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SummaryClimate change alters relationships among environmental conditions and thus has the potential to change the selection pressures acting on adaptive gene variants. Using a landscape genomic approach, we show that the southern beech speciesNothofagus pumiliohas notable genetic adaptations to climate along its 2000-kilometer-long range in the Andes. We screened 47,336 SNP loci in 1,632 contigs and found that high-latitude sampling sites have lower genetic diversity, likely due to greater impact of glacial oscillations at high latitudes. Using four genome scan methods, we identified 457 outlier SNPs that are either strongly differentiated among subpopulations or associated with environmental covariates related to temperature, day length, and precipitation. Temperature and day length parameters were associated with notably more outliers than precipitation (n = 133, 113, and 61 outliers, respectively), and almost half of all annotated outliers were related to stress response (n=38, 21%) or catabolism-metabolism (n=43, 24%). Our findings suggest thatNothofagus pumiliois an ideal Andean model of genetic adaptation to climate change because it is locally adapted to extant climate conditions, and shifting patterns among environmental parameters may be detrimental to its future survival and adaptation potential.

When environmental conditions differ both within and among populations, multiscale adaptation results from processes at both scales and interference across scales. We hypothesize that within-population environmental heterogeneity influences the chance of success of migration events, both within and among populations, and maintains within-population adaptive differentiation. We used a simulation approach to analyse the joint effects of environmental heterogeneity patterns, selection intensity and number of QTL controlling a selected trait on local adaptation in a hierarchical metapopulation design. We show the general effects of within-population environmental heterogeneity: (i) it increases occupancy rate at the margins of distribution ranges, under extreme environments and high levels of selection; (ii) it increases the adaptation lag in all environments; (iii) it impacts the genetic variance in each environment, depending on the ratio of within- to between-populations environmental heterogeneity; (iv) it reduces the selection-induced erosion of adaptive gene diversity. Most often, the smaller the number of QTL involved, the stronger are these effects. We also show that both within- and between-populations phenotypic differentiation (Q

19 Pág., 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., Agence Nationale de la Recherche, Grant/ Award Number: FLAG project (ANR-12- ADAP-0007-01); European Commission, Grant/Award Number: TOPWOOD project (MSCA-RISE-2014-645654- TOPWOOD) and grant agreement No. 676876 (GenTree); Ministère de l'Écologie, du Développement Durable et de l'Énergie, Grant/Award Number: GRAAL project (10-MCGOT-GICC-8-CVS-139)

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.

[Motivation] Trait variation within species can reveal plastic and/or genetic responses to environmental gradients, and may indicate where local adaptation has occurred. Here, we present a dataset of rangewide variation in leaf traits from seven of the most ecologically and economically important tree species in Europe. Sample collection and trait assessment are embedded in the GenTree project (EU-Horizon 2020), which aims at characterizing the genetic and phenotypic variability of forest tree species to optimize the management and sustainable use of forest genetic resources. Our dataset captures substantial intra- and interspecific leaf phenotypic variability, and provides valuable information for studying the relationship between ecosystem functioning and trait variability of individuals, and the response and resilience of species to environmental changes., [Main types of variable contained] We chose morphological and chemical characters linked to trade-offs between acquisition and conservation of resources and water use, namely specific leaf area, leaf size, carbon and nitrogen content and their ratio, and the isotopic signature of stable isotope 13C and 15N in leaves., [Spatial location and grain] We surveyed between 18 and 22 populations per species, 141 in total, across Europe., [Time period] Leaf sampling took place between 2016 and 2017., [Major taxa and level of measurement] We sampled at least 25 individuals in each population, 3,569 trees in total, and measured traits in 35,755 leaves from seven European tree species, i.e. the conifers Picea abies, Pinus pinaster and Pinus sylvestris, and the broadleaves Betula pendula, Fagus sylvatica, Populus nigra and Quercus petraea., [Software format] The data files are in ASCII text, tab delimited, not compressed., All authors acknowledge support from the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement no. 676876 (Project GenTree). Laboratory work was also supported by other projects: COMEDIAS (CGL2017- 83170-R, Spanish Ministry of Science, Innovation and Universities), REMEDINAL IV (TE-CM S2018/EMT-4338, Project of the Autonomous Community of Madrid, Spain), SPONFOREST (BIODIVERSA-3, PCIN-2016-055), and International Laboratory of Global Change (LINCGlobal 4540-143AP). The Swiss contribution was supported by the Swiss Secretariat for Education, Research and Innovation (SERI) under contract no. 6.0032. BC was funded by a Scholarship from Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES (Brazil).

