S. Adams, T. King, E. Bosch, and M. Jobling, The case of the unreliable SNP: Recurrent back-mutation of Y-chromosomal marker P25 through gene conversion, Forensic Science International, vol.159, issue.1, pp.14-20, 2006.
DOI : 10.1016/j.forsciint.2005.06.003

A. Auton, A. Fledel-alon, S. Pfeifer, O. Venn, L. Ségurel et al., A Fine-Scale Chimpanzee Genetic Map from Population Sequencing, Science, vol.336, issue.6078, pp.193-198, 2012.
DOI : 10.1126/science.1216872

D. Bachtrog, Y-chromosome evolution: emerging insights into processes of Y-chromosome degeneration, Nature Reviews Genetics, vol.70, issue.2, pp.113-124, 2013.
DOI : 10.1038/nrg3366

E. Betrán, J. Demuth, and A. Williford, Why Chromosome Palindromes?, International Journal of Evolutionary Biology, vol.14, issue.10a, p.207958, 2012.
DOI : 10.1017/S0016672397002899

O. Bininda-emonds, M. Cardillo, K. Jones, R. Macphee, R. Beck et al., The delayed rise of present-day mammals, Nature, vol.1, issue.7135, pp.507-512, 2007.
DOI : 10.1038/nature05634

E. Bosch, M. Hurles, A. Navarro, and M. Jobling, Dynamics of a Human Interparalog Gene Conversion Hotspot, Genome Research, vol.14, issue.5, pp.835-844, 2004.
DOI : 10.1101/gr.2177404

B. Charlesworth, The organization and evolution of the human Y chromosome, Genome Biology, vol.4, issue.9, p.226, 2003.
DOI : 10.1186/gb-2003-4-9-226

B. Charlesworth, C. Jordan, and D. Charlesworth, THE EVOLUTIONARY DYNAMICS OF SEXUALLY ANTAGONISTIC MUTATIONS IN PSEUDOAUTOSOMAL REGIONS OF SEX CHROMOSOMES, Evolution, vol.109, issue.5, pp.1339-1350, 2014.
DOI : 10.1111/evo.12364

J. Chen, D. Cooper, N. Chuzhanova, C. Férec, and G. Patrinos, Gene conversion: mechanisms, evolution and human disease, Nature Reviews Genetics, vol.98, issue.10, pp.762-775, 2007.
DOI : 10.1038/nrg2193

X. Conversion, doi:10.1093/molbev/msu155 MBE Chimpanzee Sequencing and Analysis Consortium Initial sequence of the chimpanzee genome and comparison with the human genome, Nature, vol.437, pp.69-87, 2005.

T. Connallon and A. Clark, Gene Duplication, Gene Conversion and the Evolution of the Y Chromosome, Genetics, vol.186, issue.1, pp.277-286, 2010.
DOI : 10.1534/genetics.110.116756

F. Cruciani, L. Fratta, R. Trombetta, B. Santolamazza, P. Sellitto et al., Tracing Past Human Male Movements in Northern/Eastern Africa and Western Eurasia: New Clues from Y-Chromosomal Haplogroups E-M78 and J-M12, Molecular Biology and Evolution, vol.24, issue.6, pp.1300-1311, 2007.
DOI : 10.1093/molbev/msm049

URL : https://hal.archives-ouvertes.fr/hal-00153296

F. Cruciani, B. Trombetta, V. Macaulay, and R. Scozzari, About the X-to-Y Gene Conversion Rate, The American Journal of Human Genetics, vol.86, issue.3, pp.495-497, 2010.
DOI : 10.1016/j.ajhg.2010.01.033

F. Cruciani, B. Trombetta, A. Massaia, G. Destro-bisol, D. Sellitto et al., A Revised Root for the Human Y Chromosomal Phylogenetic Tree: The Origin of Patrilineal Diversity in Africa, The American Journal of Human Genetics, vol.88, issue.6, pp.814-818, 2011.
DOI : 10.1016/j.ajhg.2011.05.002

H. Ellegren, Sex-chromosome evolution: recent progress and the influence of male and female heterogamety, Nature Reviews Genetics, vol.311, issue.3, pp.157-166, 2011.
DOI : 10.1038/nrg2948

