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The early-branching clades of Fabaceae subfamily Papilionoideae are characterized by their remarkable lability in floral architecture. In contrast, more derived papilionoid lineages are marked by evolutionary conservatism towards strongly bilateral, papilionate flowers. Here, we show an unexpected example of conservatism of a unique floral architecture during the early diversification history of the papilionoids. We built the most comprehensively sampled molecular phylogenetic tree with a focus on the early-diverging papilionoid Dipterygeae clade to evaluate conservatism of the winged papilionate architecture and associated traits related to flower specialization (e.g. zygomorphy, petal differentiation, stable stamen number and stamen sheath). Dipterygeae comprise c. 22 species of mostly giant trees from across tropical forests in Central America and the Amazon, but they are also ecologically dominant in the savannas of the Brazilian Central Plateau. Phylogenetic analyses of nuclear ribosomal ITS/5.8S and plastid matK and trnL intron sequences strongly supported inter-relationships and the monophyly of each genus (Dipteryx, Monopteryx, Pterodon and Taralea). Bayesian relaxed-clock dating and a Bayesian model of ancestral character estimation revealed c. 30 Myr of conservatism of all winged papilionate-related flower traits in a clade comprising the most recent common ancestor of Dipteryx, Pterodon and Taralea, but lability in fruit morphology during the diversification of the entire Dipterygeae clade. Despite Monopteryx and remaining Dipterygeae being florally discrepant, they are collectively defined by a floral synapomorphy that is unique among all papilionoid Fabaceae: the highly differentiated calyx, where the two upper lobes are enlarged and wing-like, whereas the other three lower lobes are reduced. We suggest that the different dispersal strategies and the ancient winged papilionate floral conservatism in Dipterygeae, which has maintained effective ecological interactions with specialized pollinators and ensured the protection of young flower buds and developing fruits, may explain successful evolutionary and ecological persistence of the clade across the main Neotropical biomes.

Mutation, the source of genetic diversity, is the raw material of evolution; however, the mutation process remains understudied, especially in plants. Using both a simulation and reanalysis framework, we set out to explore and demonstrate the improved performance of variant callers developed for cancer research compared to single nucleotide polymorphism (SNP) callers in detecting de novo somatic mutations.In anin silicoexperiment, we generated Illumina-like sequence reads spiked with simulated mutations at different allelic fractions to compare the performance of seven commonly-used variant callers to recall them. More empirically, we then reanalyzed two of the largest datasets available for plants, both developed for identifying within-individual variation in long-lived pedunculate oaks.Based on thein silicoexperiment, variant callers developed for cancer research outperform SNP callers regarding plant mutation recall and precision, especially at low allele frequency. Such variants at low allelic fractions are typically expected for within-individual de novo plant mutations, which initially appear in single cells. Reanalysis of published oak data with Strelka2, the best-performing caller based on our simulations, identified up to 3.4x more candidate somatic mutations than reported in the original studies.Our results advocate the use of cancer research callers to boost de novo mutation research in plants, and to reconcile empirical reports with theoretical expectations.This version of the article has been peer-reviewed and recommended byPeer Community in Genomicshttps://doi.org/10.24072/pci.genomics.100024

Tropical forest dynamics are driven by growth and survival strategies of tree species in relation to treefall gaps; however, the ecological and evolutionary roles of intraspecific variation in the response to forest gaps remain unexplored. Here, we associated genomic data of three related tree species of the genus Symphonia in a French Guiana forest with (1) each individual tree's growth potential, and (2) with its light and competition environment estimated based on 33 years of forest monitoring in plots covering 120 ha. We show that individual trees within species have genetically determined growth strategies that are adapted to the local light and competition environments, which are shaped by the time since the last treefall. Within species, fast-growing genotypes are more frequent in light-enriched environments and slow-growing genotypes in more shaded environments. Forest gap dynamics is thus a strong selection driver that shapes adaptive strategies and maintains genetic variation within tropical tree species.

Made available in DSpace on 2019-10-06T15:52:58Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-01-01 Illegal logging and trade of timber are major worldwide concerns, resulting in biodiversity and economic losses. Tropical tree species in the genus Cedrela, which have historically been heavily exploited, are still often illegally traded and there is an urgent need to develop tools to verify the origin of Cedrela products. A set of 351 SNP loci for Cedrela species from Bolivia, Brazil, Costa Rica, Cuba, Ecuador, French Guiana, Mexico, and Peru was developed using restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing, and adapted for MassARRAY genotyping. After screening of 94 individuals covering most of the distribution of Cedrela, a final set of 136 SNP loci which included 92 nuclear SNPs, 22 chloroplast markers (20 SNPs and 2 INDELs), and 22 mitochondrial markers (19 SNPs and 3 INDELs) was selected and tested for potential to verify Cedrela timber origin. Carrera de Ingeniería Forestal Laboratorio de Dendrocronología Facultad de Ciencias Agrícolas Universidad Autónoma Gabriel René Moreno, Km 9 carretera al Norte, El Vallecito Thünen Institute of Forest Genetics, Sieker Landstrasse 2 Instituto de Investigaciones de la Amazonía Peruana (IIAP), Av. José A. Quiñones km 2.5 Instituto Florestal de São Paulo, CP 1322 Faculdade de Engenharia Universidade Estadual Paulista (Unesp) INRA UMR0745 EcoFoG AgroParisTech Cirad CNRS Université des Antilles Université de Guyane, Campus Agronomique, Avenue de France Centre for Ecology & Hydrology Edinburgh, Bush Estate Faculdade de Engenharia Universidade Estadual Paulista (Unesp)

