. Meme-dqa-*-01, Meme-DQA*02 (HQ908098.1); Taxidea taxus: Tata-DQA*01 (HQ908102) Mus musculus sequence: Mumu-DQA (V00832.1) was used to root the tree

J. Klein, The natural history of the major histocompatibility complex, 1986.

M. Nei, X. Gu, and T. Sitnikova, Evolution by the birth-and-death process in multigene families of the vertebrate immune system, Proceedings of the National Academy of Sciences, vol.94, issue.15, pp.947799-7806, 1997.
DOI : 10.1073/pnas.94.15.7799

M. Nei and A. Hughes, Balanced polymorphism and evolution by the birth-and-death process in the MHC loci, Proceedings of the 11th histocompatibility workshop and conferrence, pp.27-38, 1992.

C. Janeway, Immunobiology: The immune system in health and disease, Current Biology Publications, 2004.

J. Brown, T. Jardetzky, M. Saper, B. Samraoui, P. Bjorkman et al., A hypothetical model of the foreign antigen binding site of Class II histocompatibility molecules, Nature, vol.85, issue.6167, pp.845-850, 1988.
DOI : 10.1016/0022-2836(82)90179-6

P. Reche and E. Reinherz, Sequence Variability Analysis of Human Class I and Class II MHC Molecules: Functional and Structural Correlates of Amino Acid Polymorphisms, Journal of Molecular Biology, vol.331, issue.3, pp.623-641, 2003.
DOI : 10.1016/S0022-2836(03)00750-2

J. Brown, T. Jardetzky, J. Gorga, L. Stern, R. Urban et al., Three-dimensional structure of the human class II histocompatibility antigen HLA-DR1, Nature, vol.364, issue.6432, pp.36433-36472, 1993.
DOI : 10.1038/364033a0

G. Snell, The H-2 locus of the mouse: observations and speculations concerning its comparative genetics and its polymorphism, Folia Biologica, vol.14, issue.5, pp.335-358, 1968.

J. Borghans, J. Beltman, D. Boer, and R. , MHC polymorphism under host-pathogen coevolution, Immunogenetics, vol.55, issue.11, pp.732-739, 2004.
DOI : 10.1007/s00251-003-0630-5
URL : https://hal.archives-ouvertes.fr/pasteur-00327350

P. Doherty and R. Zinkernagel, Enhanced immunological surveillance in mice heterozygous at the H-2 gene complex, Nature, vol.112, issue.5512, pp.50-52, 1975.
DOI : 10.1038/256050a0

E. Trachtenberg, B. Korber, C. Sollars, T. Kepler, P. Hraber et al., Advantage of rare HLA supertype in HIV disease progression, Nature Medicine, vol.9, issue.7, pp.928-935, 2003.
DOI : 10.1038/nm893

D. Penn, K. Damjanovich, and W. Potts, MHC heterozygosity confers a selective advantage against multiple-strain infections, Proceedings of the National Academy of Sciences, vol.99, issue.17, pp.9911260-11264, 2002.
DOI : 10.1073/pnas.162006499
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC123244

A. Hill, C. Allsopp, D. Kwiatkowski, N. Anstey, P. Twumasi et al., Common West African HLA antigens are associated with protection from severe malaria, Nature, vol.352, issue.6336, pp.352595-600, 1991.
DOI : 10.1038/352595a0

M. Thursz, H. Thomas, B. Greenwood, and A. Hill, Heterozygote advantage for HLA class-II type in hepatitis B virus infection, Nature Genetics, vol.89, issue.1, pp.11-12, 1997.
DOI : 10.1146/ANNUREV.IMMUNOL.13.1.29

M. Carrington, Recombination within the human MHC, Immunological Reviews, vol.55, issue.1, pp.245-256, 1999.
DOI : 10.1073/pnas.89.13.5847

J. Kaufman and H. Wallny, Chicken MHC Molecules, Disease Resistance and the Evolutionary Origin of Birds, Immunology and Developmental Biology, vol.212, pp.129-141, 1996.
DOI : 10.1007/978-3-642-80057-3_12

A. Langefors, J. Lohm, M. Grahn, O. Andersen, V. Schantz et al., Association between major histocompatibility complex class IIB alleles and resistance to Aeromonas salmonicida in Atlantic salmon, Proceedings of the Royal Society B: Biological Sciences, vol.268, issue.1466, pp.268479-485, 1466.
DOI : 10.1098/rspb.2000.1378

