitivity to drought and basal area, the highest predicted mortality rates for both species were at the ecotone between Mediterranean and cool temperate biomes, which can be explained by the combined effect of drought and competition. In the context of global warming, which is expected to be particularly strong in the Mediterranean biome, our results suggest that populations at the southern limit of species ranges may experience increased mortality rates in the near future. BIOSKETCHThe authors research is focused on functional trait ecology and global change, with special attention to mortality and demography processes. The authors use modelling multidisciplinary approaches to understand complex processes in ecology on a large geographical scale.

ecology↗

bioRxiv2019

IRE1-UBE2D3 signaling controls the recruitment of myeloid cells to glioblastoma.

Tumor cells are exposed to intrinsic and environmental challenges that trigger endoplasmic reticulum (ER) homeostasis alteration, in turn leading to ER stress. To cope with this, tumor cells engage an adaptive signaling pathway, the unfolded protein response (UPR) thus promoting the acquisition of malignant features. As such, glioblastoma multiforme (GBM), the most aggressive primary brain tumors, exhibit constitutive UPR signals to sustain growth. Herein, we showed that signaling elicited by one of the UPR sensors, IRE1, promotes GBM tumor invasion, angiogenesis and infiltration by macrophages. Hence, high IRE1 activity in tumors predicts worse outcome. We further dissect IRE1-dependent mechanisms that shape the brain tumor immune microenvironment towards myeloid cells. We identify an IRE1-dependent signaling pathway that directly controls the expression/release of proinflammatory chemokines (CXCL2, IL6, IL8) leading to tumor cell-mediated chemoattraction of neutrophils and macrophages. This pathway requires XBP1 non-conventional mRNA splicing and XBP1s-dependent expression of the E2 ubiquitin enzyme UBE2D3. The latter contributes to the degradation of the NF{kappa}B inhibitor I{kappa}B, leading to the up-regulation of proinflammatory chemokines. Our work identifies a novel IRE1/UBE2D3 proinflammatory signaling axis instrumental to pro-tumoral immune regulation of GBM.

cancer biology↗

bioRxiv2018

Evolutionary inference from QST-FST comparisons: disentangling local adaptation from altitudinal gradient selection in snapdragon plants

Phenotypic differentiation among natural populations can be explained by natural selection or by neutral processes such as drift. There are many examples in the literature where comparing the effects of these processes on multiple populations has allowed the detection of local adaptation. However, these studies rarely identify the agents of selection. Whether population adaptive divergence is caused by local features of the environment, or by the environmental demand emerging at a more global scale, for example along altitudinal gradients, is a question that remains poorly investigated. Here, we measured neutral genetic (FST) and quantitative genetic (QST) differentiation among 13 populations of snapdragon plants (Antirrhinum majus) in a common garden experiment. We found low but significant genetic differentiation at putatively neutral markers, which supports the hypothesis of either ongoing pervasive homogenisation via gene flow between diverged populations or reproductive isolation between disconnected populations. Our results also support the hypothesis of local adaptation involving phenological, morphological, reproductive and functional traits. They also showed that phenotypic differentiation increased with altitude for traits reflecting the reproduction and the phenology of plants, thereby confirming the role of such traits in their adaptation to environmental differences associated with altitude. Our approach allowed us to identify candidate traits for the adaptation to climate change in snapdragon plants. Our findings imply that environmental conditions changing with altitude, such as the climatic envelope, influenced the adaptation of multiple populations of snapdragon plants on the top of their adaptation to local environmental features. They also have implications for the study of adaptive evolution in structured populations because they highlight the need to disentangle the adaptation of plant populations to climate envelopes and altitude from the confounding effects of selective pressures acting specifically at the local scale of a population.

evolutionary biology↗

bioRxiv2018

Genotype by environment interactions for the shade avoidance syndrome in the plant Antirrhinum majus, the snapdragon

A classical example of phenotypic plasticity in plants is the set of trait changes in response to shade, i.e. the shade avoidance syndrome. There is widespread evidence that plants in low light conditions often avoid shade by growing taller or by increasing their photosynthetic efficiency. This plastic response is expected to have evolved in response to selection in several species, yet there is limited evidence for its genetic variation within populations, which is required for any evolutionary response to selection. In this study, we investigated the shade avoidance syndrome in snapdragon plants (Antirrhinum majus) by using a common garden approach on four natural populations from the Mediterranean region. Our results showed that, in the four populations, individual plants reacted strongly to the presence of shade by growing longer shoots, longer internodes, and increasing their specific leaf area. Our results also revealed genetic variation for the plastic response within these populations, as well as few genetic constraints to its evolution. Our findings imply that the plastic response to shade has the potential to evolve in response to selection in natural populations of A. majus.

evolutionary biology↗