Among ants, Myrmicinae represents the most speciose subfamily. The venom composition previously described for these social insects is extremely variable, with alkaloids predominant in some genera while, conversely, proteomics studies have revealed that some myrmicine ant venoms are peptide-rich. Using integrated transcriptomic and proteomic approaches, we characterized the venom peptidomes of six ants belonging to the different tribes of Myrmicinae. We identified a total of 79 myrmicitoxins precursors which can be classified into 38 peptide families according to their mature sequences. Myrmicine ant venom peptidomes showed heterogeneous compositions, with linear and disulfide-bonded monomers as well as dimeric toxins. Several peptide families were exclusive to a single venom whereas some were retrieved in multiple species. A hierarchical clustering analysis of precursor signal sequences led us to divide the myrmicitoxins precursors into eight families, including some that have already been described in other aculeate hymenoptera such as secapin-like peptides and voltage-gated sodium channel (Na

Marine sponges are known for their antimicrobial, antifungal, and cytotoxic activity. In this study, the activity of aqueous and ethanoic extracts of 3 sponges from Martinique were tested on 5 bacterial strains: Bascillus cereus (CIP 783), Echerichia coli (CIP 54127), Pseudomonas aeruginosa (CIP A22), Staphylococcus aureus (CIP 67.8) and Staphylococcus saprophyticus (CIP 76125). The antimicrobial activity of Agelas clathrodes, Desmapsamma anchorata, and Verongula rigida, was demonstrated using the disc diffusion method and by determining the minimum inhibitory concentration and the minimum bactericidal concentration. The ethanoic extract of Agelas clathrodes had an inhibitory activity specifically on Staphylococcus aureus and Staphylococcus saprophyticus. No activity was observed for the other extracts. Further chemical analyses will be carried out in order to identify the active molecules of these sponges.

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.

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.

Made available in DSpace on 2021-06-25T12:22:16Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-06-01 German Federal Ministry of Food and Agriculture (BMEL) by the LargeScale-project (Forderkennzeichen) Programa Nacional de Innovacion para la Competitividad y Productividad (Innovate Peru) Conseil Regional d'Aquitaine European Union, FEDER Investissements d'avenir Dipteryx timber has been heavily exploited in South America since 2000s due to the increasing international demand for hardwood. Developing tools for the genetic identification of Dipteryx species and their geographical origin can help to promote legal trading of timber. A collection of 800 individual trees, belonging to 6 different Dipteryx species, was genotyped based on 171 molecular markers. After the exclusion of markers out of Hardy Weinberg equilibrium or with no polymorphism or low amplification, 83 nuclear, 29 chloroplast, 13 mitochondrial single nucleotide polymorphisms (SNPs), and 2 chloroplast and 5 mitochondrial INDELS remained. Six genetic groups were identified using Bayesian Structure analyses of the nuclear SNPs, which corresponded to the different Dipteryx species collected in the field. Seventeen highly informative markers were identified as suitable for species identification and obtained self-assignment success rates to species level of 78-96%. An additional set of 15 molecular markers was selected to determine the different genetic clusters found in Dipteryx odorata and Dipteryx ferrea, obtaining self-assignment success rates of 91-100%. The success to assign samples to the correct country of origin using all or only the informative markers improved when using the nearest neighbor approach (69-92%) compared to the Bayesian approach (33-80%). While nuclear and chloroplast SNPs were more suitable for differentiating the different Dipteryx species, mitochondrial SNPs were ideal for determining the genetic clusters of D. odorata and D. ferrea. These 32 selected SNPs will be invaluable genetic tools for the accurate identification of species and country of origin of Dipteryx timber. Inst Invest Amazonia Peruana IIAP, Av Jose A Quinones Km 2-5, Iquitos, Peru Thunen Inst Forest Genet, Sieker Landstr 2, D-22927 Grosshansdorf, Germany Inst Florestal Sao Paulo, CP 1322, BR-01059970 Sao Paulo, SP, Brazil Univ Estadual Paulista, Fac Engn Ilha Solteira, Dept Fitotecnia, Ilha Solteira, SP, Brazil Univ Autonoma Gabriel Rene Moreno, Fac Ciencias Agr, Lab Dendrocronol, Carrera Ingn Forestal, Km 9 Carretera Norte, El Vallecito, Santa Cruz, Bolivia Univ Guyane, Univ Antilles, CNRS, INRA,UMR0745,EcoFoG,AgroParisTech,Cirad, Campus Agron,Ave France,BP97387, Kourou, France Univ Bordeaux, INRAE, BIOGECO, F-33610 Cestas, France Escola Nacl Bot Trop, Rua Pacheco Leao 2040, BR-22460030 Rio De Janeiro, RJ, Brazil Inst Pesquisas Jardim Bot Rio de Janeiro, Rua Pacheco Leao 915, BR-22460030 Rio De Janeiro, RJ, Brazil Univ Fed Bahia, Inst Biol, Rua Barao de Jeremoabo S-N, BR-40170115 Salvador, BA, Brazil Univ Estadual Paulista, Fac Engn Ilha Solteira, Dept Fitotecnia, Ilha Solteira, SP, Brazil German Federal Ministry of Food and Agriculture (BMEL) by the LargeScale-project (Forderkennzeichen): 281-001-01 Programa Nacional de Innovacion para la Competitividad y Productividad (Innovate Peru): 381-PNICP-PIAP-2014 Conseil Regional d'Aquitaine: 20030304002FA Conseil Regional d'Aquitaine: 20040305003FA European Union, FEDER: 2003227 Investissements d'avenir: ANR-10-EQPX-16-01 Investissements d'avenir: CEBA: ANR-10-LABX-25-01

Bacteria living on the cuticle of ants are generally studied for their protective role against pathogens, especially in the clade of fungus-growing ants. However, little is known regarding the diversity of cuticular bacteria in other ant host species, as well as the mechanisms leading to the composition of these communities. Here, we used 16S rRNA gene amplicon sequencing to study the influence of host species, species interactions and the pool of bacteria from the environment on the assembly of cuticular bacterial communities on two phylogenetically distant Amazonian ant species that frequently nest together inside the roots system of epiphytic plants, Camponotus femoratus and Crematogaster levior. Our results show that (a) the vast majority of the bacterial community on the cuticle is shared with the nest, suggesting that most bacteria on the cuticle are acquired through environmental acquisition, (b) 5.2% and 2.0% of operational taxonomic units (OTUs) are respectively specific to Ca. femoratus and Cr. levior, probably representing their respective core cuticular bacterial community, and (c) 3.6% of OTUs are shared between the two ant species. Additionally, mass spectrometry metabolomics analysis of metabolites on the cuticle of ants, which excludes the detection of cuticular hydrocarbons produced by the host, were conducted to evaluate correlations among bacterial OTUs and m/z ion mass. Although some positive and negative correlations are found, the cuticular chemical composition was weakly species-specific, suggesting that cuticular bacterial communities are prominently environmentally acquired. Overall, our results suggest the environment is the dominant source of bacteria found on the cuticle of ants.

