T. Aide and E. Rivera, (Moraceae): implications for the theory of Pleistocene refugia and the importance of riparian forest, Journal of Biogeography, vol.17, issue.4, pp.695-705, 1998.
DOI : 10.1046/j.1365-2699.1998.2540695.x

A. Antonelli, J. Johan, A. Nylander, C. Persson, and I. Sanmartin, Tracing the impact of the Andean uplift on Neotropical plant evolution, Proceedings of the National Academy of Sciences of the USA, pp.9749-9754, 2009.
DOI : 10.1016/j.ympev.2004.12.006

M. Aubry-kientz, B. Ayotte-tr-epanier, C. Baraloto, C. Rossi, and V. , Toward Trait-Based Mortality Models for Tropical Forests, PLoS ONE, vol.7, issue.5, p.63678, 2013.
DOI : 10.1371/journal.pone.0063678.s002

URL : https://hal.archives-ouvertes.fr/hal-01190561

C. Baraloto, C. Paine, and L. Poorter, Decoupled leaf and stem economics in rain forest trees, Ecology Letters, vol.97, issue.11, pp.1338-1347, 2010.
DOI : 10.1111/j.1461-0248.2010.01517.x

URL : https://hal.archives-ouvertes.fr/hal-00594040

M. Beaumont, Approximate Bayesian Computation in Evolution and Ecology, Annual Review of Ecology, Evolution, and Systematics, vol.41, issue.1, pp.379-405, 2010.
DOI : 10.1146/annurev-ecolsys-102209-144621

M. Beaumont, W. Zhang, and D. Balding, Approximate Bayesian computation in population genetics, Genetics, vol.162, pp.2025-2035, 2002.

B. Garz-on, M. , A. Ia, R. Robson, T. Zavala et al., Intra-specific variability and plasticity influence potential tree species distributions under climate change, Global Ecology and Biogeography, vol.188, issue.5, pp.766-778, 2011.
DOI : 10.1111/j.1466-8238.2010.00646.x

G. Bertorelle, A. Benazzo, and S. Mona, ABC as a flexible framework to estimate demography over space and time: some cons, many pros, Molecular Ecology, vol.26, issue.13, pp.2609-2625, 2010.
DOI : 10.1111/j.1365-294X.2010.04690.x

C. Birky and . Jr, Uniparental inheritance of mitochondrial and chloroplast genes: mechanisms and evolution., Proceedings of the National Academy of Sciences of the USA, pp.11331-11338, 1995.
DOI : 10.1073/pnas.92.25.11331

K. Budde, S. Gonzalez-martinez, O. Hardy, and M. Heuertz, The ancient tropical rainforest tree Symphonia globulifera L. f. (Clusiaceae) was not restricted to postulated Pleistocene refugia in Atlantic Equatorial Africa, Heredity, vol.5, issue.1, pp.66-76, 2013.
DOI : 10.1007/s10592-005-9009-5

M. Bush, D. Oliveira, and P. , The rise and fall of the Refugial hypothesis of Amazonian speciation: a paleo-ecological perspective, Biota Neotropica, vol.6, p.106012006, 2006.

M. Bush, M. Miller, D. Oliveira, P. Colinvaux, and P. , Orbital forcing signal in sediments of two Amazonian lakes, Journal of Paleolimnology, vol.27, issue.3, pp.341-352, 2002.
DOI : 10.1023/A:1016059415848

M. Bush, D. Oliveira, P. Colinvaux, P. Miller, M. Moreno et al., Amazonian paleoecological histories: one hill, three watersheds, Palaeogeography, Palaeoclimatology, Palaeoecology, vol.214, issue.4, pp.359-393, 2004.
DOI : 10.1016/S0031-0182(04)00401-8

M. Bush, M. Silman, M. Michael, C. Saatchi, and S. , Fire, climate change and biodiversity in Amazonia: a Late-Holocene perspective, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.15, issue.1, pp.1795-1802, 2008.
DOI : 10.1126/science.1064363