The European Beech is the dominant climax tree in most regions of Central Europe and valued for its ecological versatility and hardwood timber. Even though a draft genome has been published recently, higher resolution is required for studying aspects of genome architecture and recombination. Here, we present a chromosome-level assembly of the more than 300 year-old reference individual, Bhaga, from the Kellerwald-Edersee National Park (Germany). Its nuclear genome of 541 Mb was resolved into 12 chromosomes varying in length between 28 and 73 Mb. Multiple nuclear insertions of parts of the chloroplast genome were observed, with one region on chromosome 11 spanning more than 2 Mb which fragments up to 54,784 bp long and covering the whole chloroplast genome were inserted randomly. Unlike in

The European Beech is the dominant climax tree in most regions of Central Europe and valued for its ecological versatility and hardwood timber. Even though a draft genome has been published recently, higher resolution is required for studying aspects of genome architecture and recombination. Here we present a chromosome-level assembly of the more than 300 year-old reference individual, Bhaga, from the Kellerwald-Edersee National Park (Germany). Its nuclear genome of 541 Mb was resolved into 12 chromosomes varying in length between 28 Mb and 73 Mb. Multiple nuclear insertions of parts of the chloroplast genome were observed, with one region on chromosome 11 spanning more than 2 Mb of the genome in which fragments up to 54,784 bp long and covering the whole chloroplast genome were inserted randomly. Unlike in Arabidopsis thaliana, ribosomal cistrons are present in Fagus sylvatica only in four major regions, in line with FISH studies. On most assembled chromosomes, telomeric repeats were found at both ends, while centromeric repeats were found to be scattered throughout the genome apart from their main occurrence per chromosome. The genome- wide distribution of SNPs was evaluated using a second individual from Jamy Nature Reserve (Poland). SNPs, repeat elements and duplicated genes were unevenly distributed in the genomes, with one major anomaly on chromosome 4. The genome presented here adds to the available highly resolved plant genomes and we hope it will serve as a valuable basis for future research on genome architecture and for understanding the past and future of European Beech populations in a changing climate.

International audience; Trees are characterized by the large number of seeds they produce. Although most of those seeds will never germinate, plenty will. Of those which germinate, many die young, and eventually, only a minute fraction will grow to adult stage and reproduce. Is this just a random process? Do variations in germination and survival at very young stages rely on variations in adaptations to microgeographic heterogeneity? and do these processes matter at all in determining tree species distribution and abundance?We have studied these questions with the Neotropical Symphonia tree species. In the Guiana shield, Symphonia are represented by at least two sympatric taxa or ecotypes, Symphonia globulifera found almost exclusively in bottomlands, and a yet undescribed more generalist taxon/ecotype, Symphonia sp1. A reciprocal transplantation experiment (510 seeds, 16 conditions) was set up and followed over the course of 6 years to evaluate the survival and performance of individuals from different ecotypes and provenances.Germination, survival, growth, and herbivory showed signs of local adaptation, with some combinations of ecotypes and provenances growing faster and surviving better in their own habitat or provenance region. S. globulifera was strongly penalized when planted outside its home habitat but showed the fastest growth rates when planted in its home habitat, suggesting it is a specialist of a high‐risk high‐gain strategy. Conversely, S. sp1 behaved as a generalist, performing well in a variety of environments.The differential performance of seeds and seedlings in the different habitats matches the known distribution of both ecotypes, indicating that environmental filtering at the very early stages can be a key determinant of tree species distributions, even at the microgeographic level and among very closely related taxa. Furthermore, such differential performance also contributes to explain, in part, the maintenance of the different Symphonia ecotypes living in intimate sympatry despite occasional gene flow.

Plant populations are able to undergo very localized adaptive processes, that allow continuous populations to adapt to divergent habitats in spite of recurrent gene flow. Here, we carried out a genome scan for selection through whole-genome sequencing of pools of populations, sampled according to a nested sampling design, to evaluate microgeographic adaptation in the hyperdominant Amazonian tree Eperua falcata Aubl. (Fabaceae). A high-coverage genomic resource of ~250 Mb was assembled de novo and annotated, leading to 32 789 predicted genes. 97 062 bi-allelic SNPs were detected in 25 803 contigs were detected, and a custom Bayesian model we implemented to uncover candidate genomic targets of divergent selection. A set of 290 'divergence' outlier SNPs was detected at the regional scale (between study sites), while 185 SNPs located in the vicinity of 106 protein-coding genes were detected as replicated outliers between microhabitats within regions. These genes possibly underlie ecologically important phenotypes and tend to indicate that adaptation to microgeographic habitat patchiness would affect genomic regions involved in a variety of physiological processes, among which plant response to stress (for e.g., oxidative stress, hypoxia and metal toxicity) and biotic interactions. Identification of genomic targets of microgeographic adaptation in the Neotropics supports the hypothesis - frequently raised at the community level - that local adaptation would be a key driver of ecological diversification, probably operating across multiple spatial scales, from large- (i.e. regional) to microgeographic- (i.e. landscape) scales.

