(. T. Hivphyml-project, F. C. , O. G. Nrf-south-africa, and C. France, ANR6è me Extinction), NUMEV Montpellier Labex (M.J., O.G

A. Abebe, Identification of a Genetic Subcluster of HIV Type 1 Subtype C (C???) Widespread in Ethiopia, AIDS Research and Human Retroviruses, vol.16, issue.17, pp.1909-1914, 2000.
DOI : 10.1089/08892220050195865

J. P. Bollback, SIMMAP: stochastic character mapping of discrete traits on phylogenies, BMC Bioinformatics, vol.78, issue.8, 2006.

T. De-oliveira, The HIV-1 Subtype C Epidemic in South America Is Linked to the United Kingdom, PLoS ONE, vol.6, issue.2, 2010.
DOI : 10.1371/journal.pone.0009311.s004

A. J. Drummond, Bayesian Phylogenetics with BEAUti and the BEAST 1.7, Molecular Biology and Evolution, vol.29, issue.8, pp.1969-1973, 2012.
DOI : 10.1093/molbev/mss075

D. P. Faith, Conservation evaluation and phylogenetic diversity, Biological Conservation, vol.61, issue.1, pp.1-1, 1992.
DOI : 10.1016/0006-3207(92)91201-3

B. T. Grenfell, Unifying the Epidemiological and Evolutionary Dynamics of Pathogens, Science, vol.303, issue.5656, pp.327-332, 2004.
DOI : 10.1126/science.1090727

S. Guindon, New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0, Systematic Biology, vol.59, issue.3, pp.307-321, 2010.
DOI : 10.1093/sysbio/syq010

URL : https://hal.archives-ouvertes.fr/lirmm-00511784

J. Hemelaar, Global trends in molecular epidemiology of HIV-1 during 2000???2007, AIDS, vol.25, issue.5, pp.679-689, 2000.
DOI : 10.1097/QAD.0b013e328342ff93

H. Hue´ and S. , Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups, Proc. Natl Acad. Sci. USA, pp.4425-4429, 2005.
DOI : 10.1073/pnas.0407534102

H. Hue´ and S. , Demonstration of Sustained Drug-Resistant Human Immunodeficiency Virus Type 1 Lineages Circulating among Treatment-Naive Individuals, Journal of Virology, vol.83, issue.6, pp.2645-2654, 2009.
DOI : 10.1128/JVI.01556-08

M. Jung, The Origin and Evolutionary History of HIV-1 Subtype C in Senegal, PLoS ONE, vol.38, issue.2, 2012.
DOI : 10.1371/journal.pone.0033579.s007

URL : https://hal.archives-ouvertes.fr/lirmm-00715442

B. F. Keele, Chimpanzee Reservoirs of Pandemic and Nonpandemic HIV-1, Science, vol.313, issue.5786, pp.523-526, 2006.
DOI : 10.1126/science.1126531

S. W. Kembel, Picante: R tools for integrating phylogenies and ecology, Bioinformatics, vol.26, issue.11, pp.1463-1464, 2010.
DOI : 10.1093/bioinformatics/btq166

K. Pond and S. L. , An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV, 2009.

S. L. Lamers, HIV-1 phylogenetic analysis shows HIV-1 transits through the meninges to brain and peripheral tissues, Infection, Genetics and Evolution, vol.11, issue.1, pp.31-37, 2011.
DOI : 10.1016/j.meegid.2010.10.016

P. Lemey, Bayesian Phylogeography Finds Its Roots, PLoS Computational Biology, vol.90, issue.9, p.1000520, 2009.
DOI : 10.1371/journal.pcbi.1000520.s002

URL : http://doi.org/10.1371/journal.pcbi.1000520

D. Maddison and W. P. Maddison, MacClade 4: Analysis of Phylogeny and Character Evolution MacClade 4, 2003.

U. Neogi, Molecular Epidemiology of HIV-1 Subtypes in India: Origin and Evolutionary History of the Predominant Subtype C, PLoS ONE, vol.25, issue.6, p.39819, 2012.
DOI : 10.1371/journal.pone.0039819.t001

T. Pommier, RAMI: a tool for identification and characterization of phylogenetic clusters in microbial communities, Bioinformatics, vol.25, issue.6, pp.736-742, 2009.
DOI : 10.1093/bioinformatics/btp051

D. Posada, jModelTest: Phylogenetic Model Averaging, Molecular Biology and Evolution, vol.25, issue.7, pp.1253-1256, 2008.
DOI : 10.1093/molbev/msn083

R. H. Ree and S. A. Smith, Maximum Likelihood Inference of Geographic Range Evolution by Dispersal, Local Extinction, and Cladogenesis, Systematic Biology, vol.57, issue.1, pp.4-14, 2008.
DOI : 10.1080/10635150701883881

F. Ronquist, Dispersal-Vicariance Analysis: A New Approach to the Quantification of Historical Biogeography, Systematic Biology, vol.46, issue.1, pp.195-203, 1997.
DOI : 10.1093/sysbio/46.1.195

M. Salemi, High-Resolution Molecular Epidemiology and Evolutionary History of HIV-1 Subtypes in Albania, PLoS ONE, vol.79, issue.5, 2008.
DOI : 10.1371/journal.pone.0001390.s005

C. Shen, Origin and Dynamics of HIV-1 Subtype C Infection in India, PLoS ONE, vol.6, issue.10, p.25956, 2011.
DOI : 10.1371/journal.pone.0025956.s001

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

D. Swofford and W. Maddison, Reconstructing ancestral character states under Wagner parsimony, Mathematical Biosciences, vol.87, issue.2, pp.199-229, 1987.
DOI : 10.1016/0025-5564(87)90074-5

M. M. Thomson and A. Ferna´ndezferna´ndez-garc?á, Phylogenetic structure in African HIV-1 subtype C revealed by selective sequential pruning, Virology, vol.415, issue.1, pp.30-38, 2011.
DOI : 10.1016/j.virol.2011.03.021

N. M. Ve´rasve´ras, High-resolution phylogenetics and phylogeography of human immunodeficiency virus type 1 subtype C epidemic in South America, Journal of General Virology, vol.92, issue.7, pp.1698-1709, 2011.
DOI : 10.1099/vir.0.028951-0

N. Vidal, Unprecedented Degree of Human Immunodeficiency Virus Type 1 (HIV-1) Group M Genetic Diversity in the Democratic Republic of Congo Suggests that the HIV-1 Pandemic Originated in Central Africa, Journal of Virology, vol.74, issue.22, 2000.
DOI : 10.1128/JVI.74.22.10498-10507.2000

R. G. Wallace, A statistical phylogeography of influenza A H5N1, Proc. Natl Acad. Sci. USA, pp.4473-4478, 2007.
DOI : 10.1073/pnas.0700435104

L. Zaslavsky, Visualization of large influenza virus sequence datasets using adaptively aggregated trees with sampling-based subscale representation, BMC Bioinformatics, vol.9, issue.1, p.7, 2008.
DOI : 10.1186/1471-2105-9-237