Unraveling the evolutionary dynamics of high symbiont diversity in the fungus-farming ant genus Apterostigma: A phylogenomic approach

最著名的真菌养殖蚂蚁是切叶蚁属（Atta）和切叶蚁属（Acromyrmex），它们是新大陆热带地区占主导地位的植物收获动物。这些蚂蚁使用植物的叶片来培养一种最近进化的真菌物种，然后吃它们。 然而，一种更鲜为人知的真菌养殖蚂蚁，在Apterostigma属中，培养的真菌种类比所有其他真菌养殖蚂蚁的总和还要多。Apterostigma的近缘物种培育密切相关的真菌群，但在Apterostigma蚂蚁和真菌之间4000万年的共同进化中，真菌群多次发生重大转变。这项研究旨在更好地了解切叶蚁和它们培养的真菌的共同进化。这包括发展关于Apterostigma蚂蚁物种及其相关真菌的数量，多样性和分布的新知识，以及确定蚂蚁和真菌之间的进化关系。要解决的问题包括：为什么切叶蚁属Apterostigma培养的真菌种类比所有其他真菌养殖蚂蚁（切叶和非切叶）的总和更大的多样性？为什么一些Apterostigma蚂蚁物种只培育少数几种彼此密切相关的真菌，而另一些则培育多种真菌，这些真菌只是远亲？这项研究的结果可能会使整个社会受益，因为真菌养殖蚂蚁为达尔文农业和达尔文医学的新兴领域提供了一个罕见的非人类模型系统，这些领域旨在通过研究类似的自然系统来改善人类农业和疾病管理。最近，从与切叶蚁生活在一起的真菌和细菌物种中分离和描述了几种抗生素和抗疟醌，使其生物学与健康问题特别相关。此外，一些真菌与切叶蚁已成为更有效的生物燃料生产的模型。本研究将进行全面的实地收集蚂蚁和真菌的巢穴，在其分布在自然界中，并记录存在或不存在的共同形态模式，在Apterostigma蚂蚁和真菌品种，通过比较系统发育分析的基础上的蚂蚁和真菌的基因组数据。 研究人员将采用超保守遗传元件（UCEs）的目标富集来推断物种水平的遗传。这些共生性将用于检验共同进化的假设和真菌物种的保真度和宿主蚂蚁物种之间的流动性随着时间的推移。基因组UCE数据也将用于解决物种边界（确定物种）之间知之甚少的Apterostigma蚂蚁物种复合体。这是必不可少的重建物种特异性的蚂蚁-真菌的共同进化的相互作用，以及修改蚂蚁分类和生产图形识别各种蚂蚁物种的关键。

The best known fungus-farming ants are the leaf-cutting ants of the genera Atta and Acromyrmex, which are the dominant plant harvesting animals of the New World tropics. These ants use plant leaf cuttings in order to cultivate a single, recently evolved fungal species, which they then eat. However, a more poorly known group of fungus-farming ants in the genus Apterostigma, cultivate a greater diversity of fungal species than all other fungus-farming ants combined. Closely related species of Apterostigma cultivate closely related groups of fungi, but major shifts to distantly related fungal groups have occurred multiple times during 40 million years of co-evolution between Apterostigma ants and fungus. This research aims to better understand the co-evolution of leaf-cutting ants and the fungi they cultivate. This includes developing new knowledge about the numbers, diversity and distribution of Apterostigma ant species and their associated fungi, as well as determining the evolutionary relationships among both ants and fungi. Questions to be addressed include: Why do leaf-cutting ants in the genus Apterostigma cultivate a greater diversity of fungal species than all other fungus-farming ants (leaf-cutting and non-leaf-cutting) combined? Why do some Apterostigma ant species cultivate only a few fungi that are closely related to each other, while others cultivate diverse fungi that are only distant relatives? The results from this research may benefit society in general because fungus-farming ants provide a rare non-human model system for the emerging fields of Darwinian agriculture and Darwinian medicine, which aim to improve human agriculture and disease management through the study of analogous natural systems. Recently several antibiotics and antimalarial quinones have been isolated and described from fungi and bacterial species living in association with leaf-cutting ants, making their biology particularly relevant to issues of health. Further, some fungi associated with leaf-cutting ants have become models for more efficient biofuel production.This research will proceed by comprehensive field collecting of ants and fungi from nests throughout their distributions in nature, and documenting the presence or absence of co-speciation patterns in Apterostigma ants and their fungal cultivars, by comparing phylogenetic analyses based on genomic data for both ants and fungi. The researchers will employ targeted enrichment of Ultra-Conserved genetic Elements (UCEs) to infer the species-level phylogenies. These phylogenies will be used in testing hypotheses of co-evolution and fungal species fidelity and mobility among host ant species over time. The genomic UCE data will also be used to resolve species boundaries (identify species) among poorly known species-complexes of Apterostigma ants. This is essential for reconstructing species-specific ant-fungus co-evolutionary interactions as well as for revising ant taxonomy and producing pictorial identification keys to various ant species.