A. Aarnink, B. Jacquelin, A. Dauba, S. Hebrard, E. Moureaux et al., MHC polymorphism in Caribbean African green monkeys, Immunogenetics, vol.66, pp.353-360, 2014.
URL : https://hal.archives-ouvertes.fr/pasteur-02006676

A. Abyzov, A. E. Urban, M. Snyder, and M. Gerstein, CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing, Genome Res, vol.21, pp.974-984, 2011.

C. Alkan, J. M. Kidd, T. Marques-bonet, G. Aksay, F. Antonacci et al., Personalized copy number and segmental duplication maps using next-generation sequencing, Nat Genet, vol.41, pp.1061-1067, 2009.

F. S. Alkuraya, Natural human knockouts and the era of genotype to phenotype, Genome Med, vol.7, p.48, 2015.

J. S. Allan, M. Short, M. E. Taylor, S. Su, V. M. Hirsch et al., Species-specific diversity among simian immunodeficiency viruses from African green monkeys, J Virol, vol.65, pp.2816-2828, 1991.

F. Antonacci, M. Y. Dennis, J. Huddleston, P. H. Sudmant, K. M. Steinberg et al., Palindromic GOLGA8 core duplicons promote chromosome 15q13.3 microdeletion and evolutionary instability, Nat Genet, vol.46, pp.1293-1302, 2014.

J. A. Bailey and E. E. Eichler, Primate segmental duplications: crucibles of evolution, diversity and disease, Nat Rev Genet, vol.7, pp.552-564, 2006.

G. Benson, Tandem repeats finder: a program to analyze DNA sequences, Nucleic Acids Res, vol.27, pp.573-580, 1999.

M. Bonhomme, A. Blancher, S. Cuartero, L. Chikhi, and B. Crouau-roy, Origin and number of founders in an introduced insular primate: estimation from nuclear genetic data, Mol Ecol, vol.17, pp.1009-1019, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00257840

R. Cagliani, S. Riva, M. Biasin, M. Fumagalli, U. Pozzoli et al., Genetic diversity at endoplasmic reticulum aminopeptidases is maintained by balancing selection and is associated with natural resistance to HIV-1 infection, Hum Mol Genet, vol.19, pp.4705-4714, 2010.

L. Carbone, R. A. Harris, S. Gnerre, K. R. Veeramah, B. Lorente-galdos et al., Gibbon genome and the fast karyotype evolution of small apes, Nature, vol.513, pp.195-201, 2014.

G. M. Cooper, B. P. Coe, S. Girirajan, J. A. Rosenfeld, T. H. Vu et al., A copy number variation morbidity map of developmental delay, Nat Genet, vol.43, pp.838-846, 2011.

R. Daza-vamenta, G. Glusman, L. Rowen, B. Guthrie, and D. E. Geraghty, Genetic divergence of the rhesus macaque major histocompatibility complex, Genome Res, vol.14, pp.1501-1515, 2004.

J. D. Elsworth, J. D. Jentsch, S. M. Groman, R. H. Roth, E. D. Redmond et al., Low circulating levels of bisphenol-A induce cognitive deficits and loss of asymmetric spine synapses in dorsolateral prefrontal cortex and hippocampus of adult male monkeys, J Comp Neurol, vol.523, pp.1248-1257, 2015.

P. Finelli, R. Stanyon, R. Plesker, F. , M. A. et al., Reciprocal chromosome painting shows that the great difference in diploid number between human and African green monkey is mostly due to non-Robertsonian fissions, Mamm Genome, vol.10, pp.713-718, 1999.

P. Flicek, M. R. Amode, D. Barrell, K. Beal, K. Billis et al., Nucleic Acids Res, vol.42, pp.749-755, 2014.

A. Fomsgaard, J. Allan, M. Gravell, W. T. London, V. M. Hirsch et al., Molecular characterization of simian lentiviruses from east African green monkeys, J Med Primatol, vol.19, pp.295-303, 1990.

M. Fukasawa, T. Miura, A. Hasegawa, S. Morikawa, H. Tsujimoto et al., Sequence of simian immunodeficiency virus from African green monkey, a new member of the HIV/SIV group, Nature, vol.333, pp.457-461, 1988.

F. Gao, E. Bailes, D. L. Robertson, Y. Chen, C. M. Rodenburg et al., Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytes, Nature, vol.397, pp.436-441, 1999.

S. Gnerre, I. Maccallum, D. Przybylski, F. J. Ribeiro, J. N. Burton et al., High-quality draft assemblies of mammalian genomes from massively parallel sequence data, Proc Natl Acad Sci, vol.108, pp.1513-1518, 2011.

O. Gokcumen, V. Tischler, J. Tica, Q. Zhu, R. C. Iskow et al., Primate genome architecture influences structural variation mechanisms and functional consequences, Proc Natl Acad Sci, vol.110, pp.15764-15769, 2013.

