H. Schaschl, P. Wandeler, and T. Bucher, Achaz von Hardenberg and Bruno Bassano provided samples of Alpine ibex from the Gran Paradiso National Park. We are grateful to a number of hunting authorities and game wardens in Switzerland and Italy for their precious help to collect the samples. The preparation of the RAD library was carried out at the Genetic Diversity Center at ETH Zürich. Members of the International Goat Genome Consortium The International Goat Genome Consortium (www.goatgenome.org) is coordinated by Wenguang Zhang (KIZ, IMAU) and Gwenola Tosser-Klopp (INRA), Members include: Paolo Ajmone (Unicatt), Marcel Amills (UAB), Simon Boitard (INRA), Wenbin Chen (BGI), Shifeng Cheng (BGI), Yang Dong (KIZ), Thomas Faraut (INRA), Omar Faruque (BAU), Henri Heuven (UU), Zhao Jinshan (IMAU), Lv Jun (KIZ), Hans Lenstra (UU), Xin Li (KIZ), Xin Liu (BGI), Carole Moreno (INRA), Philippe Mulsant (INRA), Shengkai Pan (BGI)

A. Stella, ;. Ptp), and A. Valentini, Shuhong Zhao (HZAU) from the following organizations, vol.BGI

Y. Satta, Y. J. Li, and N. Takahata, The neutral theory and natural selection in the HLA region, Front Biosci, vol.3, pp.459-467, 1998.

S. Beck, D. Geraghty, H. Inoko, L. Rowen, and B. Aguado, Complete sequence and gene map of a human major histocompatibility complex, Nature, vol.401, pp.921-923, 1999.

S. Gaudieri, R. Dawkins, K. Habara, J. Kulski, and T. Gojobori, SNP profile within the human major histocompatibility complex reveals an extreme and interrupted level of nucleotide diversity, Genome Res, vol.10, pp.1579-1586, 2000.

J. Klein and F. Figueroa, Evolution of the major histocompatibility complex, Crit Rev Immunol, vol.6, pp.295-386, 1986.

J. W. Gregersen, K. R. Kranc, X. Ke, P. Svendsen, and L. S. Madsen, Functional epistasis on a common MHC haplotype associated with multiple sclerosis, Nature, vol.443, pp.574-577, 2006.

P. De-bakker, G. Mcvean, P. C. Sabeti, M. M. Miretti, and T. Green, A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC, Nat Genet, vol.38, pp.1166-1172, 2006.

A. Kloch, W. Babik, A. Bajer, E. Si?ski, and J. Radwan, Effects of an MHC-DRB genotype and allele number on the load of gut parasites in the bank vole Myodes glareolus, Mol Ecol, vol.19, pp.255-265, 2010.

M. K. Oliver, S. Telfer, and S. B. Piertney, Major histocompatibility complex (MHC) heterozygote superiority to natural multi-parasite infections in the water vole (Arvicola terrestris), Proc Biol Sci, vol.276, pp.1119-1128, 2009.

H. Westerdahl, M. Asghar, D. Hasselquist, and S. Bensch, Quantitative disease resistance: to better understand parasite-mediated selection on major histocompatibility complex, Proc Biol Sci, vol.279, pp.577-584, 2012.

L. Spurgin and D. S. Richardson, How pathogens drive genetic diversity: MHC, mechanisms and misunderstandings, Proc Biol Sci, vol.277, pp.979-988, 2010.

S. B. Piertney and M. K. Oliver, The evolutionary ecology of the major histocompatibility complex, Heredity, vol.96, pp.7-21, 2006.

C. Van-oosterhout, A new theory of MHC evolution: beyond selection on the immune genes, Proc Biol Sci, vol.276, pp.657-665, 2009.

N. Takahata, Y. Satta, and J. Klein, Polymorphism and balancing selection at major histocompatibility complex loci, Genetics, vol.130, pp.925-938, 1992.

M. H. Schierup, X. Vekemans, and D. Charlesworth, The effect of subdivision on variation at multi-allelic loci under balancing selection, Genet Res, vol.76, pp.51-62, 2000.

F. Figueroa, E. Günther, and J. Klein, MHC polymorphism pre-dating speciation, Nature, vol.335, pp.265-267, 1988.

P. W. Hedrick, Adaptive introgression in animals: examples and comparison to new mutation and standing variation as sources of adaptive variation, Mol Ecol, vol.22, pp.4606-4618, 2013.