J. Fawcett and H. Innan, The role of gene conversion in preserving rearrangement hotspots in the human genome, Trends in Genetics, vol.29, issue.10, pp.561-568, 2013.
DOI : 10.1016/j.tig.2013.07.002

P. Francalacci, L. Morelli, A. Angius, R. Berutti, F. Reinier et al., Low-Pass DNA Sequencing of 1200 Sardinians Reconstructs European Y-Chromosome Phylogeny, Science, vol.341, issue.6145, pp.565-569, 2013.
DOI : 10.1126/science.1237947

P. Hallast, P. Balaresque, G. Bowden, S. Ballereau, and M. Jobling, Recombination Dynamics of a Human Y-Chromosomal Palindrome: Rapid GC-Biased Gene Conversion, Multi-kilobase Conversion Tracts, and Rare Inversions, PLoS Genetics, vol.23, issue.7, p.1003666, 2013.
DOI : 10.1371/journal.pgen.1003666.s009

J. Hughes, H. Skaletsky, L. Brown, L. Brown, T. Pyntikova et al., Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes, Nature, vol.362, issue.7387, pp.82-86, 2012.
DOI : 10.1038/nature10843

M. Hurles, D. Willey, L. Matthews, and S. Hussain, Origins of chromosomal rearrangement hotspots in the human genome: evidence from the AZFa deletion hotspots, Genome Biology, vol.5, issue.8, p.55, 2004.
DOI : 10.1186/gb-2004-5-8-r55

D. Huson and D. Bryant, Application of Phylogenetic Networks in Evolutionary Studies, Molecular Biology and Evolution, vol.23, issue.2, pp.254-267, 2006.
DOI : 10.1093/molbev/msj030

M. Iwase, Y. Satta, H. Hirai, Y. Hirai, and N. Takahata, Frequent gene conversion events between the X and Y homologous chromosomal regions in primates, BMC Evolutionary Biology, vol.10, issue.1, p.225, 2010.
DOI : 10.1186/1471-2148-10-225

M. Jobling, A. Pandya, and C. Tyler-smith, The Y chromosome in forensic analysis and paternity testing, International Journal of Legal Medicine, vol.110, issue.3, pp.118-124, 1997.
DOI : 10.1007/s004140050050

C. Jordan and D. Charlesworth, THE POTENTIAL FOR SEXUALLY ANTAGONISTIC POLYMORPHISM IN DIFFERENT GENOME REGIONS, Evolution, vol.159, issue.2, pp.505-516, 2012.
DOI : 10.1111/j.1558-5646.2011.01448.x

T. Karafet, F. Mendez, M. Meilerman, P. Underhill, S. Zegura et al., New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree, Genome Research, vol.18, issue.5, 2008.
DOI : 10.1101/gr.7172008

Y. Katsura and Y. Satta, No Evidence for a Second Evolutionary Stratum during the Early Evolution of Mammalian Sex Chromosomes, PLoS ONE, vol.7, issue.10, p.45488, 2012.
DOI : 10.1371/journal.pone.0045488.s007

T. Kijima and H. Innan, On the Estimation of the Insertion Time of LTR Retrotransposable Elements, Molecular Biology and Evolution, vol.27, issue.4, pp.896-904, 2010.
DOI : 10.1093/molbev/msp295

C. Krausz, L. Quintana-murci, and G. Forti, Y chromosome polymorphisms in medicine, Annals of Medicine, vol.7, issue.8, pp.573-583, 2004.
DOI : 10.1161/01.HYP.16.3.277

B. Lahn and D. Page, Four Evolutionary Strata on the Human X Chromosome, Science, vol.286, issue.5441, pp.964-967, 1999.
DOI : 10.1126/science.286.5441.964

J. Lange, H. Skaletsky, S. Van-daalen, S. Embry, C. Korver et al., Isodicentric Y Chromosomes and Sex Disorders as Byproducts of Homologous Recombination that Maintains Palindromes, Cell, vol.138, issue.5, pp.855-869, 2009.
DOI : 10.1016/j.cell.2009.07.042

