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

P. Arctander, Comparison of a Mitochondrial Gene and a corresponding Nuclear Pseudogene, Proceedings of the Royal Society B: Biological Sciences, vol.262, issue.1363, pp.13-19, 1995.
DOI : 10.1098/rspb.1995.0170

J. Avise, Phylogeography?the history and formation of species, 2000.

M. Benton and P. Donoghue, Paleontological Evidence to Date the Tree of Life, Molecular Biology and Evolution, vol.24, issue.1, pp.26-53, 2007.
DOI : 10.1093/molbev/msl150

S. Boinski and S. Cropp, Disparate data sets resolve squirrel monkey (Saimiri) taxonomy: implications for behavioral ecology and biomedical usage, International Journal of Primatology, vol.20, issue.2, pp.237-256, 1999.
DOI : 10.1023/A:1020522519946

S. Boinski and J. Newman, Preliminary observations on squirrel monkey (Saimiri oerstedi) vocalizations in Costa Rica, American Journal of Primatology, vol.47, issue.4, pp.329-343, 1988.
DOI : 10.1002/ajp.1350140403

C. Bonvicino, B. Lemos, and H. Seuanez, Molecular phylogenetics of howler monkeys (Alouatta, Platyrrhini), Chromosoma, vol.110, issue.3, pp.241-246, 2001.
DOI : 10.1007/s004120000128

A. Coates and J. Obando, The geologic evolution of the Central American isthmus, Evolution and environment in tropical America, pp.21-56, 1996.

C. Coe, E. Smith, and S. Levine, The endocrine system of the squirrel monkey Handbook of squirrel monkey research, pp.191-218, 1985.

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

A. Collins and J. Dubach, Biogeographic and ecological forces responsible for speciation in Ateles, International Journal of Primatology, vol.21, issue.3, pp.421-444, 2000.
DOI : 10.1023/A:1005487802312

L. Cortes-ortiz, E. Bermingham, C. Rico, E. Rodriguez-luna, I. Sampaio et al., Molecular systematics and biogeography of the Neotropical monkey genus, Alouatta, Molecular Phylogenetics and Evolution, vol.26, issue.1, pp.64-81, 2003.
DOI : 10.1016/S1055-7903(02)00308-1

R. Costello, C. Dickinson, A. Rosenberger, S. Boinski, and F. Szalay, A multidisciplinary approach to squirrel monkey (genus Saimiri) species taxonomy, Species, species concepts, and primate evolution, pp.177-237, 1993.

S. Cowling, M. Maslin, and M. Sykes, Abstract, Quaternary Research, vol.46, issue.02, pp.140-149, 2001.
DOI : 10.1098/rstb.1986.0040

S. Cropp, Evolutionary diversification among tamarins (genus Saguinus), Dissertation Abstract Int B, vol.58, p.6433, 1998.

S. Cropp and S. Boinski, The Central American Squirrel Monkey (Saimiri oerstedii): Introduced Hybrid or Endemic Species?, Molecular Phylogenetics and Evolution, vol.16, issue.3, pp.350-365, 2000.
DOI : 10.1006/mpev.2000.0814

S. Cropp, A. Larson, and J. Cheverud, Historical biogeography of tamarins, genusSaguinus: the molecular phylogenetic evidence, American Journal of Physical Anthropology, vol.4, issue.1, pp.65-89, 1999.
DOI : 10.1002/(SICI)1096-8644(199901)108:1<65::AID-AJPA4>3.0.CO;2-4

D. Silva, B. Sampaio, M. Schneider, M. Schneider, H. Villavicencio et al., Preliminary analysis of genetic distance between squirrel monkeys, Int J Primatol, vol.8, p.528, 1987.

D. Silva, B. Sampaio, M. Schneider, H. Schneider, M. Montoya et al., Protein electrophoretic variability inSaimiri and the question of its species status, American Journal of Primatology, vol.22, issue.3, pp.183-193, 1993.
DOI : 10.1002/ajp.1350290304

C. Dick and M. Heuertz, THE COMPLEX BIOGEOGRAPHIC HISTORY OF A WIDESPREAD TROPICAL TREE SPECIES, Evolution, vol.28, issue.11, pp.2760-2774, 2008.
DOI : 10.1111/j.1558-5646.2008.00506.x

A. Ditchfield, The comparative phylogeography of neotropical mammals: patterns of intraspecific mitochondrial, Am. J. Primatol, 2000.

