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

K. Bennett, Continuing the debate on the role of Quaternary environmental change for macroevolution, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.359, issue.1442, pp.295-303, 2004.
DOI : 10.1098/rstb.2003.1395

I. Lovette, Glacial cycles and the tempo of avian speciation. Trends in Ecology and Evolution, pp.57-59, 2005.

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

C. Moritz, J. Patton, C. Schneider, and T. Smith, Diversification of Rainforest Faunas: An Integrated Molecular Approach, Annual Review of Ecology and Systematics, vol.31, issue.1, pp.533-563, 2000.
DOI : 10.1146/annurev.ecolsys.31.1.533

L. Croizat and . Biogeografia-analitica-y-sintética, Panbiogeografia " )d el a s Américas; tomo 1-2, Biblioteca de la Academia de Ciencias Fisicas, Matematicas y Naturales

G. Marroig and R. Cerqueira, Plio-Pleistocene South American history and the Amazon Lagoon hypothesis: a piece in the puzzle of Amazonian diversification, Journal of Computational Biology, vol.2, pp.103-119, 1997.

R. Hulbert, Late Miocene Tapirus (Mammalia, Perissodactyla) from Florida, with description of a new species, Tapirus webbi, Bulletin of the Florida Museum of Natural History, vol.45, pp.465-494, 2005.

A. Cione, E. Tonni, and L. Soibelzon, The Broken Zig-Zag: Late Cenozoic large mammal and tortoise extinction in South America, Revista del Museo Argentino de Ciencias Naturales, pp.1-19, 2003.
DOI : 10.22179/REVMACN.5.26

E. Lessa and R. Fariña, Reassessment of extinction patterns among the late Pleistocene mammals of South America, Palaeontology, vol.39, pp.651-662, 1996.

J. Fragoso and J. Huffman, Seed-dispersal and seedling recruitment patterns by the last Neotropical megafaunal element in Amazonia, the tapir, Journal of Tropical Ecology, vol.16, issue.3, pp.369-385, 2000.
DOI : 10.1017/S0266467400001462

P. Guimarães, . Jr, M. Galetti, and P. Jordano, Seed Dispersal Anachronisms: Rethinking the Fruits Extinct Megafauna Ate, PLoS ONE, vol.146, issue.3, p.1745, 2008.
DOI : 10.1371/journal.pone.0001745.s001

A. Taber, S. Chalukian, M. Altrichter, K. Minkowski, L. Lizárraga et al., Wildlife Conservation Society; and Wildlife Trust, El Destino de los Arquitectos de los Bosques Neotropicales: Evaluación de la Distribución y el Estado de Conservación de los Pecaríes Labiados y los Tapires de Tierras Bajas. Pigs, Peccaries and Hippos Specialist Group (IUCN/SSC); Tapir Specalist Group, 2008.

R. Bodmer and D. Brooks, Status and action plan of the lowland tapir (Tapirus terrestris) In Tapirs?Status survey and conservation action plan, Brooks DM, pp.46-56, 1997.

E. Holanda and M. Cozzuol, New records of Tapirus from the late Pleistocene of southwestern Amazonia, Brazil, Revista Brasileira de Paleontologia, vol.9, issue.2, pp.192-200, 2006.
DOI : 10.4072/rbp.2006.2.03

B. Ferrero and J. Noriega, El registro fósil de los tapires (Perissodactyla: Tapiridae) en el Pleistoceno de Entre Ríos, Ameghiniana, vol.40, p.84, 2003.

M. Ubilla, D. Perea, G. Aguilar, C. Lorernzo, and N. , Late Pleistocene vertebrates from northern Uruguay: tools for biostratigraphic, climatic and environmental reconstruction, Quaternary International, vol.114, issue.1, pp.129-142, 2004.
DOI : 10.1016/S1040-6182(03)00048-X

J. Norman and M. Ashley, Phylogenetics of Perissodactyla and Tests of the Molecular Clock, Journal of Molecular Evolution, vol.50, issue.1, pp.11-21, 2000.
DOI : 10.1007/s002399910002

G. Simpson, Splendid isolation: The curious history of south American mammals, 1980.

L. Marshall, Land mammals and the great American interchange, American Scientist, vol.76, pp.380-388, 1988.

R. Hulbert and . Jr, The giant tapir, Tapirus haysii, from Leisey Shell Pit 1A and other Florida Invingtonian localities, Bulletin of Florida Museum of Natural History, vol.37, pp.515-551, 1995.

