Data from: Extensive variation at MHC DRB in the New Zealand sea lion (Phocarctos hookeri) provides evidence for balancing selection

Marine mammals are often reported to possess reduced variation of major histocompatibility complex (MHC) genes compared with their terrestrial counterparts. We evaluated diversity at two MHC class II B genes, DQB and DRB, in the New Zealand sea lion (Phocarctos hookeri, NZSL) a species that has suffered high mortality owing to bacterial epizootics, using Sanger sequencing and haplotype reconstruction, together with next-generation sequencing. Despite this species’ prolonged history of small population size and highly restricted distribution, we demonstrate extensive diversity at MHC DRB with 26 alleles, whereas MHC DQB is dimorphic. We identify four DRB codons, predicted to be involved in antigen binding, that are evolving under adaptive evolution. Our data suggest diversity at DRB may be maintained by balancing selection, consistent with the role of this locus as an antigen-binding region and the species’ recent history of mass mortality during a series of bacterial epizootics. Phylogenetic analyses of DQB and DRB sequences from pinnipeds and other carnivores revealed significant allelic diversity, but little phylogenetic depth or structure among pinniped alleles; thus, we could neither confirm nor refute the possibility of trans-species polymorphism in this group. The phylogenetic pattern observed however, suggests some significant evolutionary constraint on these loci in the recent past, with the pattern consistent with that expected following an epizootic event. These data may help further elucidate some of the genetic factors underlying the unusually high susceptibility to bacterial infection of the threatened NZSL, and help us to better understand the extent and pattern of MHC diversity in pinnipeds.与陆生同类相比，海洋哺乳动物的主要组织相容性复合体（major histocompatibility complex, MHC）基因的变异程度普遍更低。本研究针对曾因细菌性动物流行病遭遇高死亡率的新西兰海狮（Phocarctos hookeri, NZSL），采用桑格测序（Sanger sequencing）结合单倍型重构（haplotype reconstruction）并辅以下一代测序（next-generation sequencing）的方法，对其两类MHC II类B基因——DQB与DRB的多样性进行了评估。尽管该物种种群长期维持较小规模且分布高度受限，本研究仍发现MHC DRB基因存在丰富多样性，共鉴定出26个等位基因；而MHC DQB基因仅呈现二态性。我们鉴定出4个预测参与抗原结合的DRB密码子，这些位点正处于适应性进化之下。本研究数据表明，DRB基因的多样性或许由平衡选择（balancing selection）所维持，这与该位点作为抗原结合区域的功能，以及该物种近期在多轮细菌性流行病中遭遇大规模死亡的历史相符。对鳍足类（pinnipeds）与其他食肉目（carnivores）动物的DQB和DRB序列进行系统发育分析后发现，等位基因多样性较为显著，但鳍足类等位基因的系统发育深度与结构却十分有限；因此，我们既无法证实也无法排除该类群存在跨物种多态性（trans-species polymorphism）的可能。不过，所观测到的系统发育模式暗示，这些位点在近期经历了显著的进化约束，该模式与流行病事件后预期的演化特征一致。本研究数据或有助于进一步阐明受威胁物种新西兰海狮对细菌感染异常易感的部分遗传机制，也能帮助我们更好地理解鳍足类动物MHC多样性的范围与模式。