International audience; Plant populations can undergo very localized adaptation, allowing widely distributed populations to adapt to divergent habitats in spite of recurrent gene flow. Neotropical trees –whose large and undisturbed populations often span a variety of environmental conditions and local habitats – are particularly good models to study this process. Here, we explore patterns of adaptive divergence from large (i.e. regional) to small (i.e. microgeographic) spatial scales in the hyperdominant Amazonian tree Eperua falcata Aubl. (Fabaceae) under a replicated design involving two microhabitats (~300 m apart) in two study sites (~300 km apart). A three-year reciprocal transplant illustrates that, beyond strong maternal effects and phenotypic plasticity, genetically driven divergence in seedling growth and leaf traits was detected both between seedlings originating from different regions, and between seedlings from different microhabitats. In parallel, a complementary genome scan for selection was carried out through whole-genome sequencing of tree population pools. A set of 290 divergence outlier SNPs was detected at the regional scale (between study sites), while 185 SNPs located in the vicinity of 106 protein-coding genes were detected as replicated outliers between microhabitats within regions. Outlier-surrounding genomic regions are involved in a variety of physiological processes, including plant responses to stress (e.g., oxidative stress, hypoxia and metal toxicity) and biotic interactions. Together with evidence of microgeographic divergence in functional traits, the discovery of genomic candidates for microgeographic adaptive divergence represents a promising advance in our understanding of local adaptation, which likely operates across multiple spatial scales and underpins divergence and diversification in Neotropical trees.

Phylogenetic patterns and the underlying speciation processes can be deduced from morphological, functional, and ecological patterns of species similarity and divergence. In some cases, though, species retain multiple similarities and remain almost indistinguishable; in other cases, evolutionary convergence can make such patterns misleading; very often in such cases, the “true” picture only emerges from carefully built molecular phylogenies, which may come with major surprises. In addition, closely related species may experience gene flow after divergence, thus potentially blurring species delimitation. By means of advanced inferential methods, we studied molecular divergence between species of the Virola genus (Myristicaceae): widespread Virola michelii and recently described, endemic V. kwatae, using widespread V. surinamensis as a more distantly related outgroup with different ecology and morphology—although with overlapping range. Contrary to expectations, we found that the latter, and not V. michelii, was sister to V. kwatae. Therefore, V. kwatae probably diverged from V. surinamensis through a recent morphological and ecological shift, which brought it close to distantly related V. michelii. Through the modeling of the divergence process, we inferred that gene flow between V. surinamensis and V. kwatae stopped soon after their divergence and resumed later, in a classical secondary contact event which did not erase their ecological and morphological differences. While we cannot exclude that initial divergence occurred in allopatry, current species distribution and the absence of geographical barriers make complete isolation during speciation unlikely. We tentatively conclude that (a) it is possible that divergence occurred in allopatry/parapatry and (b) secondary contact did not suppress divergence., We studied molecular divergence between species of the Neotropical Virola genus: widespread Virola michelii and recently described, endemic V. kwatae, using widespread V. surinamensis as a more distantly related outgroup with different ecology and morphology—although with overlapping range. We found that the latter, and not V. michelii, is sister to V. kwatae. This partial reassessment of the phylogeny in the Virola genus led us to investigate and to assess, by using coalescent theory and Bayesian modelling, the presence of gene flow after speciation in the pair V. kwatae/V. surinamensis, indicating the existence of phylogenetic radiation without strict reproductive isolation.

Devant l’inéluctable dépérissement de certaines espèces d’arbres, des chercheurs s’interrogentet étudient les capacités adaptatives des différentes essences

Sequences have been deposited in the R-SYST databank (https://github.com/r-syst/databases/tree/master/r-syst::plants) and NCBI under accession number KX247940–KX249593. The list of studied species, including genus size, seed dispersal syndrome and cpDNA variation, is available at https://github.com/r-syst/databases/tree/master/r-syst::plants. In this list, chloroplast haplotype designation is consistent within each genus.; International audience; We investigate chloroplast DNA variation in a hyperdiverse community of tropical rainforest trees in French Guiana, focusing on patterns of intraspecific and interspecific variation. We test whether a species genetic diversity is higher when it has congeners in the community with which it can exchange genes and if shared haplotypes are more frequent in genetically diverse species, as expected in the presence of introgression. We sampled a total of 1,681 individual trees from 472 species corresponding to 198 genera and sequenced them at a noncoding chloroplast DNA fragment. Polymorphism was more frequent in species that have congeneric species in the study site than in those without congeners (30% vs. 12%). Moreover, more chloroplast haplotypes were shared with congeners in polymorphic species than in monomorphic ones (44% vs. 28%). Despite large heterogeneities caused by genus-specific behaviors in patterns of hybridization, these results suggest that the higher polymorphism in the presence of congeners is caused by local introgression rather than by incomplete lineage sorting. Our findings suggest that introgression has the potential to drive intraspecific genetic diversity in species-rich tropical forests.