S. Goldstein, I. Ourmanov, C. R. Brown, B. E. Beer, W. R. Elkins et al., Wide range of viral load in healthy African green monkeys naturally infected with simian immunodeficiency virus, J Virol, vol.74, pp.11744-11753, 2000.

M. G. Grabherr, B. J. Haas, M. Yassour, J. Z. Levin, D. A. Thompson et al., Full-length transcriptome assembly from RNA-Seq data without a reference genome, Nat Biotechnol, vol.29, pp.644-652, 2011.

K. Guschanski, J. Krause, S. Sawyer, L. M. Valente, S. Bailey et al., Next-generation museomics disentangles one of the largest primate radiations, Syst Biol, vol.62, pp.539-554, 2013.

M. V. Han, G. W. Thomas, J. Lugo-martinez, and M. W. Hahn, Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3, Mol Biol Evol, vol.30, pp.1987-1997, 2013.

R. ;. Harris, . Pa, V. M. Hirsch, R. A. Olmsted, M. Murphey-corb et al., An African primate lentivirus (SIVsm) closely related to HIV-2, Nature, vol.339, pp.389-392, 1989.

V. M. Hirsch, C. Mcgann, G. Dapolito, S. Goldstein, A. Ogen-odoi et al., Identification of a new subgroup of SIVagm in tantalus monkeys, Virology, vol.197, pp.426-430, 1993.

J. F. Hughes, H. Skaletsky, L. G. Brown, T. Pyntikova, T. Graves et al., Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes, Nature, vol.483, pp.82-86, 2012.

, Initial sequencing and analysis of the human genome, Nature, vol.409, pp.860-921, 2001.

A. J. Jasinska, S. Service, M. Levinson, E. Slaten, O. Lee et al., A genetic linkage map of the vervet monkey (Chlorocebus aethiops sabaeus), Mamm Genome, vol.18, pp.347-360, 2007.

A. J. Jasinska, M. K. Lin, S. Service, O. W. Choi, J. Deyoung et al., A non-human primate system for large-scale genetic studies of complex traits, Hum Mol Genet, vol.21, pp.3307-3316, 2012.

A. J. Jasinska, C. A. Schmitt, S. K. Service, R. M. Cantor, K. Dewar et al., Systems biology of the vervet monkey, ILAR J, vol.54, pp.122-143, 2013.

J. W. Jdo, A. Baldini, D. C. Ward, S. T. Reeders, and R. A. Wells, Origin of human chromosome 2: an ancestral telomere-telomere fusion, Proc Natl Acad Sci, vol.88, pp.9051-9055, 1991.

M. J. Jin, H. Hui, D. L. Robertson, M. C. Muller, F. Barre-sinoussi et al., Mosaic genome structure of simian immunodeficiency virus from West African green monkeys, EMBO J, vol.13, pp.2935-2947, 1994.

J. J. Johnston, K. L. Lewis, D. Ng, L. N. Singh, J. Wynter et al., Individualized iterative phenotyping for genome-wide analysis of loss-of-function mutations, Am J Hum Genet, vol.96, pp.913-925, 2015.

Y. Kapustin, A. Souvorov, T. Tatusova, and D. Lipman, Splign: algorithms for computing spliced alignments with identification of paralogs, Biol Direct, vol.3, p.20, 2008.

H. Kehrer-sawatzki and D. N. Cooper, Molecular mechanisms of chromosomal rearrangement during primate evolution, Chromosome Res, vol.16, pp.41-56, 2008.

W. J. Kent, BLAT-the BLAST-like alignment tool, Genome Res, vol.12, pp.656-664, 2002.

J. Kingdon, East African mammals: an atlas of evolution, 1984.

S. Kurtz, A. Phillippy, A. L. Delcher, M. Smoot, M. Shumway et al., Versatile and open software for comparing large genomes, Genome Biol, vol.5, p.12, 2004.

R. M. Layer, C. Chiang, A. R. Quinlan, and I. M. Hall, LUMPY: a probabilistic framework for structural variant discovery, Genome Biol, vol.15, p.84, 2014.

H. Li and R. Durbin, Fast and accurate short read alignment with BurrowsWheeler transform, Bioinformatics, vol.25, pp.1754-1760, 2009.

J. Long, Introduced mammals of the world, 2003.

D. Ma, A. Jasinska, J. Kristoff, J. P. Grobler, T. Turner et al., SIVagm infection in wild African green monkeys from South Africa: epidemiology, natural history, and evolutionary considerations, PLoS Pathog, vol.9, p.1003011, 2013.

D. Ma, A. J. Jasinska, F. Feyertag, V. Wijewardana, J. Kristoff et al., Factors associated with simian immunodeficiency virus transmission in a natural African nonhuman primate host in the wild, J Virol, vol.88, pp.5687-5705, 2014.

T. Marques-bonet, O. A. Ryder, and E. E. Eichler, Sequencing primate genomes: what have we learned?, Annu Rev Genomics Hum Genet, vol.10, pp.355-386, 2009.