C. Bonneaud, J. Perez-tris, P. Federici, O. Chastel, and G. Sorci, MAJOR HISTOCOMPATIBILITY ALLELES ASSOCIATED WITH LOCAL RESISTANCE TO MALARIA IN A PASSERINE, Evolution, vol.135, issue.2, pp.383-389, 2006.
DOI : 10.1073/pnas.0409454102
URL : https://hal.archives-ouvertes.fr/hal-00185020

C. Eizaguirre, S. Yeates, T. Lenz, M. Kalbe, and M. Milinski, MHC-based mate choice combines good genes and maintenance of MHC polymorphism, Molecular Ecology, vol.144, issue.30
DOI : 10.1111/j.1365-294X.2009.04243.x

G. Froeschke and S. Sommer, MHC Class II DRB Variability and Parasite Load in the Striped Mouse (Rhabdomys pumilio) in the Southern Kalahari, Molecular Biology and Evolution, vol.22, issue.5, pp.1254-1259, 2005.
DOI : 10.1093/molbev/msi112

C. Loiseau, R. Zoorob, A. Robert, O. Chastel, R. Julliard et al., Plasmodium relictum infection and MHC diversity in the house sparrow (Passer domesticus), Proceedings of the Royal Society B: Biological Sciences, vol.11, issue.3, pp.2781264-1272, 1709.
DOI : 10.1111/j.1461-0248.2007.01141.x
URL : https://hal.archives-ouvertes.fr/hal-00580373

K. Yamazaki, E. Boyse, V. Mike, H. Thaler, B. Mathieson et al., Control of mating preferences in mice by genes in the major histocompatibility complex, Journal of Experimental Medicine, vol.144, issue.5, pp.1324-1335, 1976.
DOI : 10.1084/jem.144.5.1324

J. Radwan, A. Tkacz, and A. Kloch, MHC and Preferences for Male Odour in the Bank Vole, Ethology, vol.109, issue.9, pp.827-833, 2008.
DOI : 10.1111/j.1439-0310.2008.01528.x

C. Wedekind, T. Seebeck, F. Bettens, and A. Paepke, MHC-Dependent Mate Preferences in Humans, Proceedings of the Royal Society B: Biological Sciences, vol.260, issue.1359, pp.245-249, 1359.
DOI : 10.1098/rspb.1995.0087

M. Olsson, T. Madsen, J. Nordby, E. Wapstra, and B. Ujvari, Major histocompatibility complex and mate choice in sand lizards, Proceedings of the Royal Society B: Biological Sciences, vol.270, issue.Suppl_2, pp.254-256, 2003.
DOI : 10.1098/rsbl.2003.0079

P. Hedrick, Female choice and variation in the major histocompatibility complex, Genetics, vol.132, issue.2, pp.575-581, 1992.

J. Klein, Origin of major histocompatibility complex polymorphism: The trans-species hypothesis, Human Immunology, vol.19, issue.3, pp.155-162, 1987.
DOI : 10.1016/0198-8859(87)90066-8

A. Hughes and M. Nei, Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection, Nature, vol.335, issue.6186, pp.167-170, 1988.
DOI : 10.1038/335167a0

L. Bernatchez and C. Landry, MHC studies in nonmodel vertebrates: what have we learned about natural selection in 15???years?, Journal of Evolutionary Biology, vol.15, issue.3, pp.363-377, 2003.
DOI : 10.1046/j.1420-9101.2003.00531.x

A. Hughes and M. Nei, Nucleotide substitution at major histocompatibility complex class II loci: evidence for overdominant selection., Proceedings of the National Academy of Sciences, vol.86, issue.3, pp.958-962, 1989.
DOI : 10.1073/pnas.86.3.958
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC286598

D. Garrigan and P. Hedrick, PERSPECTIVE: DETECTING ADAPTIVE MOLECULAR POLYMORPHISM: LESSONS FROM THE MHC, Evolution, vol.57, issue.8, pp.1707-1722, 2003.
DOI : 10.1554/02-732

J. Klein and F. Figueroa, The major histocompatibility complex and human evolution, Trends in Genetics, vol.6, issue.4, pp.295-386, 1986.
DOI : 10.1016/0168-9525(90)90042-5

K. Takahashi, A. Rooney, and M. Nei, Origins and divergence times of mammalian class II MHC gene clusters, Journal of Heredity, vol.91, issue.3, pp.198-204, 2000.
DOI : 10.1093/jhered/91.3.198

