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International audience; Forest inventories in Amazonia include around 5000 described tree species belonging to more than 800 genera. Numerous species-rich genera share genetic variation among species because of recent speciation and/or recurrent hybridisation, forming species complexes. Despite the key role that tree species complexes play in understanding Neotropical diversification, and their need to exploit a diversity of niches, little is known about the mechanisms that allow local coexistence of tree species complexes and their species in sympatry. In this study, we explored the fine-scale distribution of five tree species complexes and 22 species within these complexes. Combining forest inventories, botanical determination, and LiDAR-derived topographic data over 120 ha of permanent plots in French Guiana, we used a Bayesian modelling framework to test the role of fine-scale topographic wetness and tree neighbourhood on the occurrence of species complexes and the relative distribution of species within complexes. Species complexes of Neotropical trees were widely spread across the topographic wetness gradient at the local scale. Species within complexes showed pervasive niche differentiation along with topographic wetness and competition gradients. Similar patterns of species-specific habitat preferences were observed within several species complexes: species more tolerant to competition for resources grow in drier and less fertile plateaus and slopes. If supported by partial reproductive isolation of species and adaptive introgression at the species complex level, our results suggest that both species-specific habitat specialisation within species complexes and the broad ecological distribution of species complexes might explain the success of these species complexes at the regional scale.

ispartof: BIOLOGICAL CONSERVATION vol:253 status: published

The most remarkable feature of our planet is the diversity of its life forms, ranging from viruses and nanobacteria to blue whales and giant sequoias to satanic leaf‐tailed geckos and leafy seadragons (look them up!). Life is found in essentially all environments on earth, and the number of species living on our planet is many times greater than we could have imagined a century ago. A well‐regarded estimate pegs the number of eukaryotic species on earth at 8.7 million (±1.3 million), of which fewer than 15% are currently described (Mora et al., 2011). The diversity of prokaryotes is less clear (and highly controversial), but an analysis of 1.6 billion 16S ribosomal RNA sequences estimated that 0.8–1.6 million prokaryotic operational taxonomic units exist globally (Louca et al., 2019). While we do not know how many species are currently extant, or have existed in the past, we do know that this biodiversity is valuable, providing food, fibre and medicine, furnishing ecosystem services such as water and air purification, nutrient cycling, pollination and carbon uptake, and contributing to technological innovations ranging from biotechnology to robotics to material science. Moreover, biodiversity underlies the cultural identity of human populations and is important to human health and well‐being. Geographically, species richness increases from the Polar Regions to the tropics in terrestrial and surface marine ecosystems. Thus, some countries, especially those in tropical and subtropical regions, are endowed with much greater biodiversity than others. Unfortunately, benefits arising from the access and utilization of this biodiversity have been unequally shared, with (paradoxically) biodiversity‐poor countries often accruing the lion's share of economic gains. There can be imbalances within countries as well, wherein some segments of the population obtain greater economic benefits from biodiversity and associated traditional knowledge than indigenous peoples. The “Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization,” which came into force in 2014, is an international agreement designed to ensure that the benefits arising from biodiversity are shared equitably (https://www.cbd.int/abs/). However, few scientific journals require compliance with the Nagoya Protocol or the reporting of benefits from biodiversity research. In this editorial, we (the editors of Molecular Ecology and Molecular Ecology Resources) express support for the Nagoya Protocol and the principle of benefit sharing. We believe that scientific journals publishing research on biodiversity can play an important role in implementing the Nagoya Protocol and in reporting on benefits generated from such research. Below, we provide background on the Nagoya Protocol, discuss the kinds of benefits that may arise from biodiversity research, describe the rationale for reporting on these benefits and introduce changes to the journals’ Data Accessibility Statements to incorporate the requirements and goals of the Nagoya Protocol.