There is a high international demand for timber from the genus Dipteryx, or “shihuahuaco” as it is known in Peru. Developing tools that allow the identification and discrimination of Dipteryx species is therefore important for supporting management of natural populations and to underpin legal trade of its timber. The objective of this study was the molecular characterization of Dipteryx species in the Peruvian Amazonia. Two plastid regions (cpDNA: trnH–psbA and matK) were sequenced and 11 microsatellite markers (nDNA) were genotyped for 32 individuals identified as Dipteryx charapilla, D. micrantha morphotype 1 and D. micrantha morphotype 2. Using the concatenated sequences of the plastid genes, we identified ten haplotypes that were not shared between the species or between the D. micrantha morphotypes. Haplotypic diversity was greater in D. micrantha morphotype 2 and D. charapilla than in D. micrantha morphotype 1, which presented only one haplotype with a wide distribution in Peru. The microsatellites allowed the discrimination of the same three clades and identified diagnostic alleles for each clade. These results allowed us to demonstrate that the two morphotypes of D. micrantha are different at both the plastid and nuclear markers, which supports the existence of three genetically distinct species in Peru. This study provides information for the genetic discrimination of Dipteryx species and emphasises the importance of conserving the genetic variability of this genus in the Peruvian Amazonia. Programa Nacional de Innovación para la Competitividad y Productividad Innóvate-Perú (contrato 381-PNICP-PIAP-2014); German Federal Ministry of Food and Agriculture (BMEL, Large Scale Project, Grant 28I-001-01) Revisión por pares.

International audience; Tropical forests shelter the highest species diversity worldwide, although genus diversity is lower than expected. In the species-rich genera, species complexes are composed of closely-related species that share large amounts of genetic variation. Despite the key role of species complexes in diversification, evolution and functioning of ecological communities, little is known on why species complexes arise and how they are maintained in Neotropical forests. Examining how individual phenotypes vary along environmental gradients, within and among closely-related species within species complexes, can reveal processes allowing species coexistence within species complexes. We examined leaf functional trait variation with topography in a hyperdiverse tropical forest of the Guiana Shield. We collected leaf functional traits from 766 trees belonging to five species in two species complexes in permanent plots encompassing a diversity of topographic positions. We tested the role of topography on leaf functional trait variation with a hierarchical Bayesian model, controlling for individual tree diameter effect. We show that, mirroring what has been previously observed among species and communities, individual leaf traits covary from acquisitive to conservative strategy within species. Moreover, decreasing wetness from bottomlands to plateaus was associated with a shift of leaf traits from an acquisitive to a conservative strategy both across and within closely-related species. Our results suggest that intraspecific trait variability widens species' niches and converges at species' margins where niches overlap, potentially implying local neutral processes. Intraspecific trait variability favors local adaptation and divergence of closely-related species within species complexes. It is potentially maintained through interspecific sharing of genetic variation through hybridization.

Trait-environment relationships have been described at the community level across tree species. However, whether interspecific trait-environment relationships are consistent at the intraspecific level is yet unknown. Moreover, we do not know how consistent is the response between organ vs. whole-tree level.We examined phenotypic variability for 16 functional leaf (dimensions, nutrient, chlorophyll) and wood traits (density) across two soil types, Ferralitic Soil (FS) vs. White Sands (WS), on two sites for 70 adult trees of Cecropia obtusa Trécul (Urticaceae) in French Guiana. Cecropia is a widespread pioneer Neotropical genus that generally dominates early successional forest stages. To understand how soil types impact resource-use through the processes of growth and branching, we examined the architectural development with a retrospective analysis of growth trajectories. We expect soil types to affect both, functional traits in relation to resource acquisition strategy as already described at the interspecific level, and growth strategies due to resource limitations with reduced growth on poor soils.Functional traits were not involved in the soil response, as only two traits-leaf residual water content and K content-showed significant differences across soil types. Soil effects were stronger on growth trajectories, with WS trees having the slowest growth trajectories and less numerous branches across their lifespan.The analysis of growth trajectories based on architectural analysis improved our ability to characterise the response of trees with soil types. The intraspecific variability is higher for growth trajectories than functional traits for C. obtusa, revealing the complementarity of the architectural approach with the functional approach to gain insights on the way trees manage their resources over their lifetime. Soil-related responses of Cecropia functional traits are not the same as those at the interspecific level, suggesting that the effects of the acting ecological processes are different between the two levels. Apart from soil differences, much variation was found across sites, which calls for further investigation of the factors shaping growth trajectories in tropical forests.