N. Goda, T. Mano, and R. Masuda, ) on Hokkaido, Northern Japan, Zoological Science, vol.26, issue.8, pp.530-535, 2009.
DOI : 10.2108/zsj.26.530

N. Goda, T. Mano, P. Kosintsev, A. Vorobiev, and R. Masuda, Allelic diversity of the MHC class II DRB genes in brown bears (Ursus arctos) and a comparison of DRB sequences within the family Ursidae, Tissue Antigens, vol.67, issue.5, pp.76404-410, 2010.
DOI : 10.1111/j.1399-0039.2010.01528.x

A. Bjärvall and F. Sandegren, Early Experiences with the First Radio-Marked Brown Bears in Sweden, Bears: Their Biology and Management, vol.7, pp.9-12, 1987.
DOI : 10.2307/3872600

L. Waits, P. Taberlet, J. Swenson, F. Sandegren, and R. Franzen, Nuclear DNA microsatellite analysis of genetic diversity and gene flow in the Scandinavian brown bear (Ursus arctos), Molecular Ecology, vol.28, issue.4, pp.421-431, 2000.
DOI : 10.1046/j.1523-1739.1995.951255.x
URL : https://hal.archives-ouvertes.fr/halsde-00280562

E. Bellemain, J. Swenson, O. Tallmon, S. Brunberg, and P. Taberlet, Estimating Population Size of Elusive Animals with DNA from Hunter-Collected Feces: Four Methods for Brown Bears, Conservation Biology, vol.46, issue.1, pp.150-161, 2005.
DOI : 10.1046/j.1365-2664.2003.00835.x
URL : https://hal.archives-ouvertes.fr/halsde-00276314

M. Zagalska-neubauer, W. Babik, M. Stuglik, L. Gustafsson, M. Cicho? et al., 454 sequencing reveals extreme complexity of the class II Major Histocompatibility Complex in the collared flycatcher, BMC Evolutionary Biology, vol.10, issue.1, p.454395, 2010.
DOI : 10.1186/1471-2148-10-395

W. Babik, M. Pabijan, and J. Radwan, Contrasting patterns of variation in MHC loci in the Alpine newt, Molecular Ecology, vol.22, issue.10, pp.2339-2355, 2008.
DOI : 10.1111/j.1365-294X.2008.03757.x

M. Stuglik, J. Radwan, and W. Babik, jMHC: software assistant for multilocus genotyping of gene families using next-generation amplicon sequencing, Molecular Ecology Resources, vol.148, issue.4, pp.739-742, 2011.
DOI : 10.1111/j.1755-0998.2011.02997.x

T. Hall, Bioedit: an user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposia Series, pp.95-98, 1999.

T. Lenz and S. Becker, Simple approach to reduce PCR artefact formation leads to reliable genotyping of MHC and other highly polymorphic loci ??? Implications for evolutionary analysis, Gene, vol.427, issue.1-2, pp.117-123, 2008.
DOI : 10.1016/j.gene.2008.09.013

W. Babik, P. Taberlet, M. Ejsmond, and J. Radwan, New generation sequencers as a tool for genotyping of highly polymorphic multilocus MHC system, Molecular Ecology Resources, vol.76, issue.3, pp.713-719, 2009.
DOI : 10.1111/j.1755-0998.2009.02622.x

M. Galan, E. Guivier, G. Caraux, N. Charbonnel, and J. Cosson, A 454 multiplex sequencing method for rapid and reliable genotyping of highly polymorphic genes in large-scale studies, BMC Genomics, vol.11, issue.1, p.296, 2010.
DOI : 10.1186/1471-2164-11-296
URL : https://hal.archives-ouvertes.fr/lirmm-00487231

W. Babik, Methods for MHC genotyping in non-model vertebrates, Molecular Ecology Resources, vol.76, issue.2, pp.237-251
DOI : 10.1111/j.1755-0998.2009.02788.x

J. Radwan, M. Zagalska-neubauer, M. Cicho?, J. Sendecka, K. Kulma et al., MHC diversity, malaria and lifetime reproductive success in collared flycatchers, Molecular Ecology, vol.22, issue.10, pp.2469-2479
DOI : 10.1111/j.1365-294X.2012.05547.x

J. Klein, R. Bontrop, R. Dawkins, H. Erlich, U. Gyllensten et al., Nomenclature for the major histocompatibility complexes of different species: a proposal, Immunogenetics, issue.4, pp.31217-219, 1990.