V. Castric, J. Bechsgaard, M. H. Schierup, and X. Vekemans, Repeated adaptive introgression at a gene under multiallelic balancing selection, PLoS Genet, vol.4, p.1000168, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00305315

P. Feulner, J. Gratten, J. W. Kijas, P. M. Visscher, and J. M. Pemberton, Introgression and the fate of domesticated genes in a wild mammal population, Mol Ecol, vol.22, pp.4210-4221, 2013.

K. M. Wegner and C. Eizaguirre, New(t)s and views from hybridizing MHC genes: introgression rather than trans-species polymorphism may shape allelic repertoires, Mol Ecol, vol.21, pp.779-781, 2012.

L. Abi-rached, M. J. Jobin, S. Kulkarni, A. Mcwhinnie, and K. Dalva, The shaping of modern human immune systems by multiregional admixture with archaic humans, Science, vol.334, pp.89-94, 2011.

C. Vila, J. Seddon, and H. Ellegren, Genes of domestic mammals augmented by backcrossing with wild ancestors, Trends Genet, vol.21, pp.214-218, 2005.

K. Nadachowska-brzyska, P. Zieli?ski, J. Radwan, and W. Babik, Interspecific hybridization increases MHC class II diversity in two sister species of newts, Mol Ecol, vol.21, pp.887-906, 2012.

S. Naderi, H. Rezaei, F. Pompanon, M. Blum, and R. Negrini, The goat domestication process inferred from large-scale mitochondrial DNA analysis of wild and domestic individuals, Proc Natl Acad Sci U S A, vol.105, pp.17659-17664, 2008.
URL : https://hal.archives-ouvertes.fr/halsde-00377989

C. Maudet, C. Miller, B. Bassano, C. Breitenmoser-wursten, and D. Gauthier, Microsatellite DNA and recent statistical methods in wildlife conservation management: applications in Alpine ibex (Capra ibex ibex), Mol Ecol, vol.11, pp.421-436, 2002.
URL : https://hal.archives-ouvertes.fr/halsde-00279796

I. Biebach and L. F. Keller, A strong genetic footprint of the re-introduction history of Alpine ibex (Capra ibex ibex), Mol Ecol, vol.18, pp.5046-5058, 2009.

I. Biebach and L. F. Keller, Inbreeding in reintroduced populations: the effects of early reintroduction history and contemporary processes, Conserv Genet, vol.11, pp.527-538, 2010.

H. Schaschl, P. Wandeler, F. Suchentrunk, G. Obexer-ruff, and S. J. Goodman, Selection and recombination drive the evolution of MHC class II DRB diversity in ungulates, Heredity, vol.97, pp.427-437, 2006.

S. Alasaad, I. Biebach, C. Grossen, R. C. Soriguer, and J. M. Pérez, Microsatellite-based genotyping of MHC class II DRB1 gene in Iberian and Alpine ibex, Eur J Wildl Res, vol.58, pp.743-748, 2012.

T. Takada, Y. Kikkawa, H. Yonekawa, and T. Amano, Analysis of goat MHC class II DRA and DRB genes: identification of the expressed gene and new DRB alleles, Immunogenetics, vol.48, pp.408-412, 1998.

H. Schaschl, F. Suchentrunk, S. Hammer, and S. J. Goodman, Recombination and the origin of sequence diversity in the DRB MHC class II locus in chamois (Rupicapra spp.), Immunogenetics, vol.57, pp.108-115, 2005.

S. Mona, B. Crestanello, S. Bankhead-dronnet, E. Pecchioli, and S. Ingrosso, Disentangling the effects of recombination, selection, and demography on the genetic variation at a major histocompatibility complex class II gene in the alpine chamois, Mol Ecol, vol.17, pp.4053-4067, 2008.

F. Schwaiger, J. Buitkamp, E. Weyers, and J. Epplen, Typing of Artiodactyl MHC-DRB genes with the help of intronic simple repeated DNA-sequences, Mol Ecol, vol.2, pp.55-59, 1993.

J. Klein, Natural history of the major histocompatibility complex, vol.1, p.pp, 1986.

A. Ropiquet and A. Hassanin, Hybrid origin of the Pliocene ancestor of wild goats, Mol Phylogenet Evol, vol.41, pp.395-404, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00174869

M. Hernández-fernández and E. S. Vrba, A complete estimate of the phylogenetic relationships in Ruminantia: a dated species-level supertree of the extant ruminants, Biol Rev, vol.80, pp.269-302, 2005.