Made available in DSpace on 2019-10-04T12:40:45Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-09-01 German Federal Ministry of Food and Agriculture (BMEL) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Investissements d'Avenir, Convention attributive d'aide EquipEx Xyloforest European Union, FEDER We developed nuclear and chloroplastic single nucleotide polymorphism (SNP) and INDEL (insertion/deletion) markers using restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing to set up a genetic tracking method of the geographical origin of Hymenaea sp. From two initial sets of 358 and 32 loci used to genotype at least 94 individuals, a final set of 75 nSNPs, 50 cpSNPs and 6 INDELs identifying significant population structure was developed. Univ Sao Paulo, Luiz de Queiroz Coll Agr, Dept Forest Sci, Ave Padua Dias,11,POB 9, BR-13418900 Sao Paulo, Brazil Thunen Inst Forest Genet, Sieker Landstr 2, D-22927 Grosshansdorf, Germany Inst Florestal Sao Paulo, CP 1322, BR-01059970 Sao Paulo, SP, Brazil Univ Autonoma Gabriel Rene Moreno, Fac Ciencias Agr, Lab Dendrocronol, Carrera Ingn Forestal, Km 9 Carretera Norte, El Vallecito, Santa Cruz, Bolivia IIAP, LBGM, Ave Jose A Quinones Km 2-5, Iquitos, Peru Univ Guyane, Univ Antilles, CNRS, INRA,UMR0745 EcoFoG,AgroParisTech,Cirad, Campus Agron,Ave France,BP97387, Kourou, France Univ Bordeaux, INRA, BIOGECO, 69 Route Arcachon, F-33610 Cestas, France Univ Estadual Paulista, Dept Fitotecnia, Fac Engn Ilha Solteira, Ilha Solteira, SP, Brazil Univ Estadual Paulista, Dept Fitotecnia, Fac Engn Ilha Solteira, Ilha Solteira, SP, Brazil Investissements d'Avenir, Convention attributive d'aide EquipEx Xyloforest: ANR-10-EQPX-16-01 European Union, FEDER: ANR-10-EQPX-16-01 European Union, FEDER: 2003227 European Union, FEDER: ANR-10-LABX-25-01

Made available in DSpace on 2019-10-04T12:40:46Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-09-01 German Federal Ministry of Food and Agriculture Conseil Regional d'Aquitaine European Union FEDER Investissements d'avenir Nuclear and plastidial single nucleotide polymorphism (SNP) and INDEL markers were developed using restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing for population genetics and timber tracking purposes in the Neotropical timber species Jacaranda copaia. We used 407 nuclear SNPs, 29 chloroplast, and 31 mitochondrial loci to genotype 92 individuals from Brazil, Bolivia, French Guiana, and Peru. Based on high amplification rates and genetic differentiation among populations, 113 nuclear SNPs, 11 chloroplast, and 4 mitochondrial loci were selected, and their use validated for genetic tracking of timber origin. Inst Florestal Sao Paulo, CP 1322, BR-01059970 Sao Paulo, SP, Brazil Thunen Inst Forest Genet, Sieker Landstr 2, D-22927 Grosshansdorf, Germany Univ Estadual Paulista, Fac Engn Ilha Solteira, Dept Fitotecnia, Ilha Solteira, SP, Brazil Univ Autonoma Gabriel Rene Moreno, Fac Ciencias Agr, Lab Dendrocronol, Carrera Ingn Forestal, Km 9 Carretera Norte, El Vallecito, Santa Cruz, Bolivia IIAP, Ave Jose A Quinones Km 2-5, Iquitos, Peru Univ Guyane, Univ Antilles, CNRS, INRA,UMR0745 EcoFoG,AgroParisTech,Cirad, Campus Agron,Ave France,BP97387, Kourou, France Univ Bordeaux, INRA, BIOGECO, F-33610 Cestas, France Univ Estadual Paulista, Fac Engn Ilha Solteira, Dept Fitotecnia, Ilha Solteira, SP, Brazil Conseil Regional d'Aquitaine: 20030304002FA Conseil Regional d'Aquitaine: 20040305003FA FEDER: 2003227 Investissements d'avenir: ANR-10-EQPX-16-01 Investissements d'avenir: CEBA: ANR-10-LABX-25-01 : 001-2016-SERFOR-DGGSPFFS-DGSPF

Made available in DSpace on 2019-10-06T15:45:24Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-09-15 Bundesministerium für Ernährung und Landwirtschaft Conseil Régional Aquitaine Agence Nationale de la Recherche Low coverage MiSeq genome sequencing and restriction associated DNA sequencing (RADseq) were used to identify nuclear and plastid SNP and INDEL genetic markers in Carapa guianensis. 261 genetic markers including 237 nuclear SNPs, 22 plastid SNPs, and 2 plastid INDELs are described based on 96 genotyped individuals from French Guiana, Brazil, Peru, and Bolivia. The best 117 SNPs for identifying population structure and performing individual assignment are assembled into four multiplexes for MassARRAY genotyping. INRA UMR0745 EcoFoG AgroParisTech Cirad CNRS Université des Antilles Université de Guyane, Campus Agronomique, Avenue de France Thünen Institute of Forest Genetics, Sieker Landstrasse 2 School of Natural Sciences and Engineering São Paulo State University (UNESP) Carrera de Ingeniería Forestal Laboratorio de Dendrocronología Facultad de Ciencias Agrícolas Universidad Autónoma Gabriel René Moreno, Km 9 carretera al Norte, El Vallecito Instituto de Investigaciones de la Amazonía Peruana (IIAP), Av. José A. Quiñones km 2.5 Instituto Florestal de São Paulo, CP 1322 BIOGECO INRA University Bordeaux School of Natural Sciences and Engineering São Paulo State University (UNESP) Conseil Régional Aquitaine: 20030304002FA Conseil Régional Aquitaine: 20040305003FA Agence Nationale de la Recherche: ANR-10-EQPX-16-01 Agence Nationale de la Recherche: ANR-10-LABX-25-01