H. Caron, S. Dumas, and G. Marque, Spatial and temporal distribution of chloroplast DNA polymorphism in a tropical tree species, Molecular Ecology, vol.42, issue.4, pp.1089-1098, 2000.
DOI : 10.1046/j.1365-294x.2000.00970.x

URL : https://hal.archives-ouvertes.fr/hal-01032205

P. Charles-dominique, P. Blanc, and D. Larpin, Forest perturbations and biodiversity during the last ten thousand years in French Guiana, Acta Oecologica, vol.19, issue.3, pp.295-302, 1998.
DOI : 10.1016/S1146-609X(98)80033-7

P. Colinvaux, Amazon diversity in light of the paleoecological record, Quaternary Science Reviews, vol.6, issue.2, pp.93-114, 1987.
DOI : 10.1016/0277-3791(87)90028-X

P. Colinvaux, D. Oliveira, P. Moreno, J. Miller, M. Bush et al., A Long Pollen Record from Lowland Amazonia: Forest and Cooling in Glacial Times, Science, vol.13, issue.1-2, pp.85-88, 1996.
DOI : 10.1016/0031-0182(94)90178-3

P. Colinvaux, D. Oliveira, P. Bush, and M. , Amazonian and neotropical plant communities on glacial time-scales: The failure of the aridity and refuge hypotheses, Quaternary Science Reviews, vol.19, issue.1-5, pp.141-169, 2000.
DOI : 10.1016/S0277-3791(99)00059-1

N. Colpaert, S. Cavers, E. Bandou, H. Caron, G. Gheysen et al., Sampling tissue for DNA analysis of trees: trunk cambium as an alternative to canopy leaves, Silvae Genetica, vol.54, pp.265-269, 2005.

J. Cornuet, F. Santos, and M. Beaumont, Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation, Bioinformatics, vol.24, issue.23, pp.2713-2719, 2008.
DOI : 10.1093/bioinformatics/btn514

K. Csill-ery, M. Blum, and O. Gaggiotti, Approximate Bayesian Computation (ABC) in practice, Trends in Ecology & Evolution, vol.25, issue.7, pp.410-418
DOI : 10.1016/j.tree.2010.04.001

K. Da?-inou, J. Bizoux, J. Doucet, G. Mahy, O. Hardy et al., Forest refugia revisited: nSSRs and cpDNA sequences support historical isolation in a wide-spread African tree with high colonization capacity, Milicia excelsa (Moraceae), Molecular Ecology, vol.24, issue.113, pp.4462-4477, 2010.
DOI : 10.1111/j.1365-294X.2010.04831.x

J. Duminil, H. Caron, I. Scotti, S. Cazal, and R. Petit, Blind population genetics survey of tropical rainforest trees, Molecular Ecology, vol.11, issue.12, pp.3505-3513, 2006.
DOI : 10.1111/j.1365-294X.2006.03040.x

URL : https://hal.archives-ouvertes.fr/hal-01031226

C. Dutech, L. Maggia, C. Tardy, H. Joly, and P. Jarne, TRACKING A GENETIC SIGNAL OF EXTINCTION-RECOLONIZATION EVENTS IN A NEOTROPICAL TREE SPECIES: VOUACAPOUA AMERICANA AUBLET IN FRENCH GUIANA, Evolution, vol.57, issue.12, pp.2753-2764, 2003.
DOI : 10.1111/j.0014-3820.2003.tb01517.x

URL : https://hal.archives-ouvertes.fr/hal-01032194

C. Dutech, H. Joly, and P. Jarne, Gene flow, historical population dynamics and genetic diversity within French Guianan populations of a rainforest tree species, Vouacapoua americana, Heredity, vol.92, issue.2, pp.69-77, 2004.
DOI : 10.1038/sj.hdy.6800384

H. Ellegren, Microsatellites: simple sequences with complex evolution, Nature Reviews Genetics, vol.164, issue.6, pp.435-445, 2004.
DOI : 10.1016/S0379-0738(01)00564-3