Premise: Few studies have addressed the evolutionary history of tree species from African savannahs. Afzelia contains economically important timber species, including two species widely distributed in African savannahs: A. africana in the Sudanian region and A. quanzensis in the Zambezian region. We aimed to infer whether these species underwent range fragmentation and/or demographic changes, possibly reflecting how savannahs responded to Quaternary climate changes. Methods: We characterized the genetic diversity and structure of these species across their distribution ranges using nuclear microsatellites (SSRs) and genotyping-by-sequencing (GBS) markers. Six SSR loci were genotyped in 241 A. africana and 113 A. quanzensis individuals, while 2800 high-quality single nucleotide polymorphisms (SNPs) were identified in 30 A. africana individuals. Results: Both species appeared to be mainly outcrossing. The kinship between individuals decayed with the logarithm of the distance at similar rates across species and markers, leading to relatively small Sp statistics (0.0056 for SSR and 0.0054 for SNP in A. africana, 0.0075 for SSR in A. quanzensis). The patterns were consistent with isolation by distance expectations in the absence of large-scale geographic gradients. Bayesian clustering of SSR genotypes did not detect genetic clusters within species. In contrast, SNP data resolved intraspecific genetic clusters in A. africana, illustrating the higher resolving power of GBS. However, these clusters revealed low levels of differentiation and no clear geographical entities, so that they were interpreted as resulting from the isolation by distance pattern rather than from past population fragmentation. Conclusions: These results suggest that populations have remained connected throughout the large, continuous savannah landscapes. The absence of clear phylogeographic discontinuities, also found in a few other African savannah trees, indicates that their distribution ranges have not been significantly fragmented during the climatic oscillations of the Pleistocene, in contrast to patterns commonly found in African rainforest trees., SCOPUS: ar.j, info:eu-repo/semantics/published

International audience; A recommendation – based on reviews by Marcela Van Loo, David Macaya-Sanz and one anonymous reviewer – of the article: Stoeckel, S., Porro, B., and Arnaud-Haond, S. (2019). The discernible and hidden effects of clonality on the genotypic and genetic states of populations: improving our estimation of clonal rates. ArXiv:1902.09365 [q-Bio] v4 peer-reviewed and recommended by Peer Community in Evolutionary Biology. Retrieved from http://arxiv.org/abs/1902.09365v4

Contexte et buts visés – Le chêne faginé, Quercus faginea Lam. (Fagaceae), représente un intérêt patrimonial, écologique et taxonomique remarquable en Algérie, mais malheureusement l’espèce est menacée et peu étudiée. L’objectif de ce travail est d’étudier la variabilité morphologique et le potentiel germinatif des glands de Q. faginea en Algérie, d’examiner la variabilité de la croissance des semis et d’évaluer l’influence des traitements physiques sur le potentiel germinatif et le développement ultérieur des semis, tant au niveau intra- qu’inter-stationnel. Méthodes – Des glands mûrs de chêne faginé récoltés sur quatre stations de l’espèce en Algérie ont été utilisés. Sur chaque station, dix arbres ont été sélectionnés, représentés par 100 glands chacun. Une analyse de traits phénotypiques a été réalisée sur les glands ; ensuite un ensemble de traitements physiques ont été effectués afin de tester leur effet sur la germination. Les semis issus de la germination ont été transplantés dans des sachets en polyéthylène et plusieurs caractères de croissance ont été mesurés. Résultats-clés – L’étude comparative morphologique et germinative révèle des glands plus longs et plus lourds à la station de Baloul, et des feuilles plus petites et plus légères à la station de Chélia, en comparaison avec les autres stations. Un effet significatif des traitements sur la germination a été montré dans toutes les stations. La taille des glands n’a aucune influence sur le développement des jeunes semis. Conclusions – Nos résultats montrent une variabilité morphologique inter-stationnelle des feuilles et des glands du chêne faginé. Cette diversité est probablement la conséquence de variations génétiques et/ou des conditions environnementales des stations. L’étude de la germination et de l’évolution de plants révèle un potentiel germinatif et de croissance considérables. Compte tenu de l’ensemble des facteurs qui menacent la pérennité du chêne faginé en Algérie, nous recommandons des actions pour la conservation de l’espèce telles que des reboisements, des plantations ex situ et des clôtures de protection pour éviter une régression réelle et irréversible des peuplements qui conduirait très probablement à sa disparition., Background and aims – The Portuguese Oak, Quercus faginea Lam. (Fagaceae) forms part of iconic Mediterranean forest communities and is of great ecological and taxonomic value in Algeria. Unfortunately, the species is under threat and its populations remain poorly characterized. The aim of this paper is to study the variability of acorn morphology and germination potential of Q. faginea in Algeria, to examine variability in the growth of seedlings and to evaluate the influence of physical treatments on germination capacity and the subsequent development of seedlings at the intra- and inter-provenance levels. Methods – Mature acorns from four Q. faginea provenances of the species in Algeria were used for this work. In each provenance, ten trees were selected, and 100 acorns collected from each tree. Prior to germination, phenotypic seed traits were measured and a set of physical treatments was performed. The germinated seedlings were transplanted into polyethylene bags and several characteristics of plant growth were measured. Key results – The comparative analysis on acorn morphology and germination features revealed heavier acorns in the Baloul provenance and smaller and lighter leaves in the Chelia provenance, in comparison with other provenances. Germination features and seedling growth showed that the size of the acorns had no influence on seedling development. Conclusions – Our results show a morphological variability of leaves and acorns of the Portuguese Oak at the inter-provenance level. This diversity is probably a consequence of genetic variation and / or variable environmental conditions of the provenances. The study of the germination and seedling development reveals a considerable potential for germination and growth. Given all the factors that threaten the persistence of Portuguese Oak in Algeria, we recommend conservation action for the species through reforestation, ex situ plantations and protective fences to avoid genuine and irreversible population regression, which would most likely lead to its disappearance.

