Data from: Evolution of the immune system influences speciation rates in teleost fishes

Teleost fishes constitute the most species-rich vertebrate clade and exhibit extensive genetic and phenotypic variation, including diverse immune defense strategies. The genomic basis of a particularly aberrant strategy is exemplified by Atlantic cod, in which a loss of major histocompatibility complex (MHC) II functionality coincides with a marked expansion of MHC I genes. Through low-coverage genome sequencing (9–39×), assembly and comparative analyses for 66 teleost species, we show here that MHC II is missing in the entire Gadiformes lineage and thus was lost once in their common ancestor. In contrast, we find that MHC I gene expansions have occurred multiple times, both inside and outside this clade. Moreover, we identify an association between high MHC I copy number and elevated speciation rates using trait-dependent diversification models. Our results extend current understanding of the plasticity of the adaptive immune system and suggest an important role for immune-related genes in animal diversification.真骨鱼类（Teleost fishes）是物种多样性最高的脊椎动物支系，展现出广泛的遗传与表型变异，涵盖多种差异化的免疫防御策略。一类极具特殊性的免疫策略的基因组基础，以大西洋鳕（Atlantic cod）为典型范例：该物种的主要组织相容性复合体（major histocompatibility complex, MHC）II型功能发生缺失，同时伴随MHC I型基因的显著扩增。本研究通过对66种真骨鱼类开展低覆盖度基因组测序（9–39×）、基因组组装与比较分析，证实MHC II型在整个鳕形目（Gadiformes）支系中均缺失，因此该复合体功能在其共同祖先中仅发生过一次丢失事件。与之形成鲜明对比的是，本研究发现MHC I型基因的扩增事件曾多次独立发生，既存在于该支系内部，也出现在该支系之外。此外，本研究借助性状依赖的物种分化模型，证实MHC I型基因高拷贝数与物种形成速率提升之间存在显著关联。本研究结果拓展了学界对适应性免疫系统可塑性的现有认知，并提示免疫相关基因在动物演化多样化进程中发挥着重要作用。