Made available in DSpace on 2019-10-04T12:40:45Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-09-01 German Federal Ministry of Food and Agriculture (BMEL) Programa Nacional de Innovacion para la Competitividad y Productividad Conseil Regional d'Aquitaine European Union, FEDER We developed nuclear and plastid single nucleotide polymorphism (SNP) and insertion/deletion (INDEL) markers for Dipteryx species using a combination of restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing. Of the total 315 loci genotyped using a MassARRAY platform, 292 loci were variable and polymorphic among the 73 sampled individuals from French Guiana, Brasil, Peru, and Bolivia. A final set of 56 nuclear SNPs, 26 chloroplast SNPs, 2 chloroplast INDELs, and 32 mitochondrial SNPs identifying significant population structure was developed. This set of loci will be useful for studies on population genetics of Dipteryx species in Amazonia. IIAP, Ave Jose A Quinones Km 2-5, Iquitos, Peru Thunen Inst Forest Genet, Sieker Landstr 2, D-22927 Grosshansdorf, Germany Inst Florestal Sao Paulo, CP 1322, BR-01059970 Sao Paulo, SP, Brazil Univ Estadual Paulista, Fac Engn Ilha Solteira, Dept Fitotecnia, Ilha Solteira, SP, Brazil Univ Autonoma Gabriel Rene Moreno, Fac Ciencias Agr, Lab Dendrocronol, Carrera Ingn Forestal, Km 9 Carretera Norte, El Vallecito, Santa Cruz, Bolivia Univ Guyane, Univ Antilles, CNRS, INRA,UMR0745 EcoFoG,AgroParisTech,Cirad, Campus Agron,Ave France,BP97387, Kourou, France INRA, Plateforme Genome Transcriptome Bordeaux, Site Pierroton Batiment Artiga,69 Route Arcachon, F-33610 Cestas, France Univ Estadual Paulista, Fac Engn Ilha Solteira, Dept Fitotecnia, Ilha Solteira, SP, Brazil Programa Nacional de Innovacion para la Competitividad y Productividad: 381-PNICP-PIAP-2014 Conseil Regional d'Aquitaine: 20030304002FA Conseil Regional d'Aquitaine: 20040305003FA European Union, FEDER: 2003227 European Union, FEDER: ANR-10-EQPX-16-01 European Union, FEDER: ANR-10-LABX-25-01

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.

Understanding the key drivers of population connectivity in the marine environment is essential for the effective management of natural resources. Although several different approaches to evaluating connectivity have been used, they are rarely integrated quantitatively. Here, we use a ‘seascape genetics’ approach, by combining oceanographic modelling and microsatellite analyses, to understand the dominant influences on the population genetic structure of two Antarctic fishes with contrasting life histories, Champsocephalus gunnari and Notothenia rossii. The close accord between the model projections and empirical genetic structure demonstrated that passive dispersal during the planktonic early life stages is the dominant influence on patterns and extent of genetic structuring in both species. The shorter planktonic phase of C. gunnari restricts direct transport of larvae between distant populations, leading to stronger regional differentiation. By contrast, geographic distance did not affect differentiation in N. rossii, whose longer larval period promotes long‐distance dispersal. Interannual variability in oceanographic flows strongly influenced the projected genetic structure, suggesting that shifts in circulation patterns due to climate change are likely to impact future genetic connectivity and opportunities for local adaptation, resilience and recovery from perturbations. Further development of realistic climate models is required to fully assess such potential impacts.

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)

Made available in DSpace on 2019-10-04T12:34:45Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-12-01 German Federal Ministry of Food and Agriculture Conseil Regional d'Aquitaine European Union, FEDER Investissements d'avenir Chico Mendes Biodiversity Institute A combination of restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing was used for the development of single nucleotide polymorphisms (SNP) and INDEL (insertion/deletions) genetic markers for Ipe (Handroanthus sp.). Of the 402 putative loci identified, 389 SNPs and INDELs (315 nuclear SPNs, six chloroplast INDELs, 15 chloroplast SNPs, 12 mitochondrial INDELs and 41 mitochondrial SNPs) were successfully genotyped at 93 individuals from Brazil, Bolivia and French Guiana using a - MassARRAY (R) iPLEX (TM) platform. This set of markers will be invaluable for population genetics, phylogeography and DNA fingerprinting studies. Univ Estadual Paulista, Dept Fitotecnia Tecnol Alimentos & Socioecon, Fac Engn Ilha Solteira, Ilha Solteira, SP, Brazil Thunen Inst Forest Genet, Sieker Landstr 2, D-22927 Grosshansdorf, Germany Univ Autonoma Gabriel Rene Moreno, Fac Ciencias Agr, Carrera Ingn Forestal, Lab Dendrocronol, Km 6 Carretera Norte, El Vallecito, Santa Cruz, Bolivia Univ Guyane, Univ Antilles, INRA, UMR0745 EcoFoG,AgroParisTech,Cirad,CNRS, Campus Agron,Ave France,BP97387, Kourou, France Inst Florestal Sao Paulo, CP 1322, BR-01059970 Sao Paulo, SP, Brazil INRA Pierroton, Plateforme Genome Transcriptome Bordeaux, 69 Route Arcachon, F-33610 Cestas, France Univ Estadual Paulista, Dept Fitotecnia Tecnol Alimentos & Socioecon, Fac Engn Ilha Solteira, Ilha Solteira, SP, Brazil Conseil Regional d'Aquitaine: 20030304002FA Conseil Regional d'Aquitaine: 20040305003FA European Union, FEDER: 2003227 Investissements d'avenir: ANR-10-EQPX-16-01 Investissements d'avenir: CEBA: ANR-10-LABX-25-01 Chico Mendes Biodiversity Institute: 47960 Chico Mendes Biodiversity Institute: 49369

Understanding characteristics, causes and consequences of biodiversity is a fundamental challenge in ecology and evolution. Biodiversity presents three nested levels, from individuals, over species, to ecosystems. Intraspecific variability affects the individual level of biodiversity. High levels of intraspecific variability, notably in ecologically important traits has been reported. Intraspecific variability is shaped by the interaction between (1) genetic variability, (2) environmental heterogeneity and (3) stochastic factors. However, we still know little about the effects of this variability on population dynamics, species interactions and ecosystem processes. Interestingly though, variability at the level of genotypes and traits has been suggested to promote local adaptation of populations and to promote species coexistence at the community level, thus suggesting a role for this variability in the origin and maintenance of biodiversity. We here present the conceptual framework of the recently started PhD thesis of S. Schmitt. The main objective of the thesis is to further explore the genotype-environment interactions in shaping the intraspecific trait variability of biodiversity. The study site for the thesis is the lowland rainforest in the research station of Paracou, French Guiana, where detailed inventory and tree growth data, as well as environmental characterization are available. We specifically wish to consider the intraspecific genomic variability as a continuum within structured populations of closely related species, and measure its role on individual tree performance through growth over time, while accounting for effects of a finely-characterized environment at the abiotic and biotic level. Eventually, we expect to help building a theory of community ecology starting with individuals, because interactions with environment is based at the individual level.