A. Estoup, P. Jarne, and J. Cornuet, Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis, Molecular Ecology, vol.92, issue.9, pp.1591-1604, 2002.
DOI : 10.1007/s004140050272

G. Evanno, S. Regnaut, and J. Goudet, Detecting the number of clusters of individuals using the software structure: a simulation study, Molecular Ecology, vol.16, issue.8, pp.2611-2620, 2005.
DOI : 10.1098/rspb.2001.1600

L. Excoffier and H. Lischer, Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows, Molecular Ecology Resources, vol.127, issue.3, pp.564-567, 2010.
DOI : 10.1111/j.1755-0998.2010.02847.x

N. Flanagan, A. Tobler, and A. Davison, Historical demography of M? ullerian mimicry in the neotropical Heliconius butterflies, Proceedings of the National Academy of Sciences, pp.9704-9709, 2004.

V. Freycon, M. Krencker, D. Schwartz, R. Nasi, and D. Bonal, The impact of climate changes during the Holocene on vegetation in northern French Guiana, Quaternary Research, vol.315, issue.02, pp.220-225, 2010.
DOI : 10.1016/S1146-609X(98)80033-7

URL : https://hal.archives-ouvertes.fr/halshs-00551758

S. Ghirotto, S. Mona, A. Benazzo, F. Paparazzo, D. Caramelli et al., Inferring Genealogical Processes from Patterns of Bronze-Age and Modern DNA Variation in Sardinia, Molecular Biology and Evolution, vol.27, issue.4, pp.875-886, 2010.
DOI : 10.1093/molbev/msp292

S. Haberle, R. Flood, D. Piper, K. A. Peterson, and L. , Upper Quaternary vegetation and climate history of the Amazon Basin: correlating marine and terrestrial pollen records, Proceedings of the Ocean Drilling Program, pp.381-396, 1997.
DOI : 10.2973/odp.proc.sr.155.225.1997

J. Haffer, Speciation in Amazonian Forest Birds, Science, vol.165, issue.3889, pp.131-137, 1969.
DOI : 10.1126/science.165.3889.131

T. Hall, BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95, NT. Nucleic Acids Symposium Series, vol.98, issue.41, pp.95-98, 1999.

B. Hardesty, C. Dick, J. Hamrick, B. Degen, S. Hubbell et al., Geographic Influence on Genetic Structure in the Widespread Neotropical Tree Simarouba amara (Simaroubaceae), Tropical Plant Biology, vol.28, issue.1, pp.28-39, 2010.
DOI : 10.1007/s12042-010-9044-3

M. Hasegawa, H. Kishino, and T. Yano, Dating of the human-ape splitting by a molecular clock of mitochondrial DNA, Journal of Molecular Evolution, vol.275, issue.3, pp.160-174, 1985.
DOI : 10.1007/BF02101694

H. , B. Bachelot, B. Poorter, and L. , Functional traits shape ontogenetic growth trajectories of rain forest tree species, Journal of Ecology, vol.99, pp.1431-1440, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01032387

M. Heuertz, D. Paoli, E. Kallman, and T. , Multilocus patterns of nucleotide diversity, linkage disequilibrium and demographic history of Norway Spruce, 2006.

G. Hewitt, The genetic legacy of the quaternary ice ages, Nature, vol.405, issue.6789, pp.907-913, 2000.
DOI : 10.1038/35016000

G. Hewitt, The structure of biodiversity ? insights from molecular phylogeography, Frontiers in Zoology, vol.1, pp.10-1186, 2004.