International audience; Reconstructing species trees from multi-loci datasets is becoming a standard practice in phylogenetics. Nevertheless, access to high-throughput sequencing may be costly, especially with studies of many samples. The potential high cost makes a priori assessments desirable in order to make informed decisions about sequencing. We generated twelve transcriptomes for ten species of the Brazil nut family (Lecythidaceae), identified a set of putatively orthologous nuclear loci and evaluated, in silico, their phylogenetic utility using genome skimming data of 24 species. We designed the markers using MarkerMiner, and developed a script, GoldFinder, to efficiently sub-select the best makers for sequencing. We captured, in silico, all designed 354 nuclear loci and performed a maximum likelihood phylogenetic analysis on the concatenated sequence matrix. We also calculated individual gene trees with maximum likelihood and used them for a coalescent-based species tree inference. Both analyses resulted in almost identical topologies. However, our nuclear-loci phylogenies were strongly incongruent with a published plastome phylogeny, suggesting that plastome data alone is not sufficient for species tree estimation. Our results suggest that using hundreds of nuclear markers (i.e. 354) will significantly improve the Lecythidaceae species tree. The framework described here will be useful, generally, for developing markers for species tree inference.

Evolutionary history of tropical tree species complexes: species delimitation and adaptive genetic variation in the Brazil nut clade (Lecythidaceae). European Conference of Tropical Ecology (GTOE2018)

Hybridization and patterns of adaptive genetic variation in tropical trees of the Bertholletia clade (Lecythidaceae) in French Guiana. Meeting of the German Society for Tropical Ecology (GTOE2017)

Is homoploid hybrid speciation that rare? An empiricist’s view

Background and Aims The recurrence of wildfires is predicted to increase due to global climate change, resulting in severe impacts on biodiversity and ecosystem functioning. Recurrent fires can drive plant adaptation and reduce genetic diversity; however, the underlying population genetic processes have not been studied in detail. In this study, the neutral and adaptive evolutionary effects of contrasting fire regimes were examined in the keystone tree species Pinus halepensis Mill. (Aleppo pine), a fire-adapted conifer. The genetic diversity, demographic history and spatial genetic structure were assessed at local (within-population) and regional scales for populations exposed to different crown fire frequencies. Methods Eight natural P. halepensis stands were sampled in the east of the Iberian Peninsula, five of them in a region exposed to frequent crown fires (HiFi) and three of them in an adjacent region with a low frequency of crown fires (LoFi). Samples were genotyped at nine neutral simple sequence repeats (SSRs) and at 251 single nucleotide polymorphisms (SNPs) from coding regions, some of them potentially important for fire adaptation. Key Results Fire regime had no effects on genetic diversity or demographic history. Three high-differentiation outlier SNPs were identified between HiFi and LoFi stands, suggesting fire-related selection at the regional scale. At the local scale, fine-scale spatial genetic structure (SGS) was overall weak as expected for a wind-pollinated and wind-dispersed tree species. HiFi stands displayed a stronger SGS than LoFi stands at SNPs, which probably reflected the simultaneous post-fire recruitment of co-dispersed related seeds. SNPs with exceptionally strong SGS, a proxy for microenvironmental selection, were only reliably identified under the HiFi regime. Conclusions An increasing fire frequency as predicted due to global change can promote increased SGS with stronger family structures and alter natural selection in P. halepensis and in plants with similar life history traits., This work was supported by the following projects financed by the Spanish Ministry of Science and Innovation (MICINN) VAMPIRO [CGL2008-05289-C02-01/02], LinkTree [EUI200-03713] under the ERAnet-BiodivERsA call, TREVOL [CGL2012-39938-C02-00/01] and AFFLORA [CGL2012-40129-C02-02], a PhD scholarship to K.B.B. [FPI: BES-2009-015443] and a ‘Ramón y Cajal’ fellowship [RYC2009-04537] to M.H. G.G.V. was also supported by the Italian MIUR project ‘Biodiversitalia’ [RBAP10A2T4]. M.H. acknowledges a Marie-Curie Intra-European fellowship [PIEF-GA-2012-329088] and research funding from the Research Council of Norway [203822/E40]