M. Larkin, G. Blackshields, N. Brown, R. Chenna, P. Mcgettigan et al., Clustal W and Clustal X version 2.0, Bioinformatics, vol.23, issue.21, pp.2947-2948, 2007.
DOI : 10.1093/bioinformatics/btm404

URL : https://hal.archives-ouvertes.fr/hal-00206210

A. Lee, M. Gutiérrez-arcelus, G. Perry, E. Vallender, W. Johnson et al., Analysis of copy number variation in the rhesus macaque genome identifies candidate loci for evolutionary and human disease studies, Human Molecular Genetics, vol.17, issue.8, pp.1127-1136, 2008.
DOI : 10.1093/hmg/ddn002

G. Marais, P. Campos, and I. Gordo, Can Intra-Y Gene Conversion Oppose the Degeneration of the Human Y Chromosome?: A Simulation Study, Genome Biology and Evolution, vol.2, issue.0, pp.347-357, 2010.
DOI : 10.1093/gbe/evq026

URL : https://hal.archives-ouvertes.fr/hal-00539484

F. Mendez, T. Krahn, B. Schrack, A. Krahn, K. Veeramah et al., An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree, The American Journal of Human Genetics, vol.92, issue.3, pp.454-459, 2013.
DOI : 10.1016/j.ajhg.2013.02.002

M. Nei, Molecular evolutionary genetics, 1987.

H. Niederstätter, B. Berger, D. Erhart, S. Willuweit, M. Geppert et al., Multiple recurrent mutations at four human Y-chromosomal single nucleotide polymorphism sites in a 37bp sequence tract on the ARSDP1 pseudogene, Forensic Science International: Genetics, vol.7, issue.6, pp.593-600, 2013.
DOI : 10.1016/j.fsigen.2013.05.010

N. Osada and H. Innan, Duplication and Gene Conversion in the Drosophila melanogaster Genome, PLoS Genetics, vol.16, issue.12, p.1000305, 2008.
DOI : 10.1371/journal.pgen.1000305.s004

R. Pandey, W. Sayres, M. Azad, and R. , Detecting Evolutionary Strata on the Human X Chromosome in the Absence of Gametologous Y-Linked Sequences, Genome Biology and Evolution, vol.5, issue.10, pp.1863-1871, 2013.
DOI : 10.1093/gbe/evt139

G. Poznik, B. Henn, M. Yee, E. Sliwerska, G. Euskirchen et al., Sequencing Y Chromosomes Resolves Discrepancy in Time to Common Ancestor of Males Versus Females, Science, vol.341, issue.6145, pp.562-565, 2013.
DOI : 10.1126/science.1237619

S. Ptak, A. Roeder, M. Stephens, Y. Gilad, S. Paäbo et al., Absence of the TAP2 Human Recombination Hotspot in Chimpanzees, PLoS Biology, vol.22, issue.6, pp.849-855, 2004.
DOI : 10.1371/journal.pbio.0020155.sd001

S. Repping, S. Van-daalen, L. Brown, C. Korver, J. Lange et al., High mutation rates have driven extensive structural polymorphism among human Y chromosomes, Nature Genetics, vol.67, issue.4, pp.463-467, 2006.
DOI : 10.1038/ng1754

M. Ross, D. Grafham, A. Coffey, S. Scherer, K. Mclay et al., The DNA sequence of the human X chromosome, Nature, vol.428, issue.7031, pp.325-337, 2005.
DOI : 10.1093/hmg/9.2.311

Z. Rosser, P. Balaresque, and M. Jobling, Gene Conversion between the X Chromosome and the Male-Specific Region of the Y Chromosome at a Translocation Hotspot, The American Journal of Human Genetics, vol.85, issue.1, pp.130-134, 2009.
DOI : 10.1016/j.ajhg.2009.06.009

J. Rozas, J. Sánchez-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

S. Rozen, H. Skaletsky, J. Marszalek, P. Minx, H. Cordum et al., Abundant gene conversion between arms of palindromes in human and ape Y chromosomes, Nature, vol.423, issue.6942, pp.873-876, 2003.
DOI : 10.1038/nature01723

N. Saitou and M. Nei, The neighbor-joining method: a new method for reconstructing phylogenetic trees, Mol Biol Evol, vol.4, pp.406-4425, 1987.