A. Drummond and A. Rambaut, BEAST: Bayesian evolutionary analysis by sampling trees, BMC Evolutionary Biology, vol.7, issue.1, p.214, 2007.
DOI : 10.1186/1471-2148-7-214
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2247476

J. Endler, Pleistocene forest refuges: fact or fancy? In: Prance GT, editor. Biological diversification in the tropics, pp.641-657, 1982.

J. Felsenstein, Confidence Limits on Phylogenies: An Approach Using the Bootstrap, Evolution, vol.39, issue.4, pp.783-791, 1985.
DOI : 10.2307/2408678

S. Ferrari, Biogeography of Amazonian Primates, A Primatologia no Brasil no 8, IPEMA/SBPr, pp.101-122, 2004.

J. Fleage and T. Brown, New Primate Fossils from Late Oligocene (Colhuehuapian) Localities of Chubut Province, Argentina, Folia Primatologica, vol.41, issue.3-4, pp.240-266, 1983.
DOI : 10.1159/000156135

J. Haffer, Alternative models of vertebrate speciation in Amazonia: an overview, Biodiversity and Conservation, vol.6, issue.3, pp.451-476, 1997.
DOI : 10.1023/A:1018320925954

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

F. Hayes and J. Sewlal, The Amazon River as a dispersal barrier to passerine birds: effects of river width, habitat and taxonomy, Journal of Biogeography, vol.20, issue.11, pp.1809-1818, 2004.
DOI : 10.1071/MU0007S

P. Hershkovitz, Taxonomy of squirrel monkeys genusSaimiri (Cebidae, platyrrhini): A preliminary report with description of a hitherto unnamed form, American Journal of Primatology, vol.10, issue.2, pp.155-210, 1984.
DOI : 10.1002/ajp.1350070212

N. Hubert, F. Duponchelle, J. Nunez, G. Davila, C. Paugy et al., Phylogeography of the piranha genera Serrasalmus and Pygocentrus: implications for the diversification of the Neotropical ichthyofauna, Molecular Ecology, vol.613, issue.10, pp.2115-2136, 2007.
DOI : 10.1007/BF00004815

C. Janson and S. Boinski, Morphological and behavioral adaptations for foraging in generalist primates: The case of the cebines, American Journal of Physical Anthropology, vol.2, issue.4, pp.483-498, 1992.
DOI : 10.1002/ajpa.1330880405

R. Kay, J. Fleagle, T. Mitchell, M. Colbert, T. Bown et al., The anatomy of Dolichocebus gaimanensis, a stem platyrrhine monkey from Argentina, Journal of Human Evolution, vol.54, issue.3, pp.323-382, 2008.
DOI : 10.1016/j.jhevol.2007.09.002

M. Kimura, A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences, Journal of Molecular Evolution, vol.206, issue.5, Nov., pp.111-120, 1980.
DOI : 10.1007/BF01731581

A. Lavergne, F. Catzeflis, S. Lacôte, A. Barnaud, M. Bordier et al., Genetic analysis of the Saimiri breeding colony of the Pasteur Institute (French Guiana): development of a molecular typing method using a combination of nuclear and mitochondrial DNA markers, Journal of Medical Primatology, vol.32, issue.6, pp.330-340, 2003.
DOI : 10.1046/j.1600-0684.2003.00038.x

J. Lundberg, L. Marshall, J. Guerrero, B. Horton, M. Malabarba et al., The stage for neotropical fish diversification: a history of tropical South American rivers Phylogeny and classification of neotropical fishes, pp.13-48, 1998.