International audience; No abstract available

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 ofPinus nigraand 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.HighlightsThe European black pine,Pinus nigra(Arnold), has a weak spatial genetic structure.Gene flow among populations is frequent and populations are often of admixed origin.Current genealogies result from recent, late Pleistocene or Holocene events.Seven modern genetic lineages emerged from divergence and demographic contractions.These seven lineages warrant a revision of subspecies taxonomic nomenclature.

International audience; Fragmentation acting over geological times confers wide, biogeographical scale and 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 widespread forest tree, Pinus nigra Arnold, the European black pine, and to resolve its demographic history, we described and modelled its spatial genetic structure and gene genealogy. We then tested which Pleistocene event, whether recent or ancient, could explain its widespread but patchy geographic distribution. We used a set of different genetic markers, both neutral and potentially adaptive, and either biparentally or paternally only inherited, and we sampled natural populations across the entire species range. We analysed the data using both frequentist population genetic and Bayesian inference methods to calibrate realistic, demographic timed scenarios. We also considered how habitat suitability might have affected demography by correlating climate variables at different recent Pleistocene ages with genetic diversity estimates. Species with geographically fragmented distribution areas are expected to display significant 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 result from the Late Pleistocene or Early Holocene fragmentation of one ancestral population into six distinct genetic lineages. 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 sub-species and name these six lineages using regionally accepted sub-species-level names.

International audience; Hylesia moths impact human health in South America, inducing epidemic outbreaks of lepidopterism, a puriginous dermatitis caused by the urticating properties of females' abdominal setae. The classification of the Hylesia genus is complex, owing to its high diversity in Amazonia, high intraspecific morphological variance, and lack of interspecific diagnostic traits which may hide cryptic species. Outbreaks of Hylesia metabus have been considered responsible for the intense outbreaks of lepidopterism in Venezuela and French Guiana since the C20, however, little is known about genetic variability throughout the species range, which is instrumental for establishing control strategies on H. metabus. Seven microsatellites and mitochondrial gene markers were analyzed from Hylesia moths collected from two major lepidopterism outbreak South American regions. The mitochondrial gene sequences contained significant genetic variation, revealing a single, widespread, polymorphic species with distinct clusters, possibly corresponding to populations evolving in isolation. The microsatellite markers validated the mitochondrial results, and suggest the presence of three populations: one in Venezuela, and two in French Guiana. All moths sampled during outbreak events in French Guiana were assigned to a single coastal population. The causes and implications of this finding require further research.; Las polillas del género Hylesia (Lepidoptera: Saturniidae) impactan la salud humana en Sudamérica, induciendo brotes epidémicos de lepidopterismo, una dermatitis pruriginosa causada por las propiedades urticantes de las setas abdominales de las hembras. La clasificación del género Hylesia es compleja, debido a su gran diversidad en Amazonía, la alta variabilidad morfológica intraespecífica y la falta de características diagnósticas interespecíficas que pueden ocultar especies crípticas. Se considerada a los aumentos explosivos de la población de Hylesia metabus como responsable de los intensos brotes de lepidopterismo en Venezuela y la Guayana Francesa desde el S.20, sin embargo, se sabe poco sobre la variabilidad genética en toda su área de distribución, que es fundamental para establecer estrategias de control de H. metabus. Siete microsatélites y marcadores de genes mitocondriales se analizaron en polillas de Hylesia recolectadas en dos regiones principales de brotes de Sudamérica. Los genes mitocondriales contenían una variación genética significativa, que revela una única especie, diseminada geográficamente y polimórfica con grupos distintos, posiblemente correspondiendo a poblaciones evolucionando de forma aislada. Los microsatélites validaron los resultados mitocondriales y sugieren la presencia de tres poblaciones: una en Venezuela y dos en la Guayana Francesa. Todas las polillas muestreadas durante los brotes en la Guayana Francesa fueron asignadas a una sola población costera. Las causas y las implicaciones de este hallazgo requieren más investigación.