E. Holanda, A. Porto, E. Nascimento, F. Góis, and M. Cozzuol, Registros do gênero Tapirus (Mammalia, Perissodactyla) do Pleistoceno da Amazônia Sul-Ocidental. XX Jornadas Argentinas de Paleontología de Vertebrados, p.51, 2004.

B. Ferrero and J. Noriega, A new tapir from the upper Pleistocene of Argentina: phylogenetic remarks on the neeotropical family de Thoisy et al278 diversification and paleoenvironmental inferences, BMC Evolutionary Biology Journal of Vertebrate Paleontology, vol.10, issue.27, pp.278507-511, 2007.

F. Takai, B. Arozqueta, T. Muzino, A. Yoshida, and H. Kondo, On fossil mammals from the Tajita department, Southern Bolivia. The Research Institute of Evolutionnary Biology, pp.1-63, 1984.

A. Cione and E. Tonni, Reassesment of the Pliocene-Pleistocene continental time scale of Southern South America. Correlation of the type Chapadmalalan with Bolivian sections, Journal of South American Earth Sciences, vol.9, issue.3-4, pp.221-236, 1996.
DOI : 10.1016/0895-9811(96)00008-9

L. Kerber and E. Oliveira, Sobre a presença de Tapirus (Tapiridae, Perissodatyla) na Formaçao Touro Passo (Pleistoceno Superior), oeste do Rio Grande do Sul, pp.9-14, 2008.

E. Tonni, Faunas y clima en el Cuaternario de la Mesopotamia argentina, Temas de la Biodiversidad del Litoral fluvial argentino. INSUGEO, Miscelánea Edited by: Aceñolaza GF, pp.31-38, 2004.

A. Aleixo and D. Rossetti, Avian gene trees, landscape evolution, and geology: towards a modern synthesis of Amazonian historical biogeography?, Journal of Ornithology, vol.1, issue.Suppl 1, pp.443-453, 2007.
DOI : 10.1007/s10336-007-0168-7

J. Haffer, Hypotheses to explain the origin of species in Amazonia, Brazilian Journal of Biology, vol.68, issue.4, pp.917-947, 2008.
DOI : 10.1590/S1519-69842008000500003

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

P. Vanzolini and E. Williams, South American anoles: geographic differentiation and evolution of the Anolis chrysolepis species group (Sauria, Iguanidae) Arquivos de Zoologia, pp.1-298, 1970.

L. Knowles, Did the Pleistocene glaciations promote divergence? Tests of explicit refugial models in montane grasshopprers, Molecular Ecology, vol.92, issue.3, pp.691-701, 2001.
DOI : 10.1046/j.1365-294x.2001.01206.x

L. Cortes-ortiz, E. Bermingham, C. Rico, . 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

A. Lavergne, M. Ruiz-garcía, F. Catzeflis, S. Lacote, H. Contamin et al., Phylogeny and phylogeography of squirrel monkeys (genus Saimiri) based on cytochrome b genetic analysis, American Journal of Primatology, vol.37, issue.3, pp.242-253, 2010.
DOI : 10.1002/ajp.20773
URL : https://hal.archives-ouvertes.fr/pasteur-00654004

P. Colinvaux, P. De-oliveira, and M. Bush, 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

M. Bush and P. Oliveira, The rise and fall of the Refugial Hypothesis of Amazonian speciation: a paleoecological perspective, Biota Neotropica, vol.6, issue.1, 2006.
DOI : 10.1590/S1676-06032006000100002

H. Tuomisto and K. Ruokolainen, The role of ecological knowledge in explaining biogeography and biodiversity in Amazonia, Biodiversity and Conservation, vol.6, issue.3, pp.347-357, 1997.
DOI : 10.1023/A:1018308623229

J. Ayres and T. Clutton-brock, River boundaries and species range size in Amazonian primates. The American Naturalist, pp.531-537, 1992.