M. Medeiros, R. Barros, J. Pieczarka, C. Nagamachi, M. Ponsa et al., Radiation and speciation of spider monkeys, genus Ateles, from the cytogenetic viewpoint, American Journal of Primatology, vol.42, issue.3, pp.167-178, 1997.
DOI : 10.1002/(SICI)1098-2345(1997)42:3<167::AID-AJP1>3.3.CO;2-H

C. Montgelard, F. Catzeflis, and E. Douzery, Phylogenetic relationships of artiodactyls and cetaceans as deduced from the comparison of cytochrome b and 12S rRNA mitochondrial sequences, Molecular Biology and Evolution, vol.14, issue.5, pp.550-559, 1997.
DOI : 10.1093/oxfordjournals.molbev.a025792

M. Mustrangi and J. Patton, Phylogeography and systematics of the slender mouse opossum marmosops (Marsupialia , Didelphidae), 1997.

F. Nascimento, C. Bonvicino, F. Da-silva, M. Schneider, and H. Seuanez, Cytochrome <i>b</i> polymorphisms and population structure of two species of <i>Alouatta</i> (Primates), Cytogenetic and Genome Research, vol.108, issue.1-3, pp.106-111, 2005.
DOI : 10.1159/000080808

M. Nei, Molecular evolutionary genetics, 1987.

M. Newton and A. Raftery, Approximate Bayesian inference with the weighted likelihood bootstrap (with discussion), J Royal Stat Soc Ser B, vol.56, pp.3-48, 1994.

J. Nylander, MrModeltest v2 program distributed by the author, Evolutionary Biology Centre, 2004.

J. Opazo, D. Wildman, T. Prychitko, R. Johnson, and M. Goodman, Phylogenetic relationships and divergence times among New World monkeys (Platyrrhini, Primates), Molecular Phylogenetics and Evolution, vol.40, issue.1, pp.274-280, 2006.
DOI : 10.1016/j.ympev.2005.11.015

J. Patton, D. Silva, and M. , Rivers, refuges and ridges: the geography of speciation of Amazonian mammals Endless forms: species and speciation, pp.202-213, 1998.

J. Patton, M. Da-silva, and J. Malcolm, MAMMALS OF THE RIO JURU?? AND THE EVOLUTIONARY AND ECOLOGICAL DIVERSIFICATION OF AMAZONIA, Bulletin of the American Museum of Natural History, vol.244, issue.1, pp.1-306, 2000.
DOI : 10.1206/0003-0090(2000)244<0001:MOTRJA>2.0.CO;2

D. Pearse, A. Arndt, N. Valenzuela, B. Miller, V. Cantarelli et al., Estimating population structure under nonequilibrium conditions in a conservation context: continent-wide population genetics of the giant Amazon river turtle, Podocnemis expansa (Chelonia; Podocnemididae), Molecular Ecology, vol.163, issue.4, pp.985-1006, 2006.
DOI : 10.1111/j.1365-294X.2006.02869.x

H. Philippe, MUST, a computer package of Management Utilities for Sequences and Trees, Nucleic Acids Research, vol.21, issue.22, pp.5264-5272, 1993.
DOI : 10.1093/nar/21.22.5264

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

C. Poux, P. Chevret, D. Huchon, W. De-jong, and E. Douzery, Arrival and Diversification of Caviomorph Rodents and Platyrrhine Primates in South America, Systematic Biology, vol.55, issue.2, pp.228-244, 2006.
DOI : 10.1080/10635150500481390
URL : https://hal.archives-ouvertes.fr/halsde-00252011

A. Rambaut and A. Drummond, Tracer v1, 2007.

J. Renno, N. Hubert, J. Torrico, F. Duponchelle, N. Rodriguez et al., Phylogeography of Cichla (Cichlidae) in the upper Madera basin (Bolivian Amazon), Molecular Phylogenetics and Evolution, vol.41, issue.2, pp.503-510, 2006.
DOI : 10.1016/j.ympev.2006.05.029

F. Ronquist and J. Huelsenbeck, MrBayes 3: Bayesian phylogenetic inference under mixed models, Bioinformatics, vol.19, issue.12, pp.1572-1574, 2003.
DOI : 10.1093/bioinformatics/btg180
URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/19/12/1572

A. Rosenberger, Cranial anatomy and implications of Dolichocebus, a late Oligocene ceboid primate, Nature, vol.6, issue.5712, pp.416-418, 1979.
DOI : 10.1016/0047-2484(75)90018-4

J. Rozas, J. Sanchez-delbarrio, X. Messeguer, and R. Rozas, DnaSP, DNA polymorphism analyses by the coalescent and other methods, Bioinformatics, vol.19, issue.18, pp.2496-2497, 2003.
DOI : 10.1093/bioinformatics/btg359

M. Ruiz-garcia, A. Parra, N. Romero-aleán, P. Escobar-armel, and J. Shostell, Genetic characterization and phylogenetic relationships between the Ateles species (Atelidae, primates) by means of DNA microsatellite markers and craniometric data, Primate Report, vol.73, pp.3-47, 2006.

