Dataset for co-phylogenetic analysis of Cicadas and their symbionts

Throughout the lengthy process of evolution, various animals have formed symbiotic associations with diverse microbes. Symbiotic associations between insects and microorganisms enable insects to adapt to a variety of ecological niches and exploit diverse food resources. In most cases, the host insects have evolved specialized cells and organs, called bacteriocytes and bacteriomes, in particular of the plant sap-feeding auchenorrhynchan insects of Hemiptera, to accommodate their bacterial symbionts. Recruitment of novel symbiont is a key strategy for hosts to escape dependence on outdated, inefficient symbiont. However, symbiont replacement is a dynamic process, and its occurrence – from emergence to eventual disappearance – is extremely difficult to ascertain. Prior work has indicated that, in many cicada lineages, the obligate symbiont Hodgkinia has been replaced by yeast-like fungal symbionts (YLS), and YLS replacement by another fungus or YLS has also occurred repeatedly. Considerable diversity has been observed in the genome of Hodgkinia among different cicada species, which possibly suggest that Hodgkinia independently infected the ancestors of different cicada lineages on multiple occasions.

In the present work, phylogenetic analyses reveal that Hodgkinia infected the common ancestor of cicadas and has co-diversified with its host cicadas before replaced by YLS. We demonstrate events of Hodgkinia loss in Cicadidae occurred at least seven times and YLS replaced by another Ophiocordyceps fungus or YLS occurred repeatedly at least 18 times. The most extraordinary replacements and supplementation of symbionts in Cicadidae could be closely related to that cicadas live underground usually for many years but aboveground only several days. Most importantly, we present direct evidence that the extremely genome-degraded Hodgkinia established a nested symbiosis with Karelsulcia – immigrated to the cytoplasm of Karelsulcia to seek refuge when being replaced by YLS. This answers the enduring puzzles in the life sciences of how host insects can break away from their dependence on an ancient and potentially inefficient symbiont and what adaptative or nonadaptive evolution may evolve before a symbiont is going to be replaced by another symbiont. The findings offer fresh insights into the endosymbiotic origins of cellular organelles and intensify our curiosity about the origins of life.

在漫长的演化历程中，各类动物已与多样微生物形成共生关联。昆虫与微生物的共生关系，可帮助昆虫适应多种生态位并利用多样化食物资源。多数情况下，宿主昆虫演化出特化的细胞与器官——即含菌细胞（bacteriocytes）与含菌体（bacteriomes），以容纳其细菌共生体，这在半翅目（Hemiptera）中以植物汁液为食的颈喙亚目（auchenorrhynchan）昆虫中尤为典型。招募新型共生体是宿主摆脱对老旧低效共生体依赖的关键策略。然而，共生体替换是一个动态过程，其发生（从出现到最终消失）极难确定。先前研究表明，在诸多蝉类演化支中，专性共生菌霍奇金菌（Hodgkinia）已被类酵母真菌共生体（YLS）取代，且类酵母真菌共生体YLS被其他真菌或YLS自身发生替换的事件也反复出现。不同蝉类物种的霍奇金菌基因组存在显著差异，这或许表明霍奇金菌曾多次独立侵染不同蝉类演化支的祖先。

本研究通过系统发育分析发现，霍奇金菌曾侵染蝉类的共同祖先，并在被类酵母真菌共生体YLS取代前，与宿主蝉类共同演化。我们证实，蝉科（Cicadidae）中霍奇金菌丢失的事件至少发生7次，而YLS被另一种虫草属（Ophiocordyceps）真菌取代或YLS自身替换的事件至少反复出现18次。蝉科中最为特殊的共生体替换与补充事件，或许与蝉类多数时间地下生活多年、仅在地面存活数日的生活史密切相关。尤为重要的是，我们提供了直接证据：基因组极度退化的霍奇金菌在被YLS取代时，会迁移至卡尔苏尔西亚菌（Karelsulcia）的细胞质中寻求庇护，从而与后者形成嵌套共生关系。这一发现解答了生命科学领域长期存在的两大谜题：宿主昆虫如何摆脱对古老且可能低效的共生体的依赖，以及在共生体被另一共生体取代前，宿主会演化出何种适应性或非适应性演化特征。本研究结果为细胞器的内共生起源提供了全新视角，也进一步激发了我们对生命起源的探索兴趣。