M. Giacometti, R. Roganti, D. De-tann, N. Stahlberger-saitbekova, and G. Obexer-ruff, Alpine ibex Capra ibex ibex x domestic goat C. aegagrus domestica hybrids in a restricted area of southern Switzerland, Wildlife Biol, vol.10, pp.137-143, 2004.

J. Klein, A. Sato, S. Nagl, O. 'huigín, and C. , Molecular trans-species polymorphism, Annu Rev Ecol Syst, pp.1-21, 1998.

L. Bernatchez and C. Landry, MHC studies in nonmodel vertebrates: what have we learned about natural selection in 15 years?, J Evolution Biol, vol.16, pp.363-377, 2003.

J. Pritchard, M. Stephens, and P. Donnelly, Inference of population structure using multilocus genotype data, Genetics, vol.155, pp.945-959, 2000.

Y. Dong, M. Xie, Y. Jiang, N. Xiao, and X. Du, Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus), Nat Biotechnol, vol.31, pp.135-141, 2012.
URL : https://hal.archives-ouvertes.fr/hal-02651460

T. Bruen, H. Philippe, and D. Bryant, A simple and robust statistical test for detecting the presence of recombination, Genetics, vol.172, pp.2665-2681, 2006.

G. Tosser-klopp, P. Bardou, O. Bouchez, C. Cabau, and R. Crooijmans, Design and characterization of a 52K SNP chip for goats, PLoS ONE, vol.9, p.86227, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01019568

D. H. Huson and D. Bryant, Application of phylogenetic networks in evolutionary studies, Mol Biol Evol, vol.23, pp.254-267, 2006.

M. Slatkin, Linkage disequilibrium -understanding the evolutionary past and mapping the medical future, Nat Rev Genet, vol.9, pp.477-485, 2008.

A. D. Cutter and B. A. Payseur, Genomic signatures of selection at linked sites: unifying the disparity among species, Nat Rev Genet, vol.14, pp.262-274, 2013.

P. Sabeti, D. Reich, J. Higgins, H. Levine, and D. Richter, Detecting recent positive selection in the human genome from haplotype structure, Nature, vol.419, pp.832-837, 2002.

B. Voight, S. Kudaravalli, X. Wen, and J. Pritchard, A map of recent positive selection in the human genome, Plos Biol, vol.4, pp.446-458, 2006.

F. Allendorf, R. Leary, P. Spruell, and J. Wenburg, The problems with hybrids: setting conservation guidelines, Trends Ecol Evol, vol.16, pp.613-622, 2001.

J. N. Derr, P. W. Hedrick, N. D. Halbert, L. Plough, and L. K. Dobson, Phenotypic effects of cattle mitochondrial DNA in American bison, Conserv Biol, vol.26, pp.1130-1136, 2012.

T. M. Anderson, B. M. Vonholdt, S. I. Candille, M. Musiani, and C. Greco, Molecular and evolutionary history of melanism in North American gray wolves, Science, vol.323, pp.1339-1343, 2009.

P. D. Etter, S. Bassham, P. A. Hohenlohe, E. A. Johnson, and W. A. Cresko, SNP discovery and genotyping for evolutionary genetics using RAD sequencing, Methods Mol Biol, vol.772, pp.157-178, 2011.

B. Langmead and S. L. Salzberg, Fast gapped-read alignment with Bowtie 2, Nat Methods, vol.9, pp.357-359, 2012.

M. A. Depristo, E. Banks, R. Poplin, K. V. Garimella, and J. R. Maguire, A framework for variation discovery and genotyping using next-generation DNA sequencing data, Nat Genet, vol.43, pp.491-498, 2011.

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

H. Lischer and L. Excoffier, PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs, Bioinformatics, vol.28, pp.298-299, 2012.

S. Purcell, B. Neale, K. Todd-brown, L. Thomas, and M. Ferreira, PLINK: a tool set for whole-genome association and population-based linkage analyses, Am J Hum Genet, vol.81, pp.559-575, 2007.

P. Scheet and M. Stephens, A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase, Am J Hum Genet, vol.78, pp.629-644, 2006.

W. G. Hill and B. S. Weir, Variances and covariances of squared linkage disequilibria in finite populations, Theor Popul Biol, vol.33, pp.54-78, 1988.

M. Gautier and M. Naves, Footprints of selection in the ancestral admixture of a New World Creole cattle breed, Mol Ecol, vol.20, pp.3128-3143, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01000166

K. Katoh and D. M. Standley, MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol Biol Evol, vol.30, pp.772-780, 2013.