E. Allié, R. Pélissier, J. Engel, P. Petronelli, V. Freycon et al., Pervasive local-scale tree-soil habitat association in a tropical forest community, PLoS One, vol.10, issue.11, p.141488, 2015.

A. Antonelli and I. Sanmartín, Why are there so many plant species in the Neotropics?, Taxon, vol.60, issue.2, pp.403-414, 2011.

G. Arellano, V. Cala, and M. J. Macía, Niche breadth of oligarchic species in Amazonian and Andean rain forests, Journal of Vegetation Science, vol.25, issue.6, pp.1355-1366, 2014.

G. Arellano, P. M. Jørgensen, A. F. Fuentes, M. I. Loza, V. Torrez et al., Oligarchic patterns in tropical forests: role of the spatial extent, environmental heterogeneity and diversity, Journal of Biogeography, vol.43, issue.3, pp.616-626, 2016.

C. Baraloto, O. J. Hardy, C. E. Paine, K. G. Dexter, C. Cruaud et al., Using functional traits and phylogenetic trees to examine the assembly of tropical tree communities, Journal of Ecology, vol.100, issue.3, pp.690-701, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01032423

W. Barthlott, A. Hostert, G. Kier, W. Küper, H. Kreft et al., Geographic patterns of vascular plant diversity at continental to global scales (Geographische Muster der Gefäßpflanzenvielfalt im kontinentalen und globalen Maßstab), Erdkunde, vol.61, issue.4, pp.305-315, 2007.

. Heuertz, Genetic species delimitation in Eschweilera

D. P. Buckley, D. M. O'malley, V. Apsit, G. T. Prance, and K. S. Bawa, Lecythidaceae): I. Genetic variation in natural populations, Berhollelia excelsa Humb. & Bonpl, vol.76, issue.6, pp.923-928, 1988.

H. Caron, J. Molino, D. Sabatier, P. Léger, P. Chaumeil et al., Chloroplast DNA variation in a hyperdiverse tropical tree community, Ecology and Evolution, vol.9, issue.8, pp.4897-4905, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02108230

B. C. Carstens, T. A. Pelletier, N. M. Reid, and J. D. Satler, How to fail at species delimitation, Molecular Ecology, vol.22, issue.17, pp.4369-4383, 2013.

S. Cavers, A. Telford, F. Cruz, A. J. Pérez-castañeda, R. Valencia et al., Cryptic species and phylogeographical structure in the tree Cedrela odorata L. throughout the Neotropics, Journal of Biogeography, vol.40, issue.4, pp.732-746, 2013.

B. Charlesworth, Effective population size and patterns of molecular evolution and variation, Nature Reviews Genetics, vol.10, pp.195-210, 2009.

L. V. Clark and M. Jasieniuk, POLYSAT: an R package for polyploid microsatellite analysis, Molecular Ecology Resources, vol.11, issue.3, pp.562-566, 2011.

K. Daïnou, C. Blanc-jolivet, B. Degen, P. Kimani, D. Ndiade-bourobou et al., Revealing hidden species diversity in closely related species using nuclear SNPs, SSRs and DNA sequences -a case study in the tree genus Milicia, BMC Evolutionary Biology, vol.16, p.259, 2016.

L. R. De-barros, L. H. De-oliveira-wadt, M. Mondin, . G. Pappas-junior, R. T. Rocha et al., Draft genome assembly of the tropical tree Bertholletia excelsa using long-read sequence data, XXV IUFRO World Congress, vol.39, p.201902043, 2019.

J. H. Degnan and N. A. Rosenberg, Gene tree discordance, phylogenetic inference and the multispecies coalescent, Trends in Ecology & Evolution, vol.24, issue.6, pp.332-340, 2009.

J. Dole?el, J. Greilhuber, S. Lucretti, A. Meister, M. A. Lysák et al., Plant genome size estimation by flow cytometry: interlaboratory comparison, Annals of Botany, vol.82, pp.17-26, 1998.

