Resolving a Rapid, Mega-Diverse Radiation of Insect Herbivores

该项目旨在提高我们对最大的食草昆虫群体之一-鳞翅目昆虫-的进化和分类的理解，鳞翅目昆虫由蝴蝶和蛾组成（描述了157，000种）。 鳞翅目昆虫对自然生态系统和人类都有重要影响。在自然系统中，它们作为食草动物、传粉者和鸟类及其他物种的猎物发挥着重要作用。它们也包括许多农业上的破坏性害虫，但有些种类提供了有商业价值的纤维，丝绸，毛毛虫在许多文化中是重要的食物。 一些鳞翅目昆虫是模式研究物种，用于发现遗传学、生理学、发育学、生态学和其他生命科学领域的基本原理。最后，鳞翅目昆虫，如帝王蝶，在生态系统评估、保护规划和教育公众环境保护方面具有重要作用。一个准确的家谱（系谱）是了解过去和潜在的未来演变的鳞翅目昆虫的多样性和特征，包括那些相关的害虫管理，并预测以前未研究的物种的特征的重要基础。最近利用DNA序列数据的研究已经取得了重大进展，在弄清楚鳞翅目目前划分的大约125个科之间的谱系关系。然而，有些关系，特别是那些包含大多数物种的家庭亚组内的关系，已被证明特别难以推断。该项目将尝试使用下一代DNA测序方法来解决家谱的这些问题，这些方法提供的每个物种的数据是以前方法的100倍以上。新的结果有望在许多领域，包括基础和应用。此外，该项目将帮助培训下一代比较生物学家使用这些新的DNA测序方法，其结果将被纳入新的教育材料，以推广到K-12儿童和广大公众。大多数早期分化的鳞翅目谱系之间的关系，以及几乎所有主要的超家族内部的关系，已经得到了有力的解决。然而，在包含绝大多数鳞翅目物种的高级分支Apoditrysia中，超科之间的关系只有微弱的支持。为了解决Apoditrysia超家族之间的关系，通过转录组RNA-Seq将160个样本物种的基因样本增加到2200 kb。由此产生的物种发生学将用于分析整个鳞翅目的物种多样化的分歧日期和速度，将试图确定其巨大的物种丰富度的主要因素。 Leptree项目产生了来自约900个物种的约10，000个DNA序列，代表了91%的家庭。为了测试RNA-Seq是否可以解决Leptree留下的不确定的关系，从代表Apoditrysia主要谱系的38个示例物种中获得了1579个基因（2.2+ mb）的DNA序列。在最初的最大似然系统发育分析的741个基因（764 MB）后，删除所有的基因显示任何建议的旁系，10的13个分组的树，联合两个或更多的超家族的自举支持超过85%，包括7个与100%的自举支持，与0/13只有14.8 kb。因此，计划扩大转录组采样似乎有可能大大提高Apoditrysia的遗传分辨率。 新的结果将构成有史以来第一个全面的，强有力的支持鳞翅目生物学研究的系统发育框架的顶点。

This project seeks to improve our understanding of the evolution and classification of one of the largest groups of plant-feeding insects, the order Lepidoptera, which consists of the butterflies and moths (157,000 described species). Lepidoptera have major effects on both natural ecosystems and humans. In natural systems they play important roles as herbivores, pollinators and prey for birds and other species. They also include many destructive pests of agriculture, but some species provide a commercially valuable fiber, silk, and caterpillars are important food items in many cultures. Some species of Lepidoptera are model research species used for discovering basic principles in genetics, physiology, development, ecology and other areas of life sciences. Finally, Lepidoptera such as the monarch butterfly are of central utility in ecosystem assessment, conservation planning, and in educating the public about environmental conservation. An accurate family tree (genealogy) is an essential foundation for understanding the past and potential future evolution of the diversity and traits of Lepidoptera, including those relevant to their pest management, and to predicting the traits of previously-unstudied species. Recent studies using DNA sequence data have made major progress toward figuring out the genealogical relationships among the approximately 125 families into which the Lepidoptera are currently divided. However, some relationships, particularly those within a subgroup of families containing the majority of species, have proven especially difficult to infer. This project will attempt to resolve these problematic aspects of the genealogy using next-generation methods of DNA sequencing, which provide over 100 times as much data per species studied as previous methods. The new results are expected to have applications in many fields, both basic and applied. In addition, the project will help train the next generation of comparative biologists in use of these new DNA sequencing methods, and the results will be incorporated into new educational materials for outreach to K-12 children and the public at large.Relationships among most early-diverging lepidopteran lineages, and within nearly all major superfamilies, have been strongly resolved. In the advanced clade Apoditrysia, however, which contains the great majority of lepidopteran species, relationships among superfamilies have only weak support. To resolve relationships among the superfamilies of Apoditrysia, the gene sample will be increased to 2200 kb in a subset of 160 exemplar species via transcriptome RNA-Seq. The resulting phylogeny will be used for an analysis of divergence dates and rates of species diversification across the Lepidoptera that will attempt to identify major factors contributing to their great species richness. The Leptree project produced about 10,000 kilobases of DNA sequence from ~ 900 species representing 91% of families. To test whether RNA-Seq can solve relationships left uncertain by Leptree, DNA sequence was obtained for 1579 genes (2.2+ mb) from 38 exemplar species representing the major lineages of Apoditrysia. In an initial maximum likelihood phylogenetic analysis of 741 genes (764 mb) left after removal of all genes showing any suggestion of paralogy, 10 of the 13 groupings on the tree that united two or more superfamilies had bootstrap support over 85%, including 7 with 100% bootstrap support, vs. 0/13 with 14.8 kb only. Thus, the planned expansion of transcriptome sampling seems likely to provide greatly improved phylogeny resolution for the Apoditrysia. The new results will constitute the capstone for the first-ever comprehensive, robustly supported phylogenetic framework for the study of lepidopteran biology.