Resolving