M. Ruiz-garcia, P. Escobar-armel, D. Alvarez, M. Mudry, M. Ascunce et al., Genetic Variability in Four <i>Alouatta</i> Species Measured by Means of Nine DNA Microsatellite Markers: Genetic Structure and Recent Bottlenecks, Folia Primatologica, vol.78, issue.2, pp.73-87, 2007.
DOI : 10.1159/000097058

V. Rull, Quaternary speciation in the Neotropics, Molecular Ecology, vol.359, issue.13, pp.4257-4259, 2006.
DOI : 10.1111/j.1365-294X.2006.03052.x

J. Salo, R. Kalliola, I. Hakkinen, Y. Marinen, P. Niemela et al., River dynamics and the diversity of Amazon lowland forest, Nature, vol.15, issue.21, pp.254-258, 1986.
DOI : 10.1038/322254a0

J. Sambrook, E. Fritsch, and T. Maniatis, Molecular cloning: a laboratory manual, 1989.

C. Schrago, On the time scale of new world primate diversification, American Journal of Physical Anthropology, vol.20, issue.3, pp.344-354, 2007.
DOI : 10.1002/ajpa.20459

R. Stirton, Ceboid monkeys from the Miocene of Columbia, Bull Univ California Publ Geol Sci, vol.28, pp.315-356, 1951.

D. Swofford, PAUP*. Phylogenetic analysis using parsimony (and other methods) Version 4, 2002.

F. Szalay and V. Delson, Evolutionary history of the primates, 1979.

L. Tchaika, E. Eizirk, T. De-oliveira, J. Candido, and T. Freitas, Phylogeography and population history of the crab-eating fox (Cerdocyon thous), Molecular Ecology, vol.12, issue.4, pp.819-838, 2007.
DOI : 10.1111/j.1365-294X.2006.03185.x

R. Thorington, The taxonomy and distribution of squirrel monkeys (Saimiri) The handbook of squirrel monkey research, pp.1-33, 1985.

H. Tuomisto, K. Ruokolainen, R. Kalliola, A. Linna, W. Danjoy et al., Dissecting Amazonian Biodiversity, Science, vol.269, issue.5220, pp.63-69, 1995.
DOI : 10.1126/science.269.5220.63

J. Vandeberg, M. Cheng, C. Moore, and C. Abee, Genetics of the squirrel monkeys (genus Saimiri): implications for taxonomy and research, Int J Primatol, vol.8, p.423, 1987.

J. Vandeberg, C. Moore, S. Williams-blangero, C. Min-lee, and C. Abee, Genetic relationships among three squirrel monkey types: Implications for taxonomy, biomedical research, and captive breeding, American Journal of Primatology, vol.32, issue.2, pp.101-111, 1990.
DOI : 10.1002/ajp.1350220204

L. Walker, B. Kaack, K. Brizzee, and M. Walker, Prenatal ionizing irradiaton and early postnatal growth of Colombian and Bolivian squirrel monkeys (Saimiri sciureus), American Journal of Primatology, vol.25, issue.4, pp.379-387, 1981.
DOI : 10.1002/ajp.1350010403

Q. Wan, H. Wu, T. Fujihara, and S. Fang, Which genetic marker for which conservation genetics issue?, ELECTROPHORESIS, vol.25, issue.14, pp.2165-2176, 2004.
DOI : 10.1002/elps.200305922

H. Whiteley, J. Everitt, I. Kakoma, M. James, and J. Ristic, Pathologic changes associated with fatal Plasmodium falciparum infection in the Bolivian squirrel monkey (Saimiri sciureus boliviensis), Am J Trop Med Hyg, vol.37, pp.1-8, 1987.