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 Fine-Scale Chimpanzee Genetic Map from Population Sequencing, Science, vol.336, issue.6078, pp.193-198, 2012. ,
DOI : 10.1126/science.1216872
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
Why Chromosome Palindromes?, International Journal of Evolutionary Biology, vol.14, issue.10a, p.207958, 2012. ,
DOI : 10.1017/S0016672397002899
The delayed rise of present-day mammals, Nature, vol.1, issue.7135, pp.507-512, 2007. ,
DOI : 10.1038/nature05634
Dynamics of a Human Interparalog Gene Conversion Hotspot, Genome Research, vol.14, issue.5, pp.835-844, 2004. ,
DOI : 10.1101/gr.2177404
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
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
Gene conversion: mechanisms, evolution and human disease, Nature Reviews Genetics, vol.98, issue.10, pp.762-775, 2007. ,
DOI : 10.1038/nrg2193
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. ,
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
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
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
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
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
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
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
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
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
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
Application of Phylogenetic Networks in Evolutionary Studies, Molecular Biology and Evolution, vol.23, issue.2, pp.254-267, 2006. ,
DOI : 10.1093/molbev/msj030
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
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
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
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
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
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
Y chromosome polymorphisms in medicine, Annals of Medicine, vol.7, issue.8, pp.573-583, 2004. ,
DOI : 10.1161/01.HYP.16.3.277
Four Evolutionary Strata on the Human X Chromosome, Science, vol.286, issue.5441, pp.964-967, 1999. ,
DOI : 10.1126/science.286.5441.964
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
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
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
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
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
Molecular evolutionary genetics, 1987. ,
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
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
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
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
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
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
The DNA sequence of the human X chromosome, Nature, vol.428, issue.7031, pp.325-337, 2005. ,
DOI : 10.1093/hmg/9.2.311
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
DnaSP, DNA polymorphism analyses by the coalescent and other methods, Bioinformatics, vol.19, issue.18, pp.2496-2497, 2003. ,
DOI : 10.1093/bioinformatics/btg359
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
The neighbor-joining method: a new method for reconstructing phylogenetic trees, Mol Biol Evol, vol.4, pp.406-4425, 1987. ,
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
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
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
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
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
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
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
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
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
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
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
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
Comparison of Fine-Scale Recombination Rates in Humans and Chimpanzees, Science, vol.308, issue.5718, pp.107-111, 2005. ,
DOI : 10.1126/science.1105322