In contrast to the western honey bee, Apis mellifera, other honey bee species have been largely neglected despite their importance and diversity. The genetic basis of the evolutionary diversification of honey bees remains largely unknown. Here, we provide a genome-wide comparison of three honey bee species, each representing one of the three subgenera of honey bees, namely the dwarf (Apis florea), giant (A. dorsata), and cavity-nesting (A. mellifera) honey bees with bumblebees as an outgroup. Our analyses resolve the phylogeny of honey bees with the dwarf honey bees diverging first. We find that evolution of increased eusocial complexity in Apis proceeds via increases in the complexity of gene regulation, which is in agreement with previous studies. However, this process seems to be related to pathways other than transcriptional control. Positive selection patterns across Apis reveal a trade-off between maintaining genome stability and generating genetic diversity, with a rapidly evolving piRNA pathway leading to genomes depleted of transposable elements, and a rapidly evolving DNA repair pathway associated with high recombination rates in all Apis species. Diversification within Apis is accompanied by positive selection in several genes whose putative functions present candidate mechanisms for lineage-specific adaptations, such as migration, immunity, and nesting behavior.

中文翻译：

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蜜蜂进化分化的基因组基础

与西方蜜蜂（Apis mellifera）相比，其他蜜蜂物种尽管具有重要性和多样性，但在很大程度上却被忽视了。蜜蜂进化多样化的遗传基础仍然很大程度上未知。在这里，我们提供了三种蜜蜂物种的全基因组比较，每种蜜蜂代表蜜蜂的三个亚属之一，即矮蜂（Apis florea）、巨型蜜蜂（A. dorsata）和空巢蜜蜂（A. mellifera）蜜蜂与大黄蜂为外群。我们的分析解决了蜜蜂的系统发育问题，其中矮蜜蜂首先分化。我们发现蜜蜂社会复杂性的进化是通过基因调控复杂性的增加而进行的，这与之前的研究一致。然而，这个过程似乎与转录控制以外的途径有关。蜜蜂的正选择模式揭示了维持基因组稳定性和产生遗传多样性之间的权衡，快速进化的 piRNA 途径导致基因组转座元件耗尽，而快速进化的 DNA 修复途径与所有蜜蜂物种的高重组率相关。蜜蜂体内的多样化伴随着几个基因的正向选择，这些基因的假定功能提供了谱系特异性适应的候选机制，例如迁移、免疫和筑巢行为。