D. Queiroz and K. , Species concepts and species delimitation, Systematic Biology, vol.56, issue.6, pp.879-886, 2007.

J. Doyle and J. L. Doyle, Genomic plant DNA preparation from fresh tissue-CTAB method, Phytochemical Bulletin, vol.19, issue.1, pp.11-15, 1987.

J. Duminil and M. Di-michele, Plant species delimitation: a comparison of morphological and molecular markers, Plant Biosystems, vol.143, issue.3, pp.528-542, 2009.

J. Duminil, H. Caron, I. Scotti, S. Cazal, and R. J. Petit, Blind population genetics survey of tropical rainforest trees, Molecular Ecology, vol.15, issue.12, pp.3505-3513, 2006.
URL : https://hal.archives-ouvertes.fr/hal-01031226

J. Duminil, M. Heuertz, J. Doucet, N. Bourland, C. Cruaud et al., CpD-NA-based species identification and phylogeography: application to African tropical tree species, Molecular Ecology, vol.19, issue.24, pp.5469-5483, 2010.

J. Duminil, D. Kenfack, V. Viscosi, L. Grumiau, and O. J. Hardy, Testing species delimitation in sympatric species complexes: the case of an African tropical tree, Carapa spp. (Meliaceae), Molecular Phylogenetics and Evolution, vol.62, issue.1, pp.275-285, 2012.

D. A. Earl and B. M. , STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method, Conservation Genetics Resources, vol.4, pp.359-361, 2012.

W. L. Eiserhardt, T. L. Couvreur, and W. J. Baker, Plant phylogeny as a window on the evolution of hyperdiversity in the tropical rainforest biome, New Phytologist, vol.214, issue.4, pp.1408-1422, 2017.

G. Evanno, S. Regnaut, and J. Goudet, Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study, Molecular Ecology, vol.14, issue.8, pp.2611-2620, 2005.

D. Falush, M. Stephens, and J. K. Pritchard, Inference of population structure using multilocus genotype data: dominant markers and null alleles, Molecular Ecology Notes, vol.7, issue.4, pp.574-578, 2007.

V. Funk, T. Hollowell, P. Berry, C. Kelloff, and S. N. Alexander, Checklist of the Plants of the Guiana Shield (Venezuela: Amazonas, 2007.

S. Guyana and F. Guiana, Contributions from the United States National Herbarium, vol.55

D. W. Galbraith, K. R. Harkins, J. M. Maddox, N. M. Ayres, D. P. Sharma et al., Rapid flow cytometric analysis of the cell cycle in intact plant tissues, Science, vol.220, issue.4601, pp.1049-1051, 1983.

A. H. Gentry, Neotropical floristic diversity: phytogeographical connections between Central and South America, Pleistocene climatic fluctuations, or an accident of the Andean orogeny?, Annals of the Missouri Botanical Garden, vol.69, issue.3, pp.557-593, 1982.

M. A. Gonzalez, C. Baraloto, J. Engel, S. A. Mori, P. Pétronelli et al., Identification of Amazonian trees with DNA barcodes, PloS One, vol.4, 2009.
URL : https://hal.archives-ouvertes.fr/hal-01086775

Z. A. Goodwin, D. J. Harris, D. Filer, J. R. Wood, and R. W. Scotland, Widespread mistaken identity in tropical plant collections, Current Biology, vol.25, issue.22, pp.1066-1067, 2015.

D. Grivet, J. Climent, M. Zabal-aguirre, D. B. Neale, G. G. Vendramin et al., Adaptive evolution of Mediterranean pines, Molecular Phylogenetics and Evolution, vol.68, issue.3, pp.555-566, 2013.

E. Guichoux, P. Garnier-géré, L. Lagache, T. Lang, C. Boury et al., Outlier loci highlight the direction of introgression in oaks, Molecular Ecology, vol.22, issue.2, pp.450-462, 2013.

O. J. Hardy, Population genetics of autopolyploids under a mixed mating model and the estimation of selfing rate, Molecular Ecology Resources, vol.16, issue.1, pp.103-117, 2016.

O. J. Hardy and X. Vekemans, Spagedi: a versatile computer program to analyse spatial genetic structure at the individual, 2002.