The analysis of fine-scale spatial genetic structure (FSGS) within populations can provide insights into eco-evolutionary processes. Restricted dispersal and locally occurring genetic drift are the primary causes for FSGS at equilibrium, as described in the isolation by distance (IBD) model. Beyond IBD expectations, spatial, environmental or historical factors can affect FSGS. We examined FSGS in seven African and Neotropical populations of the late-successional rain forest tree Symphonia globulifera L. f. (Clusiaceae) to discriminate the influence of drift-dispersal vs. landscape/ecological features and historical processes on FSGS. We used spatial principal component analysis and Bayesian clustering to assess spatial genetic heterogeneity at SSRs and examined its association with plastid DNA and habitat features. African populations (from Cameroon and São Tomé) displayed a stronger FSGS than Neotropical populations at both marker types (mean Sp = 0.025 vs. Sp = 0.008 at SSRs) and had a stronger spatial genetic heterogeneity. All three African populations occurred in pronounced altitudinal gradients, possibly restricting animal-mediated seed dispersal. Cyto-nuclear disequilibria in Cameroonian populations also suggested a legacy of biogeographic history to explain these genetic patterns. Conversely, Neotropical populations exhibited a weaker FSGS, which may reflect more efficient wide-ranging seed dispersal by Neotropical bats and other dispersers. The population from French Guiana displayed an association of plastid haplotypes with two morphotypes characterized by differential habitat preferences. Our results highlight the importance of the microenvironment for eco-evolutionary processes within persistent tropical tree populations., SCOPUS: ar.j, info:eu-repo/semantics/published

National audience

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

International audience

Understanding the drivers of population divergence, speciation and species persistence is of great interest to molecular ecology, especially for species-rich radiations inhabiting the world's biodiversity hotspots. The toolbox of population genomics holds great promise for addressing these key issues, especially if genomic data are analysed within a spatially and ecologically explicit context. We have studied the earliest stages of the divergence continuum in the Restionaceae, a species-rich and ecologically important plant family of the Cape Floristic Region (CFR) of South Africa, using the widespread CFR endemic Restio capensis (L.) H.P. Linder & C.R. Hardy as an example. We studied diverging populations of this morphotaxon for plastid DNA sequences and >14 400 nuclear DNA polymorphisms from Restriction site Associated DNA (RAD) sequencing and analysed the results jointly with spatial, climatic and phytogeographic data, using a Bayesian generalized linear mixed modelling (GLMM) approach. The results indicate that population divergence across the extreme environmental mosaic of the CFR is mostly driven by isolation by environment (IBE) rather than isolation by distance (IBD) for both neutral and non-neutral markers, consistent with genome hitchhiking or coupling effects during early stages of divergence. Mixed modelling of plastid DNA and single divergent outlier loci from a Bayesian genome scan confirmed the predominant role of climate and pointed to additional drivers of divergence, such as drift and ecological agents of selection captured by phytogeographic zones. Our study demonstrates the usefulness of population genomics for disentangling the effects of IBD and IBE along the divergence continuum often found in species radiations across heterogeneous ecological landscapes.