A. Capparella, Genetic variation in Neotropical birds: implications for the speciation process. Congress International Ornithology, pp.1658-1664, 1988.

D. Rossetti, P. De-toledo, and A. Goes, New geological framework for Western Amazonia (Brazil) and implications for biogeography and evolution, Quaternary Research, vol.67, issue.01, pp.78-89, 2005.
DOI : 10.1206/0003-0090(2000)244<0001:MOTRJA>2.0.CO;2

E. Eizirik, S. Bonatto, W. Johnson, P. Crawshaw, J. Vié et al., Phylogeographic Patterns and Evolution of the Mitochondrial DNA Control Region in Two Neotropical Cats (Mammalia, Felidae), Journal of Molecular Evolution, vol.47, issue.5, pp.613-624, 1998.
DOI : 10.1007/PL00006418

E. Eizirik, J. Kim, M. Menotti-raymond, P. Crawshaw, O. Brien et al., Phylogeography, population history and conservation genetics of jaguars (Panthera onca, Mammalia, Felidae), Molecular Ecology, vol.13, issue.1, pp.65-79, 2001.
DOI : 10.1093/nar/25.24.4876

J. Endler, Geographic variation, speciation, and clines, Princeton, N.J, 1977.

J. Patton and M. Smith, mtDNA Phylogeny of Andean Mice: A Test of Diversification Across Ecological Gradients, Evolution, vol.46, issue.1, pp.174-183, 1992.
DOI : 10.2307/2409812

J. Cracraft and R. Prum, Patterns and Processes of Diversification: Speciation and Historical Congruence in Some Neotropical Birds, Evolution, vol.42, issue.3, pp.603-620, 1988.
DOI : 10.2307/2409043

R. Brumfield and S. Edwards, ANTSHRIKES, Evolution, vol.68, issue.111, pp.346-367, 2007.
DOI : 10.1111/j.1558-5646.2007.00039.x

L. Emmons and F. Feer, Neotropical rainforest mammals: a field guide, 1997.

M. Bush, Amazonian Speciation: A Necessarily Complex Model, Journal of Biogeography, vol.21, issue.1, pp.5-17, 1994.
DOI : 10.2307/2845600

B. Nabholz, S. Glemin, and N. Galtier, Strong Variations of Mitochondrial Mutation Rate across Mammals--the Longevity Hypothesis, Molecular Biology and Evolution, vol.25, issue.1, pp.120-130, 2008.
DOI : 10.1093/molbev/msm248

F. Martins, A. Templeton, A. Pavan, B. Kohlbach, and J. Morgante, Phylogeography of the common vampire bat (Desmodus rotundus): Marked population structure, Neotropical Pleistocene vicariance and incongruence between nuclear and mtDNA markers, BMC Evolutionary Biology, vol.9, issue.1, p.294, 2009.
DOI : 10.1186/1471-2148-9-294

M. Ruiz-garcia, A. Murillo, C. Corrales, N. Romero-aleán, and D. Alvarez-prada, Genética de poblaciones Amazonicas: la historia evolutiva del jaguar, ocelote, delfín rosado, mono lanudo y piurí, reconstruida a partir de sus genes, Animal Biodiversity and Conservation, vol.30, pp.115-130, 2007.

L. Tchaicka, E. Eizirik, D. Oliveira, T. Candido, J. Freitas et al., Phylogeography and population history of the crab-eating fox (Cerdocyon thous) Molecular Ecology, pp.819-838, 2007.

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.