International audience; Deforestation-reinforced by illegal logging-is a serious problem in many tropical regions and causes pervasive environmental and economic damage. Existing laws that intend to reduce illegal logging need efficient, fraud resistant control methods. We developed a genetic reference database for Jatoba (Hymenaea courbaril), an important, high value timber species from the Neotropics. The data set can be used for controls on declarations of wood origin. Samples from 308 Hymenaea trees from 12 locations in Brazil, Bolivia, Peru, and French Guiana have been collected and genotyped on 10 nuclear microsatellites (nSSRs), 13 chloroplast SNPs (cpSNP), and 1 chloroplast indel marker. The chloroplast gene markers have been developed using Illumina DNA sequencing. Bayesian cluster analysis divided the individuals based on the nSSRs into 8 genetic groups. Using self-assignment tests, the power of the genetic reference database to judge on declarations on the location has been tested for 3 different assignment methods. We observed a strong genetic differentiation among locations leading to high and reliable self-assignment rates for the locations between 50% to 100% (average of 88%). Although all 3 assignment methods came up with similar mean self-assignment rates, there were differences for some locations linked to the level of genetic diversity, differentiation, and heterozygosity. Our results show that the nuclear and chloroplast gene markers are effective to be used for a genetic certification system and can provide national and international authorities with a robust tool to confirm legality of timber.

International audience; High-throughput sequencing of the 16S rRNA gene has considerably helped revealing the essential role of bacteria living on insect cuticles in the ecophysiology and behaviour of their hosts. However, our understanding of host-cuticular microbiota feedbacks remains hampered by the difficulties of working with low bacterial DNA quantities as with individual insect cuticle samples, which are more prone to molecular biases and contaminations. Herein, we conducted a methodological benchmark on the cuticular bacterial loads retrieved from two Neotropical ant species of different body size and ecology: Atta cephalotes (similar to 15mm) and Pseudomyrmex penetrator (similar to 5mm). We evaluated the richness and composition of the cuticular microbiota, as well as the amount of biases and contamination produced by four DNA extraction protocols. We also addressed how bacterial community characteristics would be affected by the number of individuals or individual body size used for DNA extraction. Most extraction methods yielded similar results in terms of bacterial diversity and composition for A.cephalotes (similar to 15mm). In contrast, greater amounts of artefactual sequences and contaminations, as well as noticeable differences in bacterial community characteristics were observed between extraction methods for P.penetrator (similar to 5mm). We also found that large (similar to 15mm) and small (similar to 5mm) A.cephalotes individuals harbour different bacterial communities. Our benchmark suggests that cuticular microbiota of single individual insects can be reliably retrieved provided that blank controls, appropriate data cleaning, and individual body size and functional role within insect society are considered in the experiment.

Microgeographic adaptation in tree stands. ATBC 2016

Dab (Limanda limanda) are the principal target fish species in offshore biomonitoring programmes in the UK; however, detailed knowledge of genetic structure and connectivity among sampling locations is unavailable. Here, the isolation and characterization of 30 polymorphic microsatellite loci for dab is described. The number of alleles per locus ranged from 2 to 42, with observed heterozygosities ranging from 0.089 to 1. These loci will enable high resolution of genetic population structure and dynamics of dab around the British Isles.

The European flounder (Platichthys flesus L.) is used in ecotoxicological studies to provide detailed information on the effects of pollution on individual fish. Data on population and evolutionary level effects are, however, limited. Here, the isolation and characterization of 28 novel species specific microsatellite loci are presented. The number of alleles ranged from 8 to 38, and observed heterozygosity from 0.542 to 1.

Genetic structure of Hylesia metabus (Lepidoptera: Saturniidae), moths responsible for lepidopterism outbreaks in French Guiana and Venezuela. . ICE 2016; XXV International Congress of Entomology

Bioindicators are species for which some quantifiable aspect of its biology, a biomarker, is assumed to be sensitive to ecosystem health. However, there is frequently a lack of information on the underlying genetic and environmental drivers shaping the spatiotemporal variance in prevalence of the biomarkers employed. Here, we explore the relative role of potential variables influencing the spatiotemporal prevalence of biomarkers in dab, Limanda limanda, a species used as a bioindicator of marine contaminants. Firstly, the spatiotemporal genetic structure of dab around UK waters (39 samples across 15 sites for four years: 2005-2008) is evaluated with 16 microsatellites. Two temporally stable groups are identified corresponding to the North and Irish Seas (average between basin [Formula: see text] = 0.007; [Formula: see text] = 0.022). Secondly, we examine the association between biomarker prevalence and several variables, including genetic structuring, age and contaminant exposure. Genetic structure had significant interactive effects, together with age and some contaminants, in the prevalence of some of the biomarkers considered, namely hyperpigmentation and liver lesions. The integration of these data sets enhanced our understanding of the relationship between biomarker prevalence, exposure to contaminants and population-specific response, thereby yielding more informative predictive models of response and prospects for environmental remediation.