A. Mckenna, M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis et al., The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data, Genome Res, vol.20, pp.1297-1303, 2010.

O. Hill and W. C. , Primates: comparative anatomy and taxonomy, vol.6, 1966.

F. Pasquau, J. Ena, R. Sanchez, J. M. Cuadrado, C. Amador et al., Leishmaniasis as an opportunistic infection in HIV-infected patients: determinants of relapse and mortality in a collaborative study of 228 episodes in a Mediterreanean region, Eur J Clin Microbiol Infect Dis, vol.24, pp.411-418, 2005.

P. Perelman, W. E. Johnson, C. Roos, H. N. Seuanez, J. E. Horvath et al., A molecular phylogeny of living primates, PLoS Genet, vol.7, p.1001342, 2011.

L. Pozzi, J. A. Hodgson, A. S. Burrell, K. N. Sterner, R. L. Raaum et al., Primate phylogenetic relationships and divergence dates inferred from complete mitochondrial genomes, Mol Phylogenet Evol, vol.75, pp.165-183, 2014.

J. Prado-martinez, P. H. Sudmant, J. M. Kidd, H. Li, J. L. Kelley et al., Great ape genetic diversity and population history, Nature, vol.499, pp.471-475, 2013.

K. D. Pruitt, G. R. Brown, S. M. Hiatt, F. Thibaud-nissen, A. Astashyn et al., RefSeq: an update on mammalian reference sequences, Nucleic Acids Res, vol.42, pp.756-763, 2014.

G. Rhesus-macaque, A. Sequencing, and . Consortium, Evolutionary and biomedical insights from the rhesus macaque genome, Science, vol.316, pp.222-234, 2007.

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

A. Ruiz-herrera, F. Garcia, M. Aguilera, M. Garcia, P. Fontanals et al., Comparative chromosome painting in Aotus reveals a highly derived evolution, Am J Primatol, vol.65, pp.73-85, 2005.

S. Schiffels and R. Durbin, Inferring human population size and separation history from multiple genome sequences, Nat Genet, vol.46, pp.919-925, 2014.

K. P. Schliep, phangorn: phylogenetic analysis in R, Bioinformatics, vol.27, pp.592-593, 2011.

S. K. Service, T. M. Teslovich, C. Fuchsberger, V. Ramensky, P. Yajnik et al., Re-sequencing expands our understanding of the phenotypic impact of variants at GWAS loci, PLoS Genet, vol.10, p.1004147, 2014.

R. Stanyon, M. Rocchi, F. Bigoni, and N. Archidiacono, Evolutionary molecular cytogenetics of catarrhine primates: past, present and future, Cytogenet Genome Res, vol.137, pp.273-284, 2012.

P. H. Sudmant, J. Huddleston, C. R. Catacchio, M. Malig, L. W. Hillier et al., Evolution and diversity of copy number variation in the great ape lineage, Genome Res, vol.23, pp.1373-1382, 2013.

M. Ventura, S. Weigl, L. Carbone, M. F. Cardone, D. Misceo et al., Recurrent sites for new centromere seeding, Genome Res, vol.14, pp.1696-1703, 2004.

M. Ventura, F. Antonacci, M. F. Cardone, R. Stanyon, D. 'addabbo et al., Evolutionary formation of new centromeres in macaque, Science, vol.316, pp.243-246, 2007.

J. Wang, D. Duncan, Z. Shi, and B. Zhang, WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013, Nucleic Acids Res, vol.41, pp.77-83, 2013.

A. Watanabe, T. Shiina, S. Shimizu, K. Hosomichi, K. Yanagiya et al., A BAC-based contig map of the cynomolgus macaque (Macaca fascicularis) major histocompatibility complex genomic region, Genomics, vol.89, pp.402-412, 2007.

R. W. Wiseman, J. A. Karl, P. S. Bohn, F. A. Nimityongskul, G. J. Starrett et al., Haplessly hoping: macaque major histocompatibility complex made easy, ILAR J, vol.54, pp.196-210, 2013.

G. Yan, G. Zhang, X. Fang, Y. Zhang, C. Li et al., Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques, Nat Biotechnol, vol.29, pp.1019-1023, 2011.

G. Yao, L. Ye, H. Gao, P. Minx, W. C. Warren et al., Graph accordance of next-generation sequence assemblies, Bioinformatics, vol.28, pp.13-16, 2012.

M. Zarrei, J. R. Macdonald, D. Merico, and S. W. Scherer, A copy number variation map of the human genome, Nature Rev Genet, vol.16, pp.172-183, 2015.

A. V. Zimin, A. S. Cornish, M. D. Maudhoo, R. M. Gibbs, X. Zhang et al., A new rhesus macaque assembly and annotation for next-generation sequencing analyses, Biol Direct, vol.9, p.20, 2014.