Key message This review highlights some of the discoveries and applications made possible by “omics” technologies over the last 10 years and provides perspectives for pioneering research to increase our understanding of tree biology. Context A decade after the first forest tree genome sequence was released into the public domain, the rapidly evolving genomics and bioinformatics toolbox has advanced our understanding of the structure, functioning, and evolution of forest tree genomes. Aims and methods This review highlights some of the discoveries and applications that “omics” technologies have made possible for forest trees over the past 10 years. Results In this review, we start by our current understanding of genome evolution and intricacies of gene regulation for reproduction, development, and responses to biotic and abiotic stresses. We then skim over advances in interactome analysis and epigenomics, the knowledge of the extent of genetic variation within and between species, revealing micro- and macro-evolutionary processes and species history, together with the complex architecture of quantitative traits. We finally end with applications in genetic resource conservation and breeding. Conclusion The knowledge gained through the use of these technologies has a huge potential impact for adapting forests to the main challenges they will have to face: changing demand from ecosystem services with potentially conflicting strategies in terms of conservation and use, as well as climate changes and associated threats. Genomics will undoubtedly play a major role over the next decade and beyond, not only to further understand the mechanisms underlying adaptation and evolution but also to develop and implement innovative management and policy actions to preserve the adaptability of natural forests and intensively managed plantations.

Demographic and evolutionary history of the European black pine (Pinus nigra Arn). Réunion du groupe AFORGEN

International audience

Whilst there are many examples of contemporary directional selection, evidence for responses to selection that match predictions are often missing in quantitative genetic studies of wild populations. This is despite genetic variation and selection pressures - theoretical prerequisites for the response to selection - being present. This conundrum can be explained by statistical issues with accurate parameter estimation, and by biological mechanisms that interfere with the response to selection. These biological mechanisms can accelerate or constrain this response. These mechanisms are generally studied independently but might act simultaneously. We therefore integrated these mechanisms to explore their potential combined effect. This has implications for explaining the apparent evolutionary stasis of wild populations and the conservation of wildlife.

International audience; Key message Forest disturbance affects the within-population distribution of genetic diversity, but not its overall levels, in a tropical pioneer tree species. In particular , clumps of related saplings with impoverished diversity are found in canopy gaps but not under forest cover. Context Forest disturbances can have long-term consequences on the genetic structure of tree populations, because they can alter the demographic properties of the regeneration process and favour some subpopulations/genotypes, both by stochastic processes and by selection. Intermediate disturbances tend to favour species diversity, at least in highly diverse communities , but their effect on intra-specific diversity is unknown. Aims In this study, we have looked at the genetic consequences of forest disturbance in a stand of the long-lived Neo-tropical pioneer species, Jacaranda copaia. Methods The study site was experimentally logged in 1984, and the canopy gaps generated by the logging were mapped. Seedlings of J. copaia colonised the gaps, as expected, at a higher density than in the surrounding forest. In 2006, we exhaustively sampled all saplings and adult trees available in a 25-ha area. The samples were genotyped at nine microsatel-lite loci, and the distribution of genetic diversity was inspected by analyses of spatial autocorrelation, automated Bayesian assignment and comparisons of diversity between cohorts by bootstrap (RaBoT). Results Spatial autocorrelation was found to extend farther in post-disturbance saplings than in the undisturbed population (100 m and beyond versus less than 50 m), and divergent clumps (F ST =0.05) of related genotypes were found; genetic Handling Editor: Ricardo Alia Contribution of the co-authors TL analysed data; RV collected samples and data, ran data analyses and wrote the paper; VT and SG collected and cured data; IS conceived the experiment, ran data analyses and wrote the manuscript. Thomas Leclerc tragically deceased in a car accident during his internship in French Guiana while carrying out this research. The remaining authors completed the study and wrote the manuscript on his behalf. This paper is dedicated to his memory and to his family and friends. Electronic supplementary material The online version of this article (diversity was found to be impoverished in each clump relative to the global population at about half of the loci. Conclusion Overall, our results suggest that forest disturbance has changed the patterns of distribution of genetic diversity , with potential consequences on long-term population viability.

Q(ST) is a differentiation parameter based on the decomposition of the genetic variance of a trait. In the case of additive inheritance and absence of selection, it is analogous to the genic differentiation measured on individual loci, F(ST). Thus, Q(ST)−F(ST) comparison is used to infer selection: selective divergence when Q(ST) > F(ST), or convergence when Q(ST) < F(ST). The definition of Q-statistics was extended to two-level hierarchical population structures with Hardy–Weinberg equilibrium. Here, we generalize the Q-statistics framework to any hierarchical population structure. First, we developed the analytical definition of hierarchical Q-statistics for populations not at Hardy–Weinberg equilibrium. We show that the Q-statistics values obtained with the Hardy–Weinberg definition are lower than their corresponding F-statistics when F(IS) > 0 (higher when FIS < 0). Then, we used an island model simulation approach to investigate the impact of inbreeding and dominance on the Q(ST)−F(ST) framework in a hierarchical population structure. We show that, while differentiation at the lower hierarchical level (Q(SR)) is a monotonic function of migration, differentiation at the upper level (Q(RT)) is not. In the case of additive inheritance, we show that inbreeding inflates the variance of Q(RT), which can increase the frequency of Q(RT) > F(RT) cases. We also show that dominance drastically reduces Q-statistics below F-statistics for any level of the hierarchy. Therefore, high values of Q-statistics are good indicators of selection, but low values are not in the case of dominance.