Indicator taxa are commonly used to identify priority areas for conservation or to measure biological responses to environmental change. Despite their widespread use, there is no general consensus about the ability of indicator taxa to predict wider trends in biodiversity. Many studies have focused on large-scale patterns of species co-occurrence to identify areas of high biodiversity, threat or endemism, but there is much less information about patterns of species co-occurrence at local scales. In this study, we assess fine-scale co-occurrence patterns of three indicator taxa (epiphytic ferns, leaf litter frogs and dung beetles) across a remotely sensed gradient of human disturbance in the Ecuadorian Amazon. We measure the relative contribution of rare and common species to patterns of total richness in each taxon and determine the ability of common and rare species to act as surrogate measures of human disturbance and each other. We find that the species richness of indicator taxa changed across the human disturbance gradient but that the response differed among taxa, and between rare and common species. Although we find several patterns of co-occurrence, these patterns differed between common and rare species. Despite showing complex patterns of species co-occurrence, our results suggest that species or taxa can act as reliable indicators of each other but that this relationship must be established and not assumed. © 2012 Oldekop et al.

Stock heterogeneity was investigated in albacore tuna (Thunnus alalunga, Bonnaterre 1788), a commercially important species in the North Atlantic Ocean and Mediterranean Sea. Twelve polymorphic microsatellite loci were examined in 581 albacore tuna from nine locations, four in the north-east Atlantic Ocean (NEA), three in the Mediterranean Sea (MED) and two in the south-western Pacific Ocean (SWP). Maximum numbers of alleles per locus ranged from 9 to 38 (sample mean, 5.2-22.6 per locus; overall mean, 14.2 +/- 0.47 SE), and observed heterozygosities per locus ranged from 0.44 to 1.00 (overall mean: 0.79 +/- 0.19 SE). Significant deficits of heterozygotes were observed in 20% of tests. Multilocus F-ST values were observed ranging from 0.00 to Theta = 0.036 and Theta' = 0.253, with a mean of Theta = 0.013 and Theta' = 0.079. Pairwise F-ST values showed that the SWP, NEA and MED stocks were significantly distinct from one another, thus corroborating findings in previous studies based on mitochondrial DNA, nuclear DNA (other than microsatellites) and allozyme analyses. Heterogeneity was observed for the first time between samples within the Mediterranean Sea. GENELAND indicated the potential presence of three populations across the NEA and two separate populations in the Mediterranean Sea. Observed genetic structure may be related to migration patterns and timing of movements of subpopulations to the feeding grounds in either summer or autumn. We suggest that a more intensive survey be conducted throughout the entire fishing season to ratify or refute the currently accepted genetic homogeneity within the NEA albacore stock.

The genus Hylesia (Lepidoptera Saturniidae) are moths of human health importance in Venezula and French Guiana, inducing epidemic outbreaks of lepidopterism, a puriginous dermatitis caused by the urticating properties of the females’ abdominal setae. Adult female releases extremely urticating setae in the surrounding air, causing itchy dermatitis known as ‘papillonite’. Hylesia are attracted by artificial light source which are increasing since the end of the 19th century due to urbanization resulting in serious invasion event in towns and villages. Despite of the impact on human health, many aspects of the biology and their ecology remain unclear. The definition of specific methods of population regulation is thus very urgent but it was necessary first of all to verify that only the species H. metabus is involved in these episodes of urtication and to specify the population structure of these insects. It was also important to clarify the mechanisms for recognizing sexual partners in this same species. These questions were the mainobjectives of this thesis.The use of molecular tools has shown that a single species, Hylesia metabus, was involved in recent episodes ofurtication in Guyana and Venezuela. The study also demonstrated that the Guyanese populations of this species aregenetically distinct from the Venezuelan populations, and especially that they are structured in 2 distinct genetic subgroupsbetween the coast and the interior of French Guiana. All insects collected during outbreaks belonged to thecoastal subset. An approach based on the study of reproductive behavior has been used to clarify the temporality ofemission of the sex pheromone and opens new perspectives for the identification of this pheromone; Les pullulations de « papillon cendre » du genre Hylesia, appartenant à la famille des Saturniidae, constituent un problème récurrent de santé publique en Guyane et au Venezuela. En effet, pour protéger ses oeufs des prédateurs, la femelle possède des soies détachables extrêmement urticantes qu’elle est susceptible de libérer dans l’atmosphère. L’augmentation des sources de lumière artificielle depuis la fin du 19ème siècle liée à l’urbanisation croissante attire ces papillons nocturnes vers les villes et les villages, où la libération des soies urticantes est susceptible d’affecter l’Homme en générant une douloureuse affection de peau, la « papillonite ». Malgré les enjeux sociaux et économiques liés à la présence récurrente de ces papillons en zones urbaines, leur biologie et leur écologie reste peu connue. Les pullulations de « papillon cendre » attribuées à l’espèce H. metabus constituent un problème récurrent de santé publique en Guyane et au Venezuela. La définition de méthodes spécifiques de régulation des populations s’avère donc très urgente mais nécessitait au préalable de vérifier que seule l’espèce H. metabus est impliquée dans ces épisodes d’urtication et de préciser la structure des populations de ces insectes. Il était également important de préciser les mécanismes de reconnaissance des partenaires sexuels chez cette même espèce. Ces questions ont été les objectifs principaux de cette thèse. L’utilisation d’outils moléculaires a permis de montrer que seule l’espèce Hylesia metabus était impliquée dans les récents épisodes d’urtication en Guyane et au Venezuela. L’étude a également démontré que les populations guyanaises de cette espèce se distinguaient au plan génétique des populations du Vénézuela, et surtout qu’elles se structuraient en 2 sousensembles génétiques distincts entre la côte et l’intérieur de la Guyane. Tous les insectes collectés durant les épisodes de pullulation appartenaient au sous-ensemble côtier. Une approche basée sur l’étude du comportement de reproduction a été utilisée afin de préciser la temporalité d’émission de la phéromone sexuelle et ouvre de nouvelles perspectives pour l’identification de cette phéromone.