Understanding the history of forests and their species' demographic responses to past disturbances is important for predicting impacts of future environmental changes. Tropical rainforests of the Guineo-Congolian region in Central Africa are believed to have survived the Pleistocene glacial periods in a few major refugia, essentially centred on mountainous regions close to the Atlantic Ocean. We tested this hypothesis by investigating the phylogeographic structure of a widespread, ancient rainforest tree species, Symphonia globulifera L. f. (Clusiaceae), using plastid DNA sequences (chloroplast DNA [cpDNA], psbA-trnH intergenic spacer) and nuclear microsatellites (simple sequence repeats, SSRs). SSRs identified four gene pools located in Benin, West Cameroon, South Cameroon and Gabon, and São Tomé. This structure was also apparent at cpDNA. Approximate Bayesian Computation detected recent bottlenecks approximately dated to the last glacial maximum in Benin, West Cameroon and São Tomé, and an older bottleneck in South Cameroon and Gabon, suggesting a genetic effect of Pleistocene cycles of forest contraction. CpDNA haplotype distribution indicated wide-ranging long-term persistence of S. globulifera both inside and outside of postulated forest refugia. Pollen flow was four times greater than that of seed in South Cameroon and Gabon, which probably enabled rapid population recovery after bottlenecks. Furthermore, our study suggested ecotypic differentiation - coastal or swamp vs terra firme - in S. globulifera. Comparison with other tree phylogeographic studies in Central Africa highlighted the relevance of species-specific responses to environmental change in forest trees. © 2013 Macmillan Publishers Limited All rights reserved.

Premise of the study New insights into the history of the African rainforest can be gathered from the phylogeographic structures of their constituent species, but few studies have been performed in this ecosystem. We studied the phylogeographic structure of Santiria trimera, a primate- and bird-dispersed, dioecious tree typical of mature African rainforests. Methods We sequenced three chloroplast DNA (cpDNA) regions (trnL-F, rbcL, and rpl36-infA-rps8) in 377 individuals from 42 populations. Results Sequence chromatograms regularly displayed double peaks of unequal heights. Cloning of PCR products and sequencing of outgroup taxa led to assigning the taller peak in ambiguous sequence positions to cpDNA. A total of 14 polymorphic cpDNA sites and 12 haplotypes were detected. Populations from three distinct biogeographic regions, namely, Upper Guinea, Lower Guinea, and the volcanic island of S ã o Tom é, did not share any haplotype, indicating allopatric divergence. In Lower Guinea, Gabonese forests had high diversity mainly from the sympatry of two genetically divergent morphotypes, whereas forests of eastern Cameroon were less diversified. The two haplotypes of the morphotype without stilt roots were distributed north and south of the Ogoou é River, suggesting refuges on both sides of the river bed. Conclusions The divergence between Upper and Lower Guinean rainforests is explained by the discontinuity of forest between those regions throughout most of the Quaternary. The distribution of rare endemic haplotypes concurred with proposed Pleistocene rainforest refuges in west and southwest Cameroon. Overall, phylogeographic structure is consistent with the biogeographic hypotheses largely based on patterns of species diversity. © 2011 Botanical Society of America.

International audience; Background and aims Species delimitation remains a difficult task in many groups of organisms. Even widespread and conspicuous tropical trees make no exception. Santiria trimera, an African rainforest tree, displays substantial morphological variability. While classical analysis of historical herbarium samples lead to the recognition of a single species, two morphotypes of S. trimera are regularly collected in Gabon and Equatorial Guinea, sometimes in sympatry: one form with stilt roots (SR) and another form without stilt roots (NSR). Methods To assess whether these forms constitute distinct taxa and to understand evolutionary processes within African Santiria, we combined a morphological and a spatial analysis of both sympatric morphotypes in northern Gabon with a phylogenetic analysis of samples from West and Central Africa, including the island of Sao Tome. Key results In Gabon, morphological traits, chloroplast DNA (cpDNA) and nuclear DNA (nuDNA) sequences congruently lead to the recognition of two well differentiated and reproductively isolated taxa corresponding to SR and NSR morphotypes. However, rare cases of the SR morphotype bearing DNA sequences typical of NSR individuals suggest that hybridization might sometimes occur. No evidence for habitat specialization of the two taxa was found. DNA sequences from Sao Tome formed monophyletic clades at both marker types and the nuDNA gene tree suggests that the Sao Tome population probably originated from Central Africa and subsequently underwent allopatric differentiation from continental populations. Conclusion In Central Africa, S. trimera is composed of at least two distinct sympatric species following the Biological Species Concept and calls for further morphological and phenological studies and experimental crosses between them to specify their taxonomic status. Our results also show that classical taxonomic species delimitation may not always be congruent with the Biological Species Concept, calling for more population-based in situ morphological and molecular genetic analyses.