C. Steiner and F. Catzeflis, Genetic variation and geographical structure of five mouse-sized opossums (Marsupialia, Didelphidae) throughout the Guiana Region, Journal of Biogeography, vol.267, issue.6, pp.959-973, 2004.
DOI : 10.1111/j.1365-2699.2004.01102.x

J. Patton, D. Silva, M. Malclom, and J. , 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.1-36, 2000.
DOI : 10.1206/0003-0090(2000)244<0001:MOTRJA>2.0.CO;2

L. Costa, The historical bridge between the Amazon and the Atlantic Forest of Brazil: a study of molecular phylogeography with small mammals, Journal of Biogeography, vol.92, issue.1, pp.71-86, 2003.
DOI : 10.1046/j.1365-2699.2003.00792.x

M. Lynch, B. Koskella, and S. Schaack, Mutation Pressure and the Evolution of Organelle Genomic Architecture, Science, vol.311, issue.5768, pp.1727-1730, 2006.
DOI : 10.1126/science.1118884

S. Ho, M. Phillips, A. Cooper, and A. Drummond, Time Dependency of Molecular Rate Estimates and Systematic Overestimation of Recent Divergence Times, Molecular Biology and Evolution, vol.22, issue.7, pp.1561-1568, 2005.
DOI : 10.1093/molbev/msi145

E. Zuckerkandl, L. Pauling, V. Bryson, and H. Vogel, Evolutionary divergence and convergence in proteins In Evolving genes and proteins, pp.97-166

S. Ho, U. Saarma, R. Barnett, J. Haile, and B. Shapiro, The Effect of Inappropriate Calibration: Three Case Studies in Molecular Ecology, PLoS ONE, vol.306, issue.2, p.1615, 2008.
DOI : 10.1371/journal.pone.0001615.t003

M. Pulquério and R. Nichols, Dates from the molecular clock: how wrong can we be? Trends in Ecology & Evolution, pp.180-184, 2007.

S. Subramanian, D. Denver, C. Millar, T. Heupink, A. Aschrafi et al., High mitogenomic evolutionary rates and time dependency, Trends in Genetics, vol.25, issue.11, pp.482-486, 2009.
DOI : 10.1016/j.tig.2009.09.005

B. Emerson, Alarm Bells for the Molecular Clock? No Support for Ho et al.'s Model of Time-Dependent Molecular Rate Estimates, Systematic Biology, vol.56, issue.2, pp.337-345, 2007.
DOI : 10.1080/10635150701258795

C. Millar, A. Dodd, J. Andeson, G. Gibb, P. Ritchie et al., Mutation and Evolutionary Rates in Ad??lie Penguins from the Antarctic, PLoS Genetics, vol.5, issue.10, p.1000209, 2008.
DOI : 10.1371/journal.pgen.1000209.s004

E. Latrubesse, M. Cozzuol, S. Da-silva-caminha, C. Rigsby, M. Absy et al., The Late Miocene paleogeography of the Amazon Basin and the evolution of the Amazon River system, Earth-Science Reviews, vol.99, issue.3-4, 2010.
DOI : 10.1016/j.earscirev.2010.02.005

D. Cossios, M. Lucherini, M. Ruiz-garcia, and B. Angers, Influence of ancient glacial periods on the Andean fauna: the case of the pampas cat (Leopardus colocolo), BMC Evolutionary Biology, vol.9, issue.1, p.68, 2009.
DOI : 10.1186/1471-2148-9-68

D. Silva, M. Patton, and J. , Molecular phylogeography and the evolution and conservation of Amazonian mammals, Molecular Ecology, vol.7, issue.4, pp.475-486, 1998.
DOI : 10.1016/0169-5347(96)10046-X

J. Avise, D. Walker, and G. Johns, Speciation durations and Pleistocene effects on vertebrate phylogeography, Proceedings of the Royal Society of London. Series B: Biological Sciences, pp.1707-1712, 1998.
DOI : 10.1098/rspb.1998.0492

L. Lisiecki and M. Raymo, A Plio-Pleistocene stack of 57 globally distributed benthic ? 18 O records, Paleoceanography, vol.20, p.1003, 2005.