Q

Microgeographic adaptation in tree stands. ATBC 2016

Population genetic studies in tropical plants are often challenging because of limited information on taxonomy, phylogenetic relationships and distribution ranges, scarce genomic information and logistic challenges in sampling. We describe a strategy to develop robust and widely applicable genetic markers based on a modest development of genomic resources in the ancient tropical tree species Symphonia globulifera L.f. (Clusiaceae), a keystone species in African and Neotropical rainforests. We provide the first low-coverage (11X) fragmented draft genome sequenced on an individual from Cameroon, covering 1.027 Gbp or 67.5% of the estimated genome size. Annotation of 565 scaffolds (7.57 Mbp) resulted in the prediction of 1046 putative genes (231 of them containing a complete open reading frame) and 1523 exact simple sequence repeats (SSRs, microsatellites). Aligning a published transcriptome of a French Guiana population against this draft genome produced 923 high-quality single nucleotide polymorphisms. We also preselected genic SSRs in silico that were conserved and polymorphic across a wide geographical range, thus reducing marker development tests on rare DNA samples. Of 23 SSRs tested, 19 amplified and 18 were successfully genotyped in four S. globulifera populations from South America (Brazil and French Guiana) and Africa (Cameroon and São Tomé island, FST = 0.34). Most loci showed only population-specific deviations from Hardy–Weinberg proportions, pointing to local population effects (e.g. null alleles). The described genomic resources are valuable for evolutionary studies in Symphonia and for comparative studies in plants. The methods are especially interesting for widespread tropical or endangered taxa with limited DNA availability. © 2016 John Wiley & Sons Ltd

How Quaternary climatic and geological disturbances influenced the composition of Neotropical forests is hotly debated. Rain fall and temperature changes during and/or immediately after the Last Glacial Maximum (LGM) are thought to have strongly affected the geographical distribution and local abundance of tree species. The paucity of the fossil records in Neotropical forests prevents a direct reconstruction of such processes. To describe community-level historical trends in forest composition, we turned therefore to inferential methods based on the reconstruction of past demographic changes. In particular, we modelled the history of rainforests in the Eastern Guiana Shield over a time scale of several thousand generations, through the application of Approximate Bayesian Computation (ABC) and Maximum Likelihood (ML) methods to diversity data at nuclear and chloroplast loci in eight species or subspecies of rainforest trees. Depending on the species and on the method applied, we detected population contraction, expansion or stability, with a general trend in favour of stability or expansion, with changes presumably having occurred during or after the LGM. These findings suggest that Guiana Shield rain forests have globally persisted, while expanding, through the Quaternary, but that different species have experienced different demographic events, with a trend towards the increase in frequency of light-demanding, disturbance-associated species.

International audience; No abstract available

Disentangling the impact of landscape features such as rivers and historical events on dispersal is a challenging but necessary task to gain a comprehensive picture of the evolution of diverse biota such as that found in Amazonia. Adenomera andreae, a small, territorial, terrestrial frog species of the Amazonian forest represents a good model for such studies. We combined cytochrome b sequences with 12 microsatellites to investigate the genetic structure at two contrasted spatial scales in French Guiana: along a similar to 6-km transect, to evaluate dispersal ability, and between paired bank populations along a similar to 65-km stretch of the Approuague river, to test the effect of rivers as barriers to dispersal. We observed significant spatial genetic structure between individuals at a remarkably small geographical scale, and conclude that the species has a restricted dispersal ability that is probably tied to its life-history traits. Mitochondrial and microsatellite data also indicate a high level of differentiation among populations on opposite banks of the river, and, in some cases, among populations on the same riverbank. These results suggest that the observed population structure in A. andreae is the result of restricted dispersal abilities combined with the action of rivers and Quaternary population isolation. Given that Amazonia hosts a great portion of anurans, as well as other small vertebrates, that display life-history traits comparable with A. andreae, we argue that our analyses provide new insights into the complex interactions among evolutionary processes shaping Amazonian biodiversity. (c) 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106, 356373.