, Pl. Ecol. Evol, vol.153, issue.1, p.2020

, Molecular Ecology Notes, vol.2, issue.4, pp.618-620

O. J. Hardy, K. Dainou, A. Donkpegan, J. Duminil, E. Ewedje et al., Are we underestimating the number of plant species in the tropics? New insights from population genetics approaches applied on African forest trees, Scientific abstracts from the 7 th International Barcode of Life Conference, vol.60, p.942, 2017.

D. Hartl, A primer of population genetics. 3 rd Ed. Sunderland, 2000.

S. Hoban, J. A. Arntzen, M. W. Bruford, J. A. Godoy, R. Hoelzel et al., Comparative evaluation of potential indicators and temporal sampling protocols for monitoring genetic erosion, Evolutionary Applications, vol.7, issue.9, pp.984-998, 2014.

A. A. Hoffmann, C. M. Sgrò, and T. N. Kristensen, Revisiting adaptive potential, population size, and conservation, Trends in Ecology & Evolution, vol.32, issue.7, pp.506-517, 2017.

X. Huang and A. Madan, CAP3: A DNA sequence assembly program, Genome Research, vol.9, p.868, 1999.

Y. Huang, S. A. Mori, and L. M. Kelly, Toward a phylogeneticbased generic classification of Neotropical Lecythidaceae -I. Status of Bertholletia, Corythophora, Eschweilera and Lecythis, Phytotaxa, vol.203, pp.85-121, 2015.

T. Jombart, adegenet: a R package for the multivariate analysis of genetic markers, Bioinformatics, vol.24, issue.11, pp.1403-1405, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00428105

N. A. Joshi and J. N. Fass, Sickle: a sliding-window, adaptive, quality-based trimming tool for FastQ files, 2011.

S. T. Kalinowski, The computer program STRUCTURE does not reliably identify the main genetic clusters within species: simulations and implications for human population structure, Heredity, vol.106, pp.625-632, 2011.

L. L. Knowles and B. C. Carstens, Delimiting species without monophyletic gene trees, Systematic Biology, vol.56, issue.6, pp.887-895, 2007.

N. M. Kopelman, J. Mayzel, M. Jakobsson, N. A. Rosenberg, and I. Mayrose, Clumpak: a program for identifying clustering modes and packaging population structure inferences across K, Molecular Ecology Resources, vol.15, issue.5, pp.1179-1191, 2015.

R. R. Kowal, Chromosome numbers of Asteranthos and the putatively related Lecythidaceae, Brittonia, vol.41, pp.131-135, 1989.

R. R. Kowal, S. A. Mori, and J. A. Kallunki, Chromosome numbers of Panamanian Lecythidaceae and their use in subfamilial classification, Brittonia, vol.29, p.399, 1977.

C. Levis, F. R. Costa, F. Bongers, M. Peña-claros, C. R. Clement et al., Persistent effects of pre-Columbian plant domestication on Amazonian forest composition, Science, vol.355, issue.6328, pp.925-931, 2017.
URL : https://hal.archives-ouvertes.fr/hal-02191535

B. A. Loiselle, V. L. Sork, J. Nason, and C. Graham, Spatial genetic structure of a tropical understory shrub, Psychotria officinalis (Rubiaceae), American Journal of Botany, vol.82, issue.11, pp.1420-1425, 1995.

M. A. Lopes, Population structure of Eschweilera coriacea (DC.) S. A. Mori in forest fragments in eastern Brazilian Amazonia, Revista Brasileira de Botânica, vol.30, issue.3, pp.509-519, 2007.

J. Loureiro, E. Rodriguez, J. Dole?el, and C. Santos, Two new nuclear isolation buffers for plant DNA flow cytometry: a test with 37 species, Annals of Botany, vol.100, issue.4, pp.875-888, 2007.

A. Luo, C. Ling, S. Y. Ho, and C. Zhu, Comparison of methods for molecular species delimitation across a range of speciation scenarios, Systematic Biology, vol.67, issue.5, pp.830-846, 2018.

