Major histocompatibility complex (MHC) genes code for key proteins of the adaptive immune system, which present antigens from intra-cellular (MHC class I) and extra-cellular (MHC class II) pathogens. Because of their unprecedented diversity, MHC genes have long been an object of scientific interest, but due to methodological difficulties in genotyping of duplicated loci, our knowledge on the evolution of the MHC across different vertebrate lineages is still limited. Here, we compared the evolution of MHC class I and class II genes in three sister clades of common passerine birds, finches (Fringillinae and Carduelinae) and buntings (Emberizidae) using a uniform methodological (genotyping and data processing) approach and uniform sample sizes. Our analyses revealed contrasting evolutionary trajectories of the two MHC classes. We found a stronger signature of pervasive positive selection and higher allele diversity (allele numbers) at the MHC class I than class II. In contrast, MHC class II genes showed greater allele divergence (in terms of nucleotide diversity) and a much stronger recombination (gene conversion) signal. Gene copy numbers at both MHC class I and class II evolved via fluctuating selection and drift (Brownian Motion evolution), but the evolutionary rate was higher at class I. Our study constitutes one of few existing examples, where evolution of MHC class I and class II genes was directly compared using a multi-species approach. We recommend that re-focusing MHC research from single-species and single-class approaches towards multi-species analyses of both MHC classes can substantially increase our understanding MHC evolution in a broad phylogenetic context.

主要组织相容性复合体 (MHC) 基因编码适应性免疫系统的关键蛋白，这些蛋白呈递来自细胞内（MHC I 类）和细胞外（MHC II 类）病原体的抗原。由于其前所未有的多样性，MHC 基因长期以来一直是科学界关注的对象，但由于重复基因座基因分型的方法学困难，我们对不同脊椎动物谱系的 MHC 进化的了解仍然有限。在这里，我们使用统一的方法（基因分型和数据处理）方法和统一的样本量，比较了常见雀形目鸟类、雀类（燕雀亚科和雀鸟亚科）和鹀科（Emberizidae）三个姐妹进化枝中 MHC I 类和 II 类基因的进化。我们的分析揭示了两个 MHC 类别的截然不同的进化轨迹。我们发现 MHC I 类比 II 类具有更强的普遍正选择特征和更高的等位基因多样性（等位基因数量）。相比之下，MHC II 类基因表现出更大的等位基因分歧（就核苷酸多样性而言）和更强的重组（基因转换）信号。MHC I 类和 II 类的基因拷贝数都是通过波动选择和漂移（布朗运动进化）进化的，但 I 类的进化率更高。我们的研究是现有的少数例子之一，其中 MHC I 类和 II 类的进化使用多物种方法直接比较 II 基因。我们建议将 MHC 研究的重点从单物种和单类别方法重新转向对两个 MHC 类别的多物种分析，可以大大增加我们在广泛的系统发育背景下对 MHC 进化的理解。