Heredity (2019) 122:205–218 https://doi.org/10.1038/s41437-018-0100-3 ARTICLE Evolution of MHC class I genes in Eurasian badgers, genus Meles (Carnivora, Mustelidae) 1 1,2 3 4 5 Shamshidin Abduriyim ● Yoshinori Nishita ● Pavel A. Kosintsev ● Evgeniy Raichev ● Risto Väinölä ● 6 7 8 1,2 Alexey P. Kryukov ● Alexei V. Abramov ● Yayoi Kaneko ● Ryuichi Masuda Received: 6 April 2018 / Revised: 30 May 2018 / Accepted: 30 May 2018 / Published online: 29 June 2018 © The Genetics Society 2018 Abstract Because of their role in immune defense against pathogens, major histocompatibility complex (MHC) genes are useful in evolutionary studies on how wild vertebrates adapt to their environments. We investigated the molecular evolution of MHC class I (MHCI) genes in four closely related species of Eurasian badgers, genus Meles. All four species of badgers showed similarly high variation in MHCI sequences compared to other Carnivora. We identified 7−21 putatively functional MHCI sequences in each of the badger species, and 2−7 sequences per individual, indicating the existence of 1−4 loci. MHCI exon 2 and 3 sequences encoding domains α1 and α2 exhibited different clade topologies in phylogenetic networks. Non- α 1234567890();,: 1234567890();,: synonymous nucleotide substitutions at codons for antigen-binding sites exceeded synonymous substitutions for domain 1 but not for domain α2, suggesting that the domains α1 and α2 likely had different evolutionary histories in these species. Positive selection and recombination seem to have shaped the variation in domain α2, whereas positive selection was dominant in shaping the variation in domain α1. In the separate phylogenetic analyses for exon 2, exon 3, and intron 2, each showed three clades of Meles alleles, with rampant trans-species polymorphism, indicative of the long-term maintenance of ancestral MHCI polymorphism by balancing selection. Electronic supplementary material The online version of this article Introduction (https://doi.org/10.1038/s41437-018-0100-3) contains supplementary material, which is available to authorized users. The major histocompatibility complex class I (MHCI) * Ryuichi Masuda proteins are expressed in all somatic cells (Bjorkman and [email protected] Parham 1990), where they perform a variety of cellular tasks by presenting self-derived and foreign cytosolic pep- 1 Department of Natural History Sciences, Graduate School of tides to receptors on CD8+ cytotoxic T lymphocytes Science, Hokkaido University, Sapporo 060-0810, Japan (Cresswell 2005). MHCI proteins thus play crucial roles in 2 Department of Biological Sciences, Faculty of Science, Hokkaido the vertebrate adaptive immune system by providing University, Sapporo 060-0810, Japan defense against various pathogens, and in autoimmunity. 3 Institute of Plant and Animal Ecology, Ural Branch, Russian The MHCI protein complex comprises two non-covalently Academy of Sciences, Ekaterinburg 620144, Russia conjugated components: the MHCI heavy chain, which is 4 Agricultural Faculty, Trakia University, 6000 Stara Zagora, encoded in the MHC region on chromosome 6 in humans, Bulgaria and on chromosome 12 or 18 in dogs (Xiao et al. 2016); a 5 Finnish Museum of Natural History, University of Helsinki, P. non-glycosylated light chain of β -microglobulin, which is a O. Box 17, FI-00014 Helsinki, Finland 2 non-MHC protein ~100 amino acids long (see York and 6 fi Federal Scienti c Center of the East Asia Terrestrial Biodiversity, Rock 1996). The MHCI glycoprotein comprises a cyto- Far Eastern Branch of the Russian Academy of Sciences, α Vladivostok 690022, Russia plasmic tail, transmembrane domain, and extracellular 1, 7 α2, and α3 domains (Bjorkman and Parham 1990) encoded Zoological Institute, Russian Academy of Sciences, α α Saint Petersburg 199034, Russia by exons 2, 3, and 4, respectively. The MHCI 1 and 2 domains are usually extensively polymorphic at both the 8 Carnivore Ecology and Conservation Research Group, Tokyo University of Agriculture and Technology, Tokyo 183-8509, nucleotide and amino-acid levels, especially for amino-acid Japan residues that function as antigen-binding sites (ABS; 206 Shamshidin Abduriyim et al. Hughes and Nei 1988), where MHCI proteins interact with with possibly the most recent population growth (Kurose intracellular peptides. Individuals and/or populations that et al. 2001; Tashima et al. 2011), whereas European and are highly polymorphic for this region have a greater chance Southwest Asian badgers underwent a historical sudden of responding to novel pathogens (Hughes and Nei 1992). population expansion during the Middle Pleistocene The genetic diversity of MHC genes thus serves as an (Marmi et al. 2006). These two badger species with a higher indicator of the immunological fitness of a population and level of diversity have effective numbers of females six its ability to respond to diseases (Sommer 2005). MHC also times greater than that of the Asian badger (Marmi et al. appears to be important in sexual selection (Sin et al. 2015; 2006). All