Tropical forests shelter the highest species diversity worldwide, a fact that remains partly unexplained and the origin of which is subject to debate. Even at the hectare-scale, tropical forests shelter species-rich genera with closely-related tree species coexisting in sympatry. Due to phylogenetic constraints, closely related species are expected to have similar niches and functional strategies, which raises questions on the mechanisms of their local coexistence. Closely related species may form a species complex, defined as morphologically similar species that share large amounts of genetic variation due to recent common ancestry and hybridization, and that can result from ecological adaptive radiation of species segregating along environmental gradients. Despite the key role of species complexes in Neotropical forest ecology, diversification, and evolution, little is known of the eco-evolutionary forces creating and maintaining diversity within Neotropical species complexes. We explored the intraspecific genomic variability as a continuum within structured populations of closely related species, and measured its role on individual tree performance through growth over time, while accounting for effects of a finely-characterized environment at the abiotic and biotic level. Combining tree inventories, LiDAR-derived topographic data, leaf functional traits, and gene capture data in the research station of Paracou, French Guiana, we used population genomics, environmental association analyses, genome-wide association studies and Bayesian modelling on the tree species complexes Symphonia and Eschweilera clade Parvifolia. We showed that the species complexes of Neotropical trees cover all local gradients of topography and competition and are therefore widespread in the study site whereas most of the species within them exhibit pervasive niche differentiation along these same gradients. Specifically, in the species complexes Symphonia and Eschweilera clade Parvifolia, the decrease in water availability due to higher topographic position, e.g., from bottomlands to plateaus, has led to a change in leaf functional traits from acquisitive strategies to conservative strategies, both among and within species. Symphonia species are genetically adapted to the distribution of water and nutrients, hence they coexist locally through exploiting a broad gradient of local habitats. Conversely, Eschweilera species are differentially adapted to soil chemistry and avoid the wettest, hydromorphic habitats. Last but not least, individual tree genotypes of Symphonia species are differentially adapted to regenerate and thrive in response to the fine spatio-temporal dynamics of forest gaps with divergent adaptive growth strategies along successional niches. Consequently, topography and the dynamics of forest gaps drive fine-scale spatio-temporal adaptations of individuals within and among distinct but genetically connected species within the species complexes Symphonia and Eschweilera clade Parvifolia. Fine-scale topography drives genetic divergence and niche differentiation with genetic adaptations among species, while forest gap dynamics maintains genetic diversity with divergent adaptive strategies within species. I suggest that adaptations of tree species and individuals to topography and dynamics of forest gaps promote coexistence within and among species within species complexes, and perhaps among mature forest tree species outside species complexes. Overall, I defend the primordial role of individuals within species in tropical forest diversity, suggesting that we should develop a theory of community ecology starting with individuals, because interactions with environments happen after all at the individual level.; Les forêts tropicales abritent la plus grande diversité d'espèces au monde, un fait qui reste en partie inexpliqué et dont l'origine est sujette à débat. Même à l'échelle de l'hectare, les forêts tropicales abritent des genres riches en espèces, avec des espèces d’arbres étroitement apparentées qui coexistent en sympatrie. En raison de contraintes phylogénétiques, on s'attend à ce que les espèces étroitement apparentées possèdent des niches et des stratégies fonctionnelles similaires, ce qui questionne les mécanismes de leur coexistence locale. Les espèces étroitement apparentées peuvent former un complexe d'espèces, composé d’espèces morphologiquement similaires ou qui partagent une importante proportion de leur variabilité génétique en raison d'une ascendance commune récente ou d'hybridation, et qui peut résulter d'une radiation écologique adaptative des espèces selon des gradients environnementaux. Malgré le rôle clé des complexes d'espèces dans l'écologie, la diversification et l'évolution des forêts néotropicales, les forces éco-évolutives qui créent et maintiennent la diversité au sein des complexes d'espèces néotropicales restent peu connues. Nous avons exploré la variabilité génétique intraspécifique comme un continuum au sein de populations structurées d'espèces étroitement apparentées, et mesuré son rôle sur la performance individuelle des arbres à travers la croissance dans le temps, tout en tenant compte des effets d'un environnement finement caractérisé au niveau abiotique et biotique. En combinant des inventaires forestiers, des données topographiques, des traits fonctionnels foliaires et des données de capture de gènes dans la station de recherche de Paracou, en Guyane Française, nous avons utilisé la génomique des populations, les analyses d'associations environnementales et génomiques, et la modélisation Bayésienne sur les complexes d'espèces Symphonia et Eschweilera clade Parvifolia. Nous avons montré que les complexes d'espèces d'arbres couvrent l’ensemble des gradients locaux de topographie et de compétition présents dans le site d'étude alors que la plupart des espèces qui les composent présentent une différenciation de niche marquée le long de ces mêmes gradients. Plus précisément, dans les complexes d'espèces étudiés, la diminution de la disponibilité en eau, par exemple depuis les bas-fonds jusqu’aux plateaux, a entraîné une modification des traits fonctionnels foliaires, depuis des stratégies d'acquisition à des stratégies conservatrices, tant entre les espèces qu'au sein de celles-ci. Les espèces de Symphonia sont génétiquement adaptées à la distribution de l'eau et des nutriments, elles coexistent donc localement en exploitant un large gradient d'habitats locaux. Inversement, les espèces d'Eschweilera sont différentiellement adaptées à la chimie du sol et évitent les habitats les plus humides et hydromorphes. Enfin, les génotypes individuels des espèces de Symphonia sont différentiellement adaptés pour se régénérer et croître en réponse à la fine dynamique spatio-temporelle des trouées forestières, avec des stratégies adaptatives de croissance divergentes le long des niches de succession. Par conséquent, la topographie et la dynamique des trouées forestières entraînent des adaptations spatio-temporelles à fine échelle des individus au sein et entre les espèces des complexes d'espèces Symphonia et Eschweilera. Je suggère que les adaptations à la topographie et à la dynamique des trouées forestières favorisent la coexistence des individus au sein et entre les espèces des complexes d'espèces, et peut-être plus généralement entre les espèces d'arbres de forêts matures. Dans l'ensemble, je soutiens le rôle primordial des individus au sein des espèces dans la diversité des forêts tropicales, et suggère que nous devrions élaborer une théorie de l'écologie des communautés en commençant par les individus, car les interactions avec les environnements se produisent après tout au niveau de l’individu.