Data from: Evolutionary origins and diversification of proteobacterial mutualists

Mutualistic bacteria infect most eukaryotic species in nearly every biome. Nonetheless, two dilemmas remain unresolved about bacterial–eukaryote mutualisms: how do mutualist phenotypes originate in bacterial lineages and to what degree do mutualists traits drive or hinder bacterial diversification? Here, we reconstructed the phylogeny of the hyperdiverse phylum Proteobacteria to investigate the origins and evolutionary diversification of mutualistic bacterial phenotypes. Our ancestral state reconstructions (ASRs) inferred a range of 34–39 independent origins of mutualist phenotypes in Proteobacteria, revealing the surprising frequency with which host-beneficial traits have evolved in this phylum. We found proteobacterial mutualists to be more often derived from parasitic than from free-living ancestors, consistent with the untested paradigm that bacterial mutualists most often evolve from pathogens. Strikingly, we inferred that mutualists exhibit a negative net diversification rate (speciation minus extinction), which suggests that mutualism evolves primarily via transitions from other states rather than diversification within mutualist taxa. Moreover, our ASRs infer that proteobacterial mutualist lineages exhibit a paucity of reversals to parasitism or to free-living status. This evolutionary conservatism of mutualism is contrary to long-standing theory, which predicts that selection should often favour mutants in microbial mutualist populations that exploit or abandon more slowly evolving eukaryotic hosts.

共生细菌几乎在所有生物群落中均可侵染多数真核生物物种。尽管如此，关于细菌-真核生物共生关系，仍存在两个尚未解决的核心难题：其一，共生表型如何在细菌谱系中起源；其二，共生菌性状在多大程度上推动或阻碍细菌的多样化进程。本研究通过重构物种多样性极高的变形菌门(Proteobacteria)系统发育树，探究共生细菌表型的起源与演化多样化历程。我们的祖先状态重构(Ancestral State Reconstructions, ASRs)结果显示，变形菌门中共生表型的独立起源次数为34至39次，揭示了该门类中宿主有益性状演化的惊人频率。研究发现，变形菌门的共生菌多起源于寄生菌祖先，而非自由生活菌祖先，这与“细菌共生关系大多起源于病原菌”这一尚未经实证的范式相符。值得注意的是，我们推断共生菌的净多样化率（物种形成率减去灭绝率）为负值，这表明共生关系的演化主要通过从其他状态向共生状态的转变实现，而非依赖共生类群内部的多样化进程。此外，我们的祖先状态重构结果显示，变形菌门的共生菌谱系极少发生向寄生状态或自由生活状态的逆转。这种共生关系的演化保守性与长期以来的经典理论相悖，该理论预测，自然选择通常会青睐那些利用或抛弃演化速率较慢的真核宿主的微生物共生菌种群突变体。