M. J. Macía and J. Svenning, Oligarchic dominance in western Amazonian plant communities, Journal of Tropical Ecology, vol.21, issue.6, pp.613-626, 2005.

W. P. Maddison, Gene trees in species trees, Systematic Biology, vol.46, issue.3, pp.523-536, 1997.

J. Mallet, N. Besansky, and M. W. Hahn, How reticulated are species, BioEssays, vol.38, issue.2, pp.140-149, 2016.

M. Martin, Cutadapt removes adapter sequences from highthroughput sequencing reads, EMBnet Journal, vol.17, issue.1, pp.10-12, 2011.

C. H. Mcmichael, K. J. Feeley, C. W. Dick, D. R. Piperno, and M. B. Bush, Comment on "Persistent effects of pre-Columbian plant domestication on Amazonian forest composition, Science, vol.358, issue.6361, p.8347, 2017.

M. Medrano, E. López-perea, and C. M. Herrera, Population genetics methods applied to a species delimitation problem: endemic trumpet daffodils (Narcissus section Pseudonarcissi) from the Southern Iberian Peninsula, International Journal of Plant Sciences, vol.175, issue.5, pp.501-517, 2015.

E. Meglécz, C. Costedoat, V. Dubut, A. Gilles, T. Malausa et al., QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects, Bioinformatics, vol.26, issue.3, pp.403-404, 2010.

S. Mirarab, R. Reaz, M. S. Bayzid, T. Zimmermann, M. S. Swenson et al., ASTRAL: genome-scale coalescent-based species tree estimation, Bioinformatics, vol.30, issue.17, pp.541-548, 2014.

S. A. Mori, The Lecythidaceae of a lowland Neotropical forest: La Fumée Mountain, French Guiana, Memoirs of the New York Botanical Garden, vol.44, 1987.

S. A. Mori and N. Lepsch-cunha, The Lecythidaceae of a Central Amazonian moist forest, Memoirs of the New York Botanical Garden, vol.75, 1995.

S. A. Mori and G. T. Prance, Lecythidaceae, Part 2. The zygomorphic-flowered New World genera (Couroupita, Corythophora, Bertholletia, Couratari, Eschweilera, & Lecythis), with a study of secondary xylem of Neotropical Lecythidaceae by Carl H. de Zeeuw. Flora Neotropica, Monograph 21 (II), 1990.

S. A. Mori, P. Becker, and D. Kincaid, Lecythidaceae of a Central Amazonian lowland forest, Lessons from Amazonia: The ecology and conservation of a fragmented forest, pp.54-67, 2001.

S. A. Mori, C. Tsou, C. Wu, B. Cronholm, and A. A. Anderberg, Evolution of Lecythidaceae with an emphasis on the Heuertz et al., Genetic species delimitation in Eschweilera circumscription of Neotropical genera: information from combined ndhF and trnL-F sequence data, Annals of Botany, vol.94, issue.3, pp.289-301, 2007.

S. A. Mori, E. A. Kiernan, N. P. Smith, L. M. Kelley, Y. Huang et al., Observations on the phytogeography of the Lecythidaceae (Brazil nut family), Phytoneuron, vol.30, pp.1-85, 2017.

M. Nordborg, Coalescent theory, Handbook of Statistical Genetics, pp.179-212, 2001.

P. Orozco-terwengel, J. Corander, and C. Schlötterer, Genealogical lineage sorting leads to significant, but incorrect Bayesian multilocus inference of population structure, Molecular Ecology, vol.20, issue.6, pp.1108-1121, 2011.

C. Parisod, R. Holderegger, and C. Brochmann, Evolutionary consequences of autopolyploidy, New Phytologist, vol.186, issue.1, pp.5-17, 2010.

R. T. Pennington and M. Lavin, The contrasting nature of woody plant species in different neotropical forest biomes reflects differences in ecological stability, New Phytologist, vol.210, issue.1, pp.25-37, 2016.

C. M. Peters, M. J. Balick, F. Kahn, and A. B. Anderson, Oligarchic forests of economic plants in Amazonia: Utilization and conservation of an important tropical resource, Conservation Biology, vol.3, issue.4, pp.341-349, 1989.