Aim Many tropical tree species have poorly delimited taxonomic boundaries and contain undescribed or cryptic species. We examined the genetic structure of a species complex in the tree genus Carapa in the Neotropics in order to evaluate age, geographic patterns of diversity and evolutionary relationships, and to quantify levels of introgression among currently recognized species. Location Lowland moist forests in the Guiana Shield, the Central and Western Amazon Basin, Chocoand Central America. Methods Genetic structure was analysed using seven nuclear simple sequence repeats (nuSSR), five chloroplast SSRs (cpSSR), and two chloroplast DNA (cpDNA) intergenic sequences (trnH-psbA and trnC-ycf6). Bayesian clustering analysis of the SSR data was used to infer population genetic structure and to assign 324 samples to their most likely genetic cluster. Bayesian coalescence analyses were performed on the two cpDNA markers to estimate evolutionary relationships and divergence times. Results Two genetic clusters (nu_guianensis and nu_surinamensis) were detected, which correspond to the Neotropical species C. guianensis (sensu latu )a nd C. surinamensis. Fourteen cpDNA haplotypes clustered into six haplogroups distributed between the two nuclear genetic clusters. Divergence between the haplogroups was initiated in the Miocene, with some haplotype structure evolving as recently as the Pleistocene. The absence of complete lineage sorting between the nuclear and chloroplast genomes and the presence of hybrid individuals suggest that interspecific reproductive barriers are incomplete. NuSSR diversity was highest in C. guianensis and, within C. guianensis, cpDNA diversity was highest in the Central and Western Amazon Basin. Regional genetic differentiation was strong but did not conform to an isolation-by-distance process or exhibit a phylogeographical signal. Main conclusions The biogeographical history of Neotropical Carapa appears to have been influenced by events that took place during the Neogene. Our results point to an Amazonian centre of origin and diversification of Neotropical Carapa, with subsequent migration to the Pacific coast of South America and Central America. Gene flow apparently occurs among species, and introgression events are supported by inconsistencies between chloroplast and nuclear lineage sorting. The absence of phylogeographical structure may be a result of the ineffectiveness of geographical barriers among populations and of reproductive isolation mechanisms among incipient and cryptic species in this species complex.

Background. In wild plant populations, genetic divergence within continuous stands is common, sometimes at very short geographical scales. While restrictions to gene flow combined with local inbreeding and genetic drift may cause neutral differentiation among subpopulations, microgeographical variations in environmental conditions can drive adaptive divergence through natural selection at some targeted loci. Such phenomena have recurrently been observed in plant populations occurring across sharp environmental boundaries, but the interplay between selective processes and neutral genetic divergence has seldom been studied.[br/]Methods. We assessed the extent of within-stand neutral and environmentally-driven divergence in the Neotropical tree [i]Eperua falcate Aubl[/i]. (Fabaceae) through a genome-scan approach. Populations of this species grow in dense stands that cross the boundaries between starkly contrasting habitats. Within-stand phenotypic and candidate-gene divergence have already been proven, making this species a suitable model for the study of genome-wide microgeographic divergence. Thirty trees from each of two habitats (seasonally flooded swamps and well-drained plateaus) in two separate populations were genotyped using thousands of AFLPs markers. To avoid genotyping errors and increase marker reliability, each sample was genotyped twice and submitted to a rigorous procedure for data cleaning, which resulted in 1196 reliable and reproducible markers.[br/]Results. Despite the short spatial distances, we detected within-populations genetic divergence, probably caused by neutral processes, such as restrictions in gene flow. Moreover, habitat-structured subpopulations belonging to otherwise continuous stands also diverge in relation to environmental variability and habitat patchiness: we detected convincing evidence of divergent selection at the genome-wide level and for a fraction of the analyzed loci (comprised between 0.25% and 1.6%). Simulations showed that the levels of differentiation for these outliers are compatible with scenarios of strong divergent selection

Rainforest tree species can be difficult to identify outside of their period of reproduction. Vascular tissues from Carapa spp. individuals were collected during a short field trip in French Guiana and analysed in the laboratory with nuclear and chloroplast markers. Using a Bayesian approach, > 90% of the samples could be assigned to one of two distinct clusters corresponding to previously described species, making it possible to estimate the genetic structure of each species and to identify cases of introgression. We argue that this blind procedure represents a first-choice rather than a fallback option whenever related taxa are investigated.

