Data from: Know your farmer: ancient origins and multiple independent domestications of ambrosia beetle fungal cultivars

Bark and ambrosia beetles are highly specialized weevils (Curculionidae) that have established diverse symbioses with fungi, most often from the order Ophiostomatales (Ascomycota, Sordariomycetes). The two types of beetles are distinguished by their feeding habits and intimacy of interactions with their symbiotic fungi. The tree tissue diet of bark beetles is facilitated by fungi, while ambrosia beetles feed solely on fungi that they farm. The farming life history strategy requires domestication of a fungus, which the beetles consume as their sole food source. Ambrosia beetles in the subfamily Platypodinae originated in the mid-Cretaceous (119-88Mya) and are the oldest known group of farming insects. However, attempts to resolve phylogenetic relationships and the timing of domestication events for fungal cultivars have been largely inconclusive. We sequenced the genomes of 12 ambrosia beetle fungal cultivars and bark beetle associates, including the devastating laurel wilt pathogen, Raffaelea lauricola, to estimate a robust phylogeny of the Ophiostomatales. We find evidence for contemporaneous diversification of the beetles and their associated fungi, followed by three independent domestication events of the ambrosia fungi genus Raffaelea. We estimate the first domestication of an Ophiostomatales fungus occurred ~86Mya, 25 million years earlier than prior estimates and in close agreement with the estimated age of farming in the Platypodinae (96Mya). Comparisons of the timing of fungal domestication events with the timing of beetle radiations support the hypothesis that the first large beetle radiations may have spread domesticated ‘ambrosia’ fungi to other fungi-associated beetle groups, perhaps facilitating the evolution of new farming lineages.树皮小蠹与食菌小蠹均为高度特化的象甲科（Curculionidae）象甲类群，它们与真菌建立了多样的共生关系，其共生真菌多隶属于长喙壳菌目（Ophiostomatales，子囊菌门Ascomycota，粪壳菌纲Sordariomycetes）。两类小蠹可根据取食习性以及与共生真菌的互作紧密程度加以区分：树皮小蠹以树木组织为食，该取食过程依赖真菌的协助；而食菌小蠹仅以自身培育的真菌作为唯一食物来源。这种培育型生活史策略需要宿主小蠹驯化一种真菌作为其专属食物。长小蠹亚科（Platypodinae）的食菌小蠹起源于白垩纪中期（119~88百万年前），是目前已知最古老的培育型昆虫类群。然而此前针对真菌共生体的系统发育关系与驯化事件定年的研究大多未能得到明确结论。本研究对12种食菌小蠹的共生真菌以及树皮小蠹的伴生真菌进行了基因组测序，其中包括毁灭性的樟枯萎病病原菌樟生拉夫霉（Raffaelea lauricola），以此重建长喙壳菌目（Ophiostomatales）的稳健系统发育关系。研究结果显示，小蠹类群与其共生真菌存在协同分化的演化模式，随后食菌真菌类群拉夫霉属（Raffaelea）共发生了三次独立的驯化事件。本研究估算长喙壳菌目真菌的首次驯化事件发生于约86百万年前，较此前的研究结果早2500万年，且与长小蠹亚科培育行为的起源估算时间（约96百万年前）高度吻合。通过对比真菌驯化事件与小蠹类群辐射演化的时间节点，本研究支持如下假说：首次大规模小蠹辐射演化可能将已驯化的“食菌”真菌传播至其他与真菌伴生的小蠹类群，进而推动了全新培育型昆虫世系的演化。