D. Funk and K. Omland, Species-Level Paraphyly and Polyphyly: Frequency, Causes, and Consequences, with Insights from Animal Mitochondrial DNA, Annual Review of Ecology, Evolution, and Systematics, vol.34, issue.1, pp.397-423, 2003.
DOI : 10.1146/annurev.ecolsys.34.011802.132421

K. Røed, Refugial origin and postglacial colonization of holarctic reindeer and caribou, Rangifer, vol.25, issue.1, pp.19-30, 2005.
DOI : 10.7557/2.25.1.334

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

D. Irwin, PHYLOGEOGRAPHIC BREAKS WITHOUT GEOGRAPHIC BARRIERS TO GENE FLOW, Evolution, vol.28, issue.12, pp.2383-2394, 2002.
DOI : 10.1080/106351502753475880

E. Rauch and Y. Bar-yam, Theory predicts the uneven distribution of genetic diversity within species, Nature, vol.56, issue.7007, pp.449-452, 2004.
DOI : 10.1016/0169-5347(94)90057-4

J. Marin, A. Spotorno, B. Gonzalez, C. Bonacic, J. Wheeler et al., Mitochondrial DNA Variation and Systematics of the Guanaco (Lama guanicoe, Artiodactyla: Camelidae), Mitochondrial DNA variation and systematics of the Guanaco (Lama guanicoe, pp.269-281, 2008.
DOI : 10.1644/06-MAMM-A-385R.1

E. Medici, A. Desbiez, G. Da-silva, A. Jerusalinsky, L. Chassot et al., Lowland tapir (Tapirus terrestris) conservation workshop: Final report, 2007.

G. Caughley, Directions in Conservation Biology, The Journal of Animal Ecology, vol.63, issue.2, pp.215-244, 1994.
DOI : 10.2307/5542

C. Moritz, Applications of mitochondrial DNA analysis in conservation: a critical review, Molecular Ecology, vol.26, issue.13, pp.401-411, 1994.
DOI : 10.1046/j.1523-1739.1992.06040559.x

K. Crandall, O. Bininda-emonds, G. Mace, and R. Wayne, Considering evolutionary processes in conservation biology, Trends in Ecology & Evolution, vol.15, issue.7, pp.290-295, 2000.
DOI : 10.1016/S0169-5347(00)01876-0

P. Lesica and F. Allendorf, When Are Peripheral Populations Valuable for Conservation?, Conservation Biology, vol.9, issue.4, pp.753-760, 1995.
DOI : 10.1046/j.1523-1739.1995.09040753.x

E. Dinerstein, A conservation assessment of the terrestrial ecoregions of Latin America and the Caribbean, 1995.
DOI : 10.1596/0-8213-3295-3

L. Salas and T. Fuller, L.) in the Tabaro River valley, southern Venezuela, Canadian Journal of Zoology, vol.74, issue.8, pp.1444-1451, 1996.
DOI : 10.1139/z96-159
URL : https://hal.archives-ouvertes.fr/hal-00656782

M. Tobler, Habitat Use and Diet of Baird's Tapirs (Tapirus bairdii) in a Montane Cloud Forest of the Cordillera de Talamanca, Costa Rica1, Biotropica, vol.64, issue.3, pp.468-474, 2002.
DOI : 10.1007/BF00320611

C. Moritz and D. Faith, Comparative phylogeography and the identification of genetically divergent areas for conservation, Molecular Ecology, vol.7, issue.4, pp.419-429, 1998.
DOI : 10.1126/science.276.5320.1855

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

C. Tougard, T. Delefosse, C. Hanni, and C. Montgelard, Phylogenetic Relationships of the Five Extant Rhinoceros Species (Rhinocerotidae, Perissodactyla) Based on Mitochondrial Cytochrome b and 12S rRNA Genes, Molecular Phylogenetics and Evolution, vol.19, issue.1, pp.34-44, 2001.
DOI : 10.1006/mpev.2000.0903
URL : https://hal.archives-ouvertes.fr/halsde-00336406

K. Tamura, J. Dudley, M. Nei, and S. Kumar, MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0, Molecular Biology and Evolution, vol.24, issue.8, pp.1596-1599, 2007.
DOI : 10.1093/molbev/msm092
URL : http://mbe.oxfordjournals.org/cgi/content/short/24/8/1596

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

M. Amato, R. Brooks, and J. Fu, A phylogeographic analysis of populations of the wood turtle (Glyptemys insculpta) throughout its range, Molecular Ecology, vol.57, issue.0, pp.570-581, 2008.
DOI : 10.1046/j.1365-294X.1996.00265.x

