Data from: Coupling of diversification and pH adaptation during the evolution of terrestrial Thaumarchaeota

The Thaumarchaeota is an abundant and ubiquitous phylum of archaea that plays a major role in the global nitrogen cycle. Previous analyses of the ammonia monooxygenase gene amoA suggest that pH is an important driver of niche specialization in these organisms. Although the ecological distribution and ecophysiology of extant Thaumarchaeota have been studied extensively, the evolutionary rise of these prokaryotes to ecological dominance in many habitats remains poorly understood. To characterize processes leading to their diversification, we investigated coevolutionary relationships between amoA, a conserved marker gene for Thaumarchaeota, and soil characteristics, by using deep sequencing and comprehensive environmental data in Bayesian comparative phylogenetics. These analyses reveal a large and rapid increase in diversification rates during early thaumarchaeotal evolution; this finding was verified by independent analyses of 16S rRNA. Our findings suggest that the entire Thaumarchaeota diversification regime was strikingly coupled to pH adaptation but less clearly correlated with several other tested environmental factors. Interestingly, the early radiation event coincided with a period of pH adaptation that enabled the terrestrial Thaumarchaeota ancestor to initially move from neutral to more acidic and alkaline conditions. In contrast to classic evolutionary models, whereby niches become rapidly filled after adaptive radiation, global diversification rates have remained stably high in Thaumarchaeota during the past 400–700 million years, suggesting an ongoing high rate of niche formation or switching for these microbes. Our study highlights the enduring importance of environmental adaptation during thaumarchaeotal evolution and, to our knowledge, is the first to link evolutionary diversification to environmental adaptation in a prokaryotic phylum.奇古菌门（Thaumarchaeota）是一类分布广泛且丰度极高的古菌类群，在全球氮循环中发挥着核心作用。此前针对氨单加氧酶基因（ammonia monooxygenase gene）amoA的分析表明，pH值是驱动这类生物生态位特化的关键因素。尽管目前已对现生奇古菌的生态分布与生态生理学开展了大量研究，但这类原核生物在诸多生境中逐步占据生态主导地位的演化起源仍有待阐明。为厘清驱动其物种分化的具体过程，本研究依托深度测序技术与涵盖全面环境数据的贝叶斯比较系统发育学（Bayesian comparative phylogenetics）方法，针对奇古菌的保守标记基因amoA与土壤环境特征之间的共演化关系展开了系统探究。分析结果显示，在奇古菌演化早期，物种分化速率曾出现大幅且快速的跃升；该结论通过针对16S rRNA的独立分析得到了验证。本研究结果表明，整个奇古菌门的物种分化模式与pH值适应存在显著关联，但与其他若干已检测环境因子的相关性则相对较弱。值得注意的是，此次早期辐射事件与一段pH值适应时期高度重合，该时期让陆生奇古菌的祖先得以从中性生境初始拓展至酸性与碱性更强的生境中。与经典演化模型——即适应辐射发生后生态位会被快速填满——不同，在过去4亿至7亿年间，奇古菌门的全球物种分化速率始终维持在较高且稳定的水平，这表明这类微生物仍在以较高的速率持续进行生态位形成或生态位转换。本研究凸显了环境适应在奇古菌演化过程中的持久重要性；据我们所知，本研究首次在原核生物门级类群中将演化分化与环境适应直接建立关联。