C. Hoorn, F. Wesselingh, and H. Ter-steege, Amazonia Through Time: Andean Uplift, Climate Change, Landscape Evolution, and Biodiversity, Science, vol.27, issue.7176, pp.927-931, 2010.
DOI : 10.1038/nature06588

URL : http://www.zora.uzh.ch/42535/10/Figure2.pdf

F. Hu, A. Hampe, and R. Petit, Paleoecology meets genetics: deciphering past vegetational dynamics, Frontiers in Ecology and the Environment, vol.55, issue.7, pp.371-379, 2009.
DOI : 10.1016/j.quascirev.2004.06.002

URL : https://digital.csic.es/bitstream/10261/64096/1/accesoRestringido.pdf

F. Jones, I. Ceron-souza, B. Hardesty, and C. Dick, Genetic evidence of Quaternary demographic changes in four rain forest tree species sampled across the Isthmus of Panama, Journal of Biogeography, vol.19, issue.4, pp.720-731, 2013.
DOI : 10.1111/jbi.12037

M. Kimura, The Neutral Theory of Molecular Evolution, 1985.

J. Kingman, On the genealogy of large populations, Journal of Applied Probability, vol.84, issue.A, pp.27-43, 1982.
DOI : 10.1016/0040-5809(75)90049-0

K. Kitajima and L. Poorter, Tissue-level leaf toughness, but not lamina thickness, predicts sapling leaf lifespan and shade tolerance of tropical tree species, New Phytologist, vol.84, issue.3, pp.708-721, 2010.
DOI : 10.1111/j.1469-8137.2010.03212.x

T. Lander, S. Oddou-muratorio, H. Prouillet-leplat, and E. Klein, Reconstruction of a beech population bottleneck using archival demographic information and Bayesian analysis of genetic data, Molecular Ecology, vol.27, issue.24, pp.5182-5196, 2011.
DOI : 10.1111/j.1365-294X.2011.05356.x

URL : https://hal.archives-ouvertes.fr/hal-01344426

C. Latouche-halle, A. Ramboer, E. Bandou, H. Caron, and S. Decroocq, Isolation and characterization of microsatellite markers in the tropical tree species Dicorynia guianensis (Caesalpinaceae), Molecular Ecology Notes, vol.38, issue.3, pp.228-230, 2002.
DOI : 10.1046/j.1365-294X.1999.00637.x

R. Leblois, P. Pudlo, F. Bertaux, C. Beeravolu, R. Vitalis et al., Maximum-Likelihood Inference of Population Size Contractions from Microsatellite Data, Molecular Biology and Evolution, vol.31, issue.10, pp.2805-2823, 2014.
DOI : 10.1093/molbev/msu212

M. Ledru, J. Bertaux, and A. Sifeddine, Absence of Last Glacial Maximum Records in Lowland Tropical Forests, Quaternary Research, vol.165, issue.3, pp.233-237, 1998.
DOI : 10.1006/qres.1993.1011

F. Mayle and M. Power, Impact of a drier Early-Mid-Holocene climate upon Amazonian forests, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.120, issue.1-2, pp.1829-1838, 2008.
DOI : 10.1016/S0034-6667(01)00148-8

F. Mayle, R. Burbridge, and T. Killeen, Millennial-Scale Dynamics of Southern Amazonian Rain Forests, Science, vol.290, issue.5500, pp.2291-2294, 2000.
DOI : 10.1126/science.290.5500.2291

F. Mayle, D. Beerling, W. Gosling, and M. Bush, Responses of Amazonian ecosystems to climatic and atmospheric carbon dioxide changes since the last glacial maximum, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.359, issue.1443, pp.499-514, 2004.
DOI : 10.1098/rstb.2003.1434

J. Molino and D. Sabatier, Tree Diversity in Tropical Rain Forests: A Validation of the Intermediate Disturbance Hypothesis, Science, vol.294, issue.5547, pp.1702-1704, 2001.
DOI : 10.1126/science.1060284

J. Motamayor, P. Lachenaud, and J. Da-silva-e-mota, Geographic and Genetic Population Differentiation of the Amazonian Chocolate Tree (Theobroma cacao L), PLoS ONE, vol.53, issue.10, p.3311, 2008.
DOI : 10.1371/journal.pone.0003311.s005