L. Excoffier and H. Lischer, Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows, Molecular Ecology Resources, vol.127, issue.3
DOI : 10.1111/j.1755-0998.2010.02847.x

M. Nei and T. Gojobori, Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions, Mol Biol Evol, vol.3, issue.5, pp.418-426, 1986.

K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei et al., MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods, Molecular Biology and Evolution, vol.28, issue.10, pp.282731-2739, 2011.
DOI : 10.1093/molbev/msr121

Z. Yang, PAML 4: Phylogenetic Analysis by Maximum Likelihood, Molecular Biology and Evolution, vol.24, issue.8, pp.1586-1591, 2007.
DOI : 10.1093/molbev/msm088

D. Posada and T. Buckley, Model Selection and Model Averaging in Phylogenetics: Advantages of Akaike Information Criterion and Bayesian Approaches Over Likelihood Ratio Tests, Systematic Biology, vol.53, issue.5, pp.793-808, 2004.
DOI : 10.1080/10635150490522304

J. Zhang, R. Nielsen, and Z. Yang, Evaluation of an Improved Branch-Site Likelihood Method for Detecting Positive Selection at the Molecular Level, Molecular Biology and Evolution, vol.22, issue.12, pp.2472-2479, 2005.
DOI : 10.1093/molbev/msi237

F. Ronquist and J. Huelsenbeck, MrBayes 3: Bayesian phylogenetic inference under mixed models, Bioinformatics, vol.19, issue.12, pp.1572-1574, 2003.
DOI : 10.1093/bioinformatics/btg180
URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/19/12/1572

B. Shum, R. Rajalingam, K. Magor, K. Azumi, W. Carr et al., A divergent non-classical class I gene conserved in salmonids, Immunogenetics, vol.49, issue.6, pp.479-490, 1999.
DOI : 10.1007/s002510050524

H. Pan, Q. Wan, and S. Fang, Molecular characterization of major histocompatibility complex class I genes from the giant panda (Ailuropoda melanoleuca), Immunogenetics, vol.8, issue.3-4, pp.3-4185, 2008.
DOI : 10.1007/s00251-008-0281-7

P. Taberlet, J. Swenson, F. Sandegren, and A. Bjarvall, Localization of a Contact Zone between Two Highly Divergent Mitochondrial DNA Lineages of the Brown Bear Ursus arctos in Scandinavia, Conservation Biology, vol.10, issue.5, pp.1255-1261, 1995.
DOI : 10.1038/358197a0

S. Manel, E. Bellemain, J. Swenson, and O. Francois, Assumed and inferred spatial structure of populations: the Scandinavian brown bears revisited, Molecular Ecology, vol.9, issue.5, pp.1327-1331, 2004.
DOI : 10.1111/j.1365-294X.2004.02074.x

Y. Chen, Y. Zhang, H. Zhang, Y. Ge, Q. Wan et al., Natural selection coupled with intragenic recombination shapes diversity patterns in the major histocompatibility complex class II genes of the giant panda, Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, vol.5, issue.3, pp.314-208, 2010.
DOI : 10.1002/jez.b.21327

A. Richman, L. Herrera, and D. Nash, MHC class II beta sequence diversity in the deer mouse (Peromyscus maniculatus): implications for models of balancing selection, Molecular Ecology, vol.26, issue.12, pp.2765-2773, 2001.
DOI : 10.1007/s002510050516

R. Furlong and Z. Yang, Diversifying and Purifying Selection in the Peptide Binding Region of DRB in Mammals, Journal of Molecular Evolution, vol.22, issue.4, pp.384-394, 2008.
DOI : 10.1007/s00239-008-9092-6

A. Aguilar, G. Roemer, S. Debenham, M. Binns, D. Garcelon et al., High MHC diversity maintained by balancing selection in an otherwise genetically monomorphic mammal, Proceedings of the National Academy of Sciences, vol.101, issue.10, pp.3490-3494, 2004.
DOI : 10.1073/pnas.0306582101

M. Ejsmond and J. Radwan, MHC diversity in bottlenecked populations: a simulation model, Conservation Genetics, vol.17, issue.1, pp.129-137, 2011.
DOI : 10.1007/s10592-009-9998-6

. Kuduk, Evolution of major histocompatibility complex class I and class II genes in the brown bear, BMC Evolutionary Biology, vol.12, issue.1, p.197, 2012.
DOI : 10.1007/s10592-009-9998-6
URL : https://hal.archives-ouvertes.fr/insu-00845224