Trinucleotide microsatellites have proven to be the markers of choice in human genetic analysis because they are easier to genotype than dinucleotides. Their development can be more time-consuming due to their lower abundance in the genome. We isolated trinucleotide microsatellites in Norway spruce ( Picea abies K.) using an enrichment procedure for the genomic-library construction. Here we report on the characterisation of 85 ATC microsatellite-containing clones, from which 39 markers were developed. Many of the clones showed the occurrence of tandem repeats of higher order than the trinucleotide ones, often resembling minisatellite repeats. The sequencing of a sample of the alleles at one of the loci revealed size homoplasy due to base substitutions within the microsatellite region. The presence of ATC motifs within repetitive sequence families was observed. We found a significant relationship between the level of polymorphism and the length of the microsatellite. The levels of variability for ATC trinucleotide markers were lower than those for dinucleotides, both when tested on all loci in a set of six individuals and on a subset of loci in four natural populations. This difference is most likely attributable to lower mutation rates for trinucleotide than for dinucleotide loci. The availability of markers with different mutation rates allows one to select the proper marker set to investigate population processes on different time scales.

Traditional measures of diversity, namely the number of species as well as Simpson's and Shannon's indices, are particular cases of Tsallis entropy. Entropy decomposition, i.e. decomposing gamma entropy into alpha and beta components, has been previously derived in the literature. We propose a generalization of the additive decomposition of Shannon entropy applied to Tsallis entropy. We obtain a self-contained definition of beta entropy as the information gain brought by the knowledge of each community composition. We propose a correction of the estimation bias allowing to estimate alpha, beta and gamma entropy from the data and eventually convert them into true diversity. We advocate additive decomposition in complement of multiplicative partitioning to allow robust estimation of biodiversity.

Background The Amazonian rainforest is predicted to suffer from ongoing environmental changes. Despite the need to evaluate the impact of such changes on tree genetic diversity, we almost entirely lack genomic resources. Results In this study, we analysed the transcriptome of four tropical tree species (Carapa guianensis, Eperua falcata, Symphonia globulifera and Virola michelii) with contrasting ecological features, belonging to four widespread botanical families (respectively Meliaceae, Fabaceae, Clusiaceae and Myristicaceae). We sequenced cDNA libraries from three organs (leaves, stems, and roots) using 454 pyrosequencing. We have developed an R and bioperl-based bioinformatic procedure for de novo assembly, gene functional annotation and marker discovery. Mismatch identification takes into account single-base quality values as well as the likelihood of false variants as a function of contig depth and number of sequenced chromosomes. Between 17103 (for Symphonia globulifera) and 23390 (for Eperua falcata) contigs were assembled. Organs varied in the numbers of unigenes they apparently express, with higher number in roots. Patterns of gene expression were similar across species, with metabolism of aromatic compounds standing out as an overrepresented gene function. Transcripts corresponding to several gene functions were found to be over- or underrepresented in each organ. We identified between 4434 (for Symphonia globulifera) and 9076 (for Virola surinamensis) well-supported mismatches. The resulting overall mismatch density was comprised between 0.89 (S. globulifera) and 1.05 (V. surinamensis) mismatches/100 bp in variation-containing contigs. Conclusion The relative representation of gene functions in the four transcriptomes suggests that secondary metabolism may be particularly important in tropical trees. The differential representation of transcripts among tissues suggests differential gene expression, which opens the way to functional studies in these non-model, ecologically important species. We found substantial amounts of mismatches in the four species. These newly identified putative variants are a first step towards acquiring much needed genomic resources for tropical tree species. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-238) contains supplementary material, which is available to authorized users.

† Background and Aims In habitat mosaics, plant populations face environmental heterogeneity over short geographical distances. Such steep environmental gradients can induce ecological divergence. Lowland rainforests of the Guiana Shield are characterized by sharp, short-distance environmental variations related to topography and soil characteristics (from waterlogged bottomlands on hydromorphic soils to well-drained terra firme on ferralitic soils). Continuous plant populations distributed along such gradients are an interesting system to study intrapopulation divergence at highly local scales. This study tested (1) whether conspecific populations growing in different habitats diverge at functional traits, and (2) whether they diverge in the same way as congeneric species having different habitat preferences. † Methods Phenotypic differentiation was studied within continuous populations occupying different habitats for two congeneric, sympatric, and ecologically divergent tree species (Eperua falcata and E. grandiflora, Fabaceae). Over 3000 seeds collected from three habitats were germinated and grown in a common garden experiment, and 23 morphological, biomass, resource allocation and physiological traits were measured. † Key Results In both species, seedling populations native of different habitats displayed phenotypic divergence for several traits (including seedling growth, biomass allocation, leaf chemistry, photosynthesis and carbon isotope composition). This may occur through heritable genetic variation or other maternally inherited effects. For a sub-set of traits, the intraspecific divergence associated with environmental variation coincided with interspecific divergence. † Conclusions The results indicate that mother trees from different habitats transmit divergent trait values to their progeny, and suggest that local environmental variation selects for different trait optima even at a very local spatial scale. Traits for which differentiation within species follows the same pattern as differentiation between species indicate that the same ecological processes underlie intra- and interspecific variation.