M. Nei, Molecular Evolutionary Genetics, 1987.

R. Petit, S. Brewer, and S. Bordacs, Identification of refugia and post-glacial colonisation routes of European white oaks based on chloroplast DNA and fossil pollen evidence, Forest Ecology and Management, vol.156, issue.1-3, pp.49-74, 2002.
DOI : 10.1016/S0378-1127(01)00634-X

D. Posada and T. Buckley, Model Selection and Model Averaging in Phylogenetics: Advantages of Akaike Information Criterion and Bayesian Approaches Over Likelihood Ratio Tests, Systematic Biology, vol.53, issue.5, pp.793-808, 2004.
DOI : 10.1080/10635150490522304

D. Posada and K. Crandall, MODELTEST: testing the model of DNA substitution, Bioinformatics, vol.14, issue.9, pp.817-818, 1998.
DOI : 10.1093/bioinformatics/14.9.817

M. Power, M. Bush, H. Behling, S. Horn, F. Mayle et al., Paleofire activity in tropical America during the last 21 ka: a regional synthesis based on sedimentary charcoal . Pages News, pp.73-75, 2010.

G. Prance, A Review of the Phytogeographic Evidences for Pleistocene Climate Changes in the Neotropics, Annals of the Missouri Botanical Garden, vol.69, issue.3, pp.594-624, 1982.
DOI : 10.2307/2399085

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

T. Pyh?-aj?-arvi, M. Garcia-gil, T. Knurr, M. Mikkonen, W. Wachowiak et al., Demographic History Has Influenced Nucleotide Diversity in European Pinus sylvestris Populations, Genetics, vol.177, issue.3, pp.1713-1724, 2007.
DOI : 10.1534/genetics.107.077099

J. Quijada-mascarenas, J. Ferguson, C. Pook, D. Grac-ßa-salomao, M. Thorpe et al., Phylogeographic patterns of trans-Amazonian vicariants and Amazonian biogeography: the Neotropical rattlesnake (Crotalus durissus complex) as an example, Journal of Biogeography, vol.14, issue.8, pp.1296-1312, 2007.
DOI : 10.1111/j.1365-2699.2007.01707.x

R. Team, R: A Language and Environment for Statistical Computing. R foundation for Statistical Computing, 2013.

D. Reich, M. Feldman, and D. Goldstein, Statistical Properties of Two Teststhat Use Multilocus Data Sets to Detect Population Expansions, Molecular Biology and Evolution, vol.16, issue.4, pp.453-466, 1999.
DOI : 10.1093/oxfordjournals.molbev.a026127

J. Richardson, R. Pennington, T. Pennington, and P. Hollingsworth, Rapid Diversification of a Species-Rich Genus of Neotropical Rain Forest Trees, Science, vol.293, issue.5538, pp.2242-2245, 2001.
DOI : 10.1126/science.1061421

D. Sabatier, M. Grimaldi, and M. Pr-evost, The influence of soil cover organization on the floristic and structural heterogeneity of a Guianan rain forest, Plant Ecology formerly `Vegetatio', vol.131, issue.1, pp.81-108, 1997.
DOI : 10.1023/A:1009775025850

M. Schuelke, An economic method for the fluorescent labeling of PCR fragments, Nature Biotechnology, vol.252, issue.2, pp.233-234, 2000.
DOI : 10.1038/72708

C. Scotti-saintagne, C. Dick, and H. Caron, (Bignoniaceae), Journal of Biogeography, vol.34, issue.4, pp.707-719, 2013.
DOI : 10.1111/j.1365-2699.2012.02797.x

URL : https://hal.archives-ouvertes.fr/hal-01032410

C. Scotti-saintagne, C. Dick, and H. Caron, , Meliaceae), Journal of Biogeography, vol.42, issue.4, pp.676-692, 2013.
DOI : 10.1111/j.1365-2699.2011.02678.x

J. Shaw, E. Lickey, and J. Beck, The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis, American Journal of Botany, vol.92, issue.1, pp.142-166, 2005.
DOI : 10.3732/ajb.92.1.142