four Meles species seem to have evolved under Gessner et al. 2017), kin recognition (Zelano and Edwards diverse pathogenic pressures, and some pathogens are 2002), individual odors (Brown et al. 1989), and pregnancy species/region-specific in these species (Hancox 1980; outcomes (Kydd et al. 2016). Harasawa et al. 2014; Moreno et al. 2015; Hornok et al. The diversity of MHC genes, particularly within exon 2 2017). A related finding is that MHCI genes in the Eur- of MHC class II and exons 2 and 3 of MHCI, is presumably opean badger have been associated with the prevalence and/ maintained by positive selection (see Akiyama et al. 2017; or intensity of certain pathogens (Sin et al. 2014). More- Saka et al. 2017), which fixes and accumulates beneficial over, these species possess several identical MHC class II point mutations through interactions between pathogens and DRB alleles, showing TSP at different taxonomic levels, their hosts. Its polymorphism is also retained by balancing and some alleles identified were novel to certain species and selection (Nishita et al. 2015, 2017)—overdominance and populations (Abduriyim et al. 2017). Comparative analyses frequency-dependent selection—which enhances the high revealed that the evolution of MHCI fundamentally differed allelic diversity within species and maintains ancestral from that of class II. Although MHC class II allelic lineages allelic diversity over long periods. Some mammalian MHC were shared, no such trans-species sharing of allelic linea- allelic lineages have persisted for more than a million years, ges was seen at the MHCI loci in some primate species even across speciation events (Figueroa et al. 1988; (Boyson et al. 1996), mostly due to the faster evolutionary Abduriyim et al. 2017). This trans-species polymorphism rate of MHC class I than that of class II (Takahashi et al. (TSP) can be detected in phylogenetic reconstructions 2000; Piontkivska and Nei 2003). Thus, all these facts (Nishita et al. 2015, 2017; Abduriyim et al. 2017; Akiyama present a compelling argument to analyze the variation and et al. 2017; Maibach et al. 2017; Saka et al. 2017), where evolution of MHCI genes in the Eurasian badger. This some alleles from one species are more closely related would also contribute to insights into whole MHC diversity (sometimes even identical) to alleles from a different spe- in these Meles species. cies than to alleles from the same species (Klein 1987; Klein The MHC class II, but not class I, gene-assortative et al. 2007). Phylogenetic analyses of MHCI genes can also mating preference was evidenced in M. meles (Sin et al. show orthologous relationships, in which sequences are 2015), although both MHC classes I and II genes have been grouped by gene or locus, rather than by species (Gu and associated with the prevalence and/or intensity of certain Nei 1999; Nei and Rooney 2005; Cao et al. 2015). The pathogens (Sin et al. 2014). Differences in the allelic orthologous relationship is yet reflected in species closely diversity of MHC class II DRB genes have been detected related (Nei and Rooney 2005; Cao et al. 2015), because among UK (Sin et al. 2012a) and continental populations of genes are diverged from their common ancestor by M. meles; 16 novel alleles were found from the continental speciation. population of M. meles, and the other 3 Meles species also Eurasian badgers, genus Meles, split into four distinct showed higher genetic diversity (Abduriyim et al. 2017). species—European badger, M. meles; Southwest Asian Sin et al. (2012b) characterized MHCI genes in M. meles badger, M. canescens; Asian badger, M. leucurus; and and found signs of separate evolutionary histories of MHCI Japanese badger, M. anakuma (Marmi et al. 2006; Sato protein domains: they studied insular population in UK and 2016)—from a common ancestor more than 2 million years biased their phylogenetic analyses toward distantly related ago (Mya) (Marmi et al. 2006; Del Cerro et al. 2010); the taxa. Thus, analyzing MHCI genes in closely related species last divergence of the Japanese badger from the continental is also needed to obtain further evidence for their findings. Asian badger occurred between 0.21–1.09 Mya (Marmi In this study we characterized highly variable MHCI et al. 2006). These species show differences in geographic exons 2 and 3 and intervening intron 2 in four Meles species variability, size, coat color and other morphological char- to compare MHCI gene content and diversity. Specifically, acteristics (Corbet 1978; Abramov 2003; Abramov and we addressed whether there are signatures of positive Puzachenko 2013; Sato 2016), and diet ecology (Kaneko selection and recombination in Meles MHC alleles; how the et al. 2006; Li et al. 2013). They also differ in demographic different alleles are related among Meles species and to histories, which might have affected the MHC diversity in alleles in other carnivorans; and whether the Meles MHCI the past: the Japanese badger revealed low genetic diversity α1 and α2 domains evolved differently.