M. Culling, K. Janko, A. Boron, V. Vasil-'ev, I. Cöté et al., European colonization by the spined loach (Cobitis taenia) from Ponto-Caspian refugia based on mitochondrial DNA variation, Molecular Ecology, vol.11, issue.6, pp.173-190, 2006.
DOI : 10.1111/j.1365-294X.2005.02790.x

C. Moritz, Defining Evolutionarily-Significant-Units for conservation. Trends in Ecology and Evolution, pp.373-375, 1994.
DOI : 10.1016/0169-5347(94)90057-4

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

R. Hudson and M. Turelli, Stochasiticity overrules the " three-times rule": genetic drift, genetic draft, and coalescence times for nuclear loci versus mitochondrial DNA, Evolution, vol.57, pp.182-90, 2003.

R. Baker and R. Bradley, SPECIATION IN MAMMALS AND THE GENETIC SPECIES CONCEPT, Journal of Mammalogy, vol.87, issue.4, pp.643-662, 2006.
DOI : 10.1644/06-MAMM-F-038R2.1

H. Bandelt, P. Forster, and A. Röhl, Median-joining networks for inferring intraspecific phylogenies, Molecular Biology and Evolution, vol.16, issue.1, pp.37-48, 1999.
DOI : 10.1093/oxfordjournals.molbev.a026036

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

D. Swofford, PAUP: A computer-program for phylogenetic inference using maximum parsimony, Journal of General Physiology, vol.102, p.9, 1993.

W. Maddison and D. Maddison, Mesquite: a modular system for evolutionary analysis, p.72, 2009.

J. Felsenstein, Distance Methods for Inferring Phylogenies: A Justification, Evolution, vol.38, issue.1, pp.16-24, 1984.
DOI : 10.2307/2408542

A. Drummond, A. Rambaut, and . Beast, 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

D. Prothero and R. Schoch, The Evolution of Perissodactyls, 1989.

D. Hooijer, V. Maglio, and H. Cooke, In Evolution of African Mammals, pp.371-378, 1978.

M. Newton and A. Raftery, Approximate Bayesian-inference with the weighted likelihood bootstrap, Journal of the Royal Statistical Society Series B-Methodological, vol.56, pp.3-48, 1994.

A. Rambaut and A. Drummond, Tracer v1.4, 2007.

A. Drummond, S. Ho, M. Phillips, and A. Rambaut, Relaxed Phylogenetics and Dating with Confidence, PLoS Biology, vol.20, issue.5, pp.699-710, 2006.
DOI : 10.1371/journal.pbio.0040088.sd001
URL : http://doi.org/10.1371/journal.pbio.0040088

L. Excoffier, G. Laval, and S. Schneider, Arlequin (version 3.0): an integrated software package for population genetics data analysis, Evolutionary Bioinformatics, vol.1, pp.47-50, 2005.

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

Y. Fu, Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection, Genetics, vol.147, pp.915-925, 1997.

D. Hartl and A. Clark, Principles of population genetics, 2007.

A. Drummond, A. Rambaut, B. Shapiro, and O. Pybus, Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences, Molecular Biology and Evolution, vol.22, issue.5, pp.1185-1192, 2005.
DOI : 10.1093/molbev/msi103

I. Dupanloup, S. Schneider, and L. Excoffier, A simulated annealing approach to define the genetic structure of populations, Molecular Ecology, vol.28, issue.12, pp.2571-2581, 2002.
DOI : 10.1046/j.1365-294X.2002.01650.x

L. Excoffier, P. Smouse, and J. Quattro, Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial-DNA restriction data, Genetics, vol.131, pp.479-491, 1992.

M. Slatkin and W. Maddison, A cladistic measure of gene flow inferred from the phylogenies of alleles, Genetics, vol.123, pp.603-613, 1989.

L. Knowles and W. Maddison, Statistical phylogeography, Molecular Ecology, vol.54, issue.12, pp.2623-2635, 2002.
DOI : 10.1006/tpbi.2000.1495

J. Wakeley, Coalescent theory: an introduction. Greenwood village, 2009.