K. Schiebel, M. Winkelmann, A. Mertz, X. Xu, D. Page et al., Abnormal XY Interchange between a Novel Isolated Protein Kinase Gene, PRKY, and Its Homologue, PRKX, Accounts for One Third of All (Y+)XX Males and (Y-)XY Females, Human Molecular Genetics, vol.6, issue.11, pp.1985-9198, 1997.
DOI : 10.1093/hmg/6.11.1985

R. Scozzari, A. Massaia, D. Atanasio, E. Myres, N. Perego et al., Molecular Dissection of the Basal Clades in the Human Y Chromosome Phylogenetic Tree, PLoS ONE, vol.50, issue.11, p.49170, 2012.
DOI : 10.1371/journal.pone.0049170.s002

R. Scozzari, A. Massaia, B. Trombetta, G. Bellusci, N. Myres et al., An unbiased resource of novel SNP markers provides a new chronology for the human Y chromosome and reveals a deep phylogenetic structure in Africa, Genome Research, vol.24, issue.3, pp.535-544, 2014.
DOI : 10.1101/gr.160788.113

P. Shen, F. Wang, P. Underhill, C. Franco, W. Yang et al., Population genetic implications from sequence variation in four Y chromosome genes, Proceedings of the National Academy of Sciences, vol.97, issue.13, pp.7354-7359, 2000.
DOI : 10.1073/pnas.97.13.7354

H. Skaletsky, T. Kuroda-kawaguchi, P. Minx, H. Cordum, L. Hillier et al., The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes, Nature, vol.423, issue.6942, pp.825-837, 2003.
DOI : 10.1038/nature01722

J. Slattery, L. Sanner-wachter, O. Brien, and S. , Novel gene conversion between X-Y homologues located in the nonrecombining region of the Y chromosome in Felidae (Mammalia), Proceedings of the National Academy of Sciences, vol.97, issue.10, pp.5307-5312, 2000.
DOI : 10.1073/pnas.97.10.5307

B. Trombetta, F. Cruciani, D. Sellitto, and R. Scozzari, A New Topology of the Human Y Chromosome Haplogroup E1b1 (E-P2) Revealed through the Use of Newly Characterized Binary Polymorphisms, PLoS ONE, vol.12, issue.1, p.16073, 2011.
DOI : 10.1371/journal.pone.0016073.s002

B. Trombetta, F. Cruciani, P. Underhill, D. Sellitto, and R. Scozzari, Footprints of X-to-Y Gene Conversion in Recent Human Evolution, Molecular Biology and Evolution, vol.27, issue.3, pp.714-725, 2010.
DOI : 10.1093/molbev/msp231

P. Underhill and T. Kivisild, Use of Y Chromosome and Mitochondrial DNA Population Structure in Tracing Human Migrations, Annual Review of Genetics, vol.41, issue.1, pp.539-564, 2007.
DOI : 10.1146/annurev.genet.41.110306.130407

F. Veyrunes, P. Waters, P. Miethke, W. Rens, D. Mcmillan et al., Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes, Genome Research, vol.18, issue.6, pp.965-973, 2008.
DOI : 10.1101/gr.7101908

D. Vollrath, S. Foote, A. Hilton, L. Brown, P. Beer-romero et al., The human Y chromosome: a 43-interval map based on naturally occurring deletions, Science, vol.258, issue.5079, pp.52-59, 1992.
DOI : 10.1126/science.1439769

W. Wei, Q. Ayub, Y. Chen, S. Mccarthy, Y. Hou et al., A calibrated human Y-chromosomal phylogeny based on resequencing, Genome Research, vol.23, issue.2, pp.388-395, 2013.
DOI : 10.1101/gr.143198.112

W. Winckler, S. Myers, D. Richter, R. Onofrio, G. Mcdonald et al., Comparison of Fine-Scale Recombination Rates in Humans and Chimpanzees, Science, vol.308, issue.5718, pp.107-111, 2005.
DOI : 10.1126/science.1105322