N. C. Pitman, J. W. Terborgh, M. R. Silman, P. Núñez, V. Neill et al., Dominance and distribution of tree species in Upper Amazonian terra firme forests, Ecology, vol.82, issue.8, pp.2101-2117, 2001.

N. C. Pitman, M. R. Silman, and J. W. Terborgh, Oligarchies in Amazonian tree communities: a ten-year review, Ecography, vol.36, issue.2, pp.114-123, 2013.

G. T. Prance and S. A. Mori, Lecythidaceae-Part 1. The actinomorphic-flowered, New World Lecythidaceae (Asteranthos, 1979.

J. K. Pritchard, M. Stephens, and P. Donnelly, Inference of population structure using multilocus genotype data, Genetics, vol.155, issue.2, pp.945-959, 2000.

, R: a language and environment for statistical computing. Vienna, Austria, R Foundation for Statistical Computing, 2008.

N. A. Rosenberg and M. Nordborg, Genealogical trees, coalescent theory and the analysis of genetic polymorphisms, Nature Reviews Genetics, vol.3, pp.380-390, 2002.

N. A. Rosenberg, S. Mahajan, S. Ramachandran, C. Zhao, J. K. Pritchard et al., Clines, clusters, and the effect of study design on the inference of human population structure, PLoS Genetics, vol.1, 2005.

F. Rousset, Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance, Genetics, vol.145, issue.4, pp.1219-1228, 1997.

S. Rozen and H. Skaletsky, Primer3 on the WWW for general users and for biologist programmers, Methods in Molecular Biology, vol.132, pp.365-386, 2000.

A. S. Santos, D. B. Borges, C. V. Vivas, C. V. Berg, P. S. Rodrigues et al., Gene pool sharing and genetic bottleneck effects in subpopulations of Eschweilera ovata (Cambess.) Mart. ex Miers (Lecythidaceae) in the Atlantic Forest of southern Bahia, Brazil. Genetics and Molecular Biology, vol.42, issue.3, pp.655-665, 2019.

T. Shi, H. Huang, and M. S. Barker, Ancient genome duplications during the evolution of kiwifruit (Actinidia) and related Ericales, Annals of Botany, vol.106, issue.3, pp.497-504, 2010.

J. D. Storey, The positive false discovery rate: a Bayesian interpretation and the q-value, The Annals of Statistics, vol.31, issue.6, pp.2013-2035, 2003.

N. Techen, R. S. Arias, N. C. Glynn, Z. Pan, I. A. Khan et al., Continental-scale patterns of canopy tree composition and function across Amazonia, Molecular Ecology Resources, vol.10, issue.3, pp.444-447, 2006.

H. Ter-steege, N. C. Pitman, D. Sabatier, C. Baraloto, R. P. Salomão et al., Hyperdominance in the Amazonian tree flora, Science, vol.342, issue.6156, p.1243092, 2013.

P. Torroba-balmori, K. B. Budde, K. Heer, S. C. González-martínez, S. Olsson et al., Altitudinal gradients, biogeographic history and microhabitat adaptation affect fine-scale spatial genetic structure in African and Neotropical populations of an ancient tropical tree species, PloS One, vol.12, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01608324

A. C. Turchetto-zolet, F. Pinheiro, F. Salgueiro, and C. Palma-silva, Phylogeographical patterns shed light on evolutionary process in South America, Molecular Ecology, vol.22, issue.5, pp.1193-1213, 2013.

X. Vekemans and O. J. Hardy, New insights from fine-scale spatial genetic structure analyses in plant populations, Molecular Ecology, vol.13, issue.4, pp.921-935, 2004.

B. S. Weir and C. C. Cockerham, Estimating F-statistics for the analysis of population structure Evolution, vol.38, pp.1358-1370, 1984.

A. Willyard, R. Cronn, and A. Liston, Reticulate evolution and incomplete lineage sorting among the ponderosa pines, Molecular Phylogenetics and Evolution, vol.52, issue.2, pp.498-511, 2009.

, Acceptance date, André Simões. Submission date: 4 Dec, 2018.