International audience; The impact of the Pleistocene climate oscillations on the structure of biodiversity in tropical regions remains poorly understood. In this study, the forest refuge theory is examined at the molecular level in Milicia excelsa, a dioecious tree with a continuous range throughout tropical Africa. Eight nuclear microsatellites (nSSRs) and two sequences and one microsatellite from chloroplast DNA (cpDNA) showed a deep divide between samples from Benin and those from Lower Guinea. This suggests that these populations were isolated in separate geographical regions, probably for several glacial cycles of the Pleistocene, and that the nuclear gene pools were not homogenized despite M. excelsa's wind-pollination syndrome. The divide could also be related to seed dispersal patterns, which should be largely determined by the migration behaviour of M. excelsa's main seed disperser, the frugivorous bat Eidolon helvum. Within Lower Guinea, a north-south divide, observed with both marker types despite weak genetic structure (nSSRs: F(ST) = 0.035, cpDNA: G(ST) = 0.506), suggested the existence of separate Pleistocene refugia in Cameroon and the Gabon/Congo region. We inferred a pollen-to-seed dispersal distance ratio of c.1.8, consistent with wide-ranging gene dispersal by both wind and bats. Simulations in an Approximate Bayesian Computation framework suggested low nSSR and cpDNA mutation rates, but imprecise estimates of other demographic parameters, probably due to a substantial gene flow between the Lower Guinean gene pools. The decline of genetic diversity detected in some Gabonese populations could be a consequence of the relatively recent establishment of a closed canopy forest, which could negatively affect M. excelsa's reproductive system.

International audience; Many tropical forest tree species have broad geographic ranges, and fossil records indicate that population disjunctions in some species were established millions of years ago. Here we relate biogeographic history to patterns of population differentiation, mutational and demographic processes in the widespread rainforest tree Symphonia globulifera using ribosomal (ITS) and chloroplast DNA sequences and nuclear microsatellite (nSSR) loci. Fossil records document sweepstakes dispersal origins of Neotropical S. globulifera populations from Africa during the Miocene. Despite historical long-distance gene flow, nSSR differentiation across 13 populations from Costa Rica, Panama, Ecuador (east and west of Andes) and French Guiana was pronounced (F(ST)= 0.14, R(ST)= 0.39, P < 0.001) and allele-size mutations contributed significantly (R(ST) > F(ST)) to the divergences between cis- and trans-Andean populations. Both DNA sequence and nSSR data reflect contrasting demographic histories in lower Mesoamerica and Amazonia. Amazon populations show weak phylogeographic structure and deviation from drift-mutation equilibrium indicating recent population expansion. In Mesoamerica, genetic drift was strong and contributed to marked differentiation among populations. The genetic structure of S. globulifera contains fingerprints of drift-dispersal processes and phylogeographic footprints of geological uplifts and sweepstakes dispersal.

International audience; We assessed the outcrossing rate of sorghum landraces sampled in situ from two fields under traditional cultivation in north-western Morocco using genotypic data from five microsatellite loci. Assuming a mixed mating model, we estimated outcrossing parameters by two methods that are based on progeny analyses. With both methods, the multilocus estimate of outcrossing rate for the overall sample was in the order of 0.1, meaning that sorghum landraces are predominantly autogamous, but with a significant proportion of outcrossing. The estimated outcrossing rate is about two times higher in field 1 (tm= 0.161) than in field 2 (tm= 0.069). This difference could be explained by distinct morphological characteristics of the inflorescence in the two fields, with predominance of loose panicles in field 1 and of very compact panicles in field 2. The distribution of outcrossing rate among progeny families showed that 30% of them were completely self-fertilized but some families showed substantial outcrossing. These results are at odds with the very low genetic differentiation observed previously among Moroccan landraces and suggest that morphological differences are maintained despite gene flow through seed exchanges among farmers.