S. Solomon, M. Bacci, J. Martins, G. Vinha, and U. Mueller, Paleodistributions and Comparative Molecular Phylogeography of Leafcutter Ants (Atta spp.) Provide New Insight into the Origins of Amazonian Diversity, PLoS ONE, vol.9, issue.7, p.2738, 2008.
DOI : 10.1371/journal.pone.0002738.s008

T. Stadler, B. Haubold, C. Merino, W. Stephan, and P. Pfaffelhuber, The Impact of Sampling Schemes on the Site Frequency Spectrum in Nonequilibrium Subdivided Populations, Genetics, vol.182, issue.1, pp.205-216, 2009.
DOI : 10.1534/genetics.108.094904

D. Swofford, PAUP: Phylogenetic Analysis Using Parsimony , Version 3.1. Computer program distributed by the Illinois Natural History Survey, 1991.

P. Taberlet, L. Fumagalli, A. Wust-saucy, and J. Cosson, Comparative phylogeography and postglacial colonization routes in Europe, Molecular Ecology, vol.7, issue.4, pp.453-464, 1998.
DOI : 10.1146/annurev.ecolsys.19.1.513

URL : https://hal.archives-ouvertes.fr/halsde-00280580

F. Tajima, The effect of change in population size on DNA polymorphism, Genetics, vol.123, pp.597-601, 1989.

F. Tajima, Statistical method for testing the neutral mutation hypothesis by DNA polymorphism, Genetics, vol.123, pp.585-595, 1989.

C. Tardy, Pal eoincendies naturels, feux anthropiques et environnements forestiers de Guyane franc ßaise du tardiglaciaire a l'holoc ene recent. Approches chronologique et anthracologique, Th ese de Doctorat, Sciences et Techniques, p.343, 1998.

B. De-thoisy, D. Silva, A. Ruiz-garcia, and M. , Population history, phylogeography, and conservation genetics of the last Neotropical mega-herbivore, the lowland tapir (Tapirus terrestris), BMC Evolutionary Biology, vol.10, issue.1, p.278, 2010.
DOI : 10.1186/1471-2148-10-278

URL : https://hal.archives-ouvertes.fr/pasteur-00654107

A. Thuillet, D. Bru, and J. David, Direct Estimation of Mutation Rate for 10 Microsatellite Loci in Durum Wheat, Triticum turgidum (L.) Thell. ssp durum desf, Molecular Biology and Evolution, vol.19, issue.1, pp.122-125, 2002.
DOI : 10.1093/oxfordjournals.molbev.a003977

Y. Vigouroux, J. Jaqueth, and Y. Matsuoka, Rate and Pattern of Mutation at Microsatellite Loci in Maize, Molecular Biology and Evolution, vol.19, issue.8, pp.1251-1260, 2002.
DOI : 10.1093/oxfordjournals.molbev.a004186

C. Vinson, V. Azevedo, I. Sampaio, and A. Ciampi, Development of microsatellite markers for Carapa guianensis (Aublet), a tree species from the Amazon forest, Molecular Ecology Notes, vol.5, issue.1, pp.33-34, 2005.
DOI : 10.1046/j.1365-294x.1998.00374.x

J. Westbrook, K. Kitajima, J. Burleigh, W. Kress, D. Erickson et al., What Makes a Leaf Tough? Patterns of Correlated Evolution between Leaf Toughness Traits and Demographic Rates among 197 Shade-Tolerant Woody Species in a Neotropical Forest, The American Naturalist, vol.177, issue.6, pp.800-811, 2011.
DOI : 10.1086/659963

K. Wolfe, W. Li, P. Sharp, and H. I. Ltd, Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs., Proceedings of the National Academy of Sciences, vol.84, issue.24, 1173.
DOI : 10.1073/pnas.84.24.9054

L. Zhivotovsky, M. Feldman, and S. Grishechkin, Biased mutations and microsatellite variation, Molecular Biology and Evolution, vol.14, issue.9, pp.926-933, 1997.
DOI : 10.1093/oxfordjournals.molbev.a025835