Evolution of major histocompatibility complex class I and class II genes in the brown bear

• Published in: BMC Evolutionary Biology
• Main Authors: Kuduk, Katarzyna, Babik, Wiesław, Bojarska, Katarzyna, Śliwińska, Ewa B, Kindberg, Jonas, Taberlet, Pierre, Swenson, Jon E, Radwan, Jacek
• Other Authors: Institute of Environmental Sciences, Uniwersytet Jagielloński w Krakowie = Jagiellonian University (UJ), Institute of Systematics and Evolution of Animals, Polska Akademia Nauk = Polish Academy of Sciences (PAN), Institute of Nature Conservation, Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences (SLU), Laboratoire d'Ecologie Alpine (LECA), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB Université de Savoie Université de Chambéry ), Department of Ecology and Natural Resource Management, Norwegian University of Life Sciences (NMBU), Norwegian Institute for Nature Research (NINA)
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2012
• Subjects: Positive selection; Antigen binding sites; MHC gene expression; Phylogenetic analysis; Orthology; Ursidae; stat; envir; Ursus arctos
• Online Access: https://doi.org/10.1186/1471-2148-12-197; https://hal-insu.archives-ouvertes.fr/insu-00845224/file/1471-2148-12-197.pdf; https://hal-insu.archives-ouvertes.fr/insu-00845224

International audience Background: Major histocompatibility complex (MHC) proteins constitute an essential component of the vertebrate immune response, and are coded by the most polymorphic of the vertebrate genes. Here, we investigated sequence variation and evolution of MHC class I and class II DRB, DQA and DQB genes in the brown bear Ursus arctos to characterise the level of polymorphism, estimate the strength of positive selection acting on them, and assess the extent of gene orthology and trans-species polymorphism in Ursidae . Results: We found 37 MHC class I, 16 MHC class II DRB, four DQB and two DQA alleles. We confirmed the expression of several loci: three MHC class I, two DRB, two DQB and one DQA. MHC class I also contained two clusters of non-expressed sequences. MHC class I and DRB allele frequencies differed between northern and southern populations of the Scandinavian brown bear. The rate of nonsynonymous substitutions (d N ) exceeded the rate of synonymous substitutions (d S ) at putative antigen binding sites of DRB and DQB loci and, marginally significantly, at MHC class I loci. Models of codon evolution supported positive selection at DRB and MHC class I loci. Both MHC class I and MHC class II sequences showed orthology to gene clusters found in the giant panda Ailuropoda melanoleuca. Conclusions: Historical positive selection has acted on MHC class I, class II DRB and DQB, but not on the DQA locus. The signal of historical positive selection on the DRB locus was particularly strong, which may be a general feature of caniforms. The presence of MHC class I pseudogenes may indicate faster gene turnover in this class through the birth-and-death process. South - north population structure at MHC loci probably reflects origin of the populations from separate glacial refugia.