The mutation process at microsatellite loci typically occurs at high rates and with stepwise changes in allele sizes, features that may introduce bias when using classical measures of population differentiation based on allele identity (e.g., FST, Nei’s Ds genetic distance). Allele size-based measures of differentiation, assuming a stepwise mutation process [e.g., Slatkin’s RST, Goldstein et al.’s (δμ)2], may better reflect differentiation at microsatellite loci, but they suffer high sampling variance. The relative efficiency of allele size- vs. allele identity-based statistics depends on the relative contributions of mutations vs. drift to population differentiation. We present a simple test based on a randomization procedure of allele sizes to determine whether stepwise-like mutations contributed to genetic differentiation. This test can be applied to any microsatellite data set designed to assess population differentiation and can be interpreted as testing whether FST = RST. Computer simulations show that the test efficiently identifies which of FST or RST estimates has the lowest mean square error. A significant test, implying that RST performs better than FST, is obtained when the mutation rate, μ, for a stepwise mutation process is (a) ≥ m in an island model (m being the migration rate among populations) or (b) ≥ 1/t in the case of isolated populations (t being the number of generations since population divergence). The test also informs on the efficiency of other statistics used in phylogenetical reconstruction [e.g., Ds and (δμ)2], a nonsignificant test meaning that allele identity-based statistics perform better than allele size-based ones. This test can also provide insights into the evolutionary history of populations, revealing, for example, phylogeographic patterns, as illustrated by applying it on three published data sets.

International audience; Spatial genetic structure was analysed with five highly polymorphic microsatellite loci in a Romanian population of common ash (Fraxinus excelsior L.), a wind-pollinated and wind-dispersed tree species occurring in mixed deciduous forests over almost all of Europe. Contributions of seed and pollen dispersal to total gene flow were investigated by analysing the pattern of decrease in kinship coefficients among pairs of individuals with geographical distance and comparing it with simulation results. Plots of kinship against the logarithm of distance were decomposed into a slope and a shape component. Simulations showed that the slope is informative about the global level of gene flow, in agreement with theoretical expectations, whereas the shape component was correlated with the relative importance of seed vs. pollen dispersal. Hence, our results indicate that insights into the relative contributions of seed and pollen dispersal to overall gene flow can be gained from details of the pattern of spatial genetic structure at biparentally inherited loci. In common ash, the slope provided an estimate of total gene dispersal in terms of Wright's neighbourhood size of Nb = 519 individuals. No precise estimate of seed vs. pollen flow could be obtained from the shape because of the stochasticity inherent to the data, but the parameter combinations that best fitted the data indicated restricted seed flow, sigmas pound 14 m, and moderate pollen flow, 70 m pound sigmap pound 140 m.

Climate change is modifying the distribution ranges of species worldwide. To better understand and more realistically predict future species ranges, it is critical to account for local adaptation and phenotypic plasticity in populations’ responses to climate. This is challenging, however, because local adaptation and phenotypic plasticity are trait dependent and because traits co-vary along climatic gradients across the range, with differential consequences for fitness. One way to address this challenge is to build models with empirical data from large-scale common-garden experiments such as those that have been established in past decades for some forest tree species. This thesis used individual measurements of several fitness-related phenotypic traits (vertical and radial tree growth, spring and autumn leaf phenology and recruit mortality) of European beech (Fagus sylvatica L.) recorded in the frame of BeechCOSTe52, the largest network of tree phenotypic traits measured in common gardens throughout Europe (>150,000 trees) for modeling the species’ likely response to recent climate change. Specifically, I pursued the following objectives: (i) to quantify range-wide variation and co-variation of local adaptation and phenotypic plasticity for four major phenotypic traits related to fitness (vertical growth, radial growth, survival, and leaf flushing phenology), and to project its species range under current and future climate based on this information (chapter 1); (ii) to quantify variation among populations in spring and autumn leaf phenology and the resulting growing season length, and to predict their patterns at the range-wide scale under current and future climate (chapter 2); and (iii) to quantify phenotypic plasticity at different development stages for vertical growth, radial growth, survival, and spring and autumn leaf flushing phenology, and to determine the extent to which inter-annual climate variation during the 20th century is related to variation in phenotypic plasticity across the species range (chapter 3). After setting up the required databases, I performed different types of linear mixed-effect models that related trait variation and co-variation to local adaptation (i.e., trait variation related to the climate of the planted populations’ origin) and phenotypic plasticity (i.e., trait variation related to the climate of plantation site). Finally, I calculated a phenotypic plasticity index for populations based on their reaction norms (i.e., the shape or specific form of the phenotypic response to the environment of an individual or genotype). My results revealed that: (i) the contribution of plasticity to intra-specific trait variation is always higher than that of local adaptation, suggesting that beech is less sensitive to (moderate) climate change than previously reported; (ii) different traits and underlying climatic drivers constrain beech populations in different parts of the species range; (iii) considering trait co-variation improves predictions based on single traits; (iv) growing season length will increase under climate change in northern beech provenances but shrink in populations from the core and the southern range; (v) northern beech populations show high phenotypic plasticity for the investigated traits; and (vi) phenotypic plasticity tends to increase with age in growth-related traits. My results underline that population responses to climate across large geographical gradients are trait-dependent, suggesting that a complete set of fitness-related traits is required to fully understand species sensitivity to climate change., Le changement climatique modifie l'aire de répartition des espèces dans le monde. Pour mieux comprendre et prévoir de façon plus réaliste les aires de répartition futures des espèces, il est essentiel de tenir compte de l'adaptation locale et de la plasticité phénotypique dans les réponses des populations au changement climatique. C'est un défi, cependant, parce que l'adaptation locale et la plasticité phénotypique dépendent des caractères et parce que les caractères varient le long des gradients climatiques dans toute la gamme, avec des conséquences différentes pour la condition physique. C'est un défi, cependant, parce que l'adaptation locale et la plasticité phénotypique dépendent des caractères et parce que les caractères varient le long des gradients climatiques dans toute la gamme, avec des conséquences différentes pour la valeur adaptative. Une façon de relever ce défi consiste à construire des modèles à partir de données empiriques issues d'expériences à grande échelle sur les jardins communs, comme celles qui ont été réalisées au cours des dernières décennies pour certaines essences forestières. Cette thèse a utilisé des mesures individuelles de plusieurs caractères phénotypiques liés à la valeur adaptative (croissance verticale et radiale des arbres, phénologie foliaire printanière et automnale et mortalité) du hêtre européen (Fagus sylvatica L.) enregistrés dans le cadre du projet BeechCOSTe52, le plus grand réseau de caractères phénotypiques d'arbres mesurés dans des jardins communs à travers l'Europe (>150 000 arbres) pour modéliser la réponse probable de l'espèce au changement climatique récent. Plus précisément, j'ai poursuivi les objectifs suivants (i) quantifier la variation et la covariation à l'échelle de l'aire de répartition de l'adaptation locale et de la plasticité phénotypique pour quatre caractères phénotypiques majeurs liés à la valeur adaptative (croissance verticale, croissance radiale, survie et phénologie des feuilles au printemps), et de projeter son aire de répartition dans le climat actuel et futur en fonction de cette information (chapitre 1) ; (ii) quantifier les variations entre les populations en ce qui concerne la phénologie foliaire printanière et automnale et la durée de la période de végétation qui en résulte, et prévoir leurs tendances à l'échelle de l'aire de répartition sous le climat actuel et futur (chapitre 2) ; et (iii) quantifier la plasticité phénotypique à différents stades de développement pour la croissance verticale, la croissance radiale, la survie et la phénologie des feuilles au printemps et à l'automne, et déterminer dans quelle mesure la variation climatique interannuelle au cours du 20e siècle est liée à la variation de la plasticité phénotypique dans l'aire de répartition des espèces (chapitre 3). Après avoir mis en place les bases de données requises, j'ai réalisé différents types de modèles linéaires à effets mixtes qui relient la variation et la covariation des caractères à l'adaptation locale (c'est-à-dire la variation des caractères liée au climat d'origine des populations plantées) et la plasticité phénotypique (c'est-à-dire la variation des caractères liée au climat du site de plantation). Finalement, j'ai calculé un indice de plasticité phénotypique pour les populations en fonction de leurs normes de réaction (la forme spécifique de la réponse phénotypique à l'environnement d'un individu ou du génotype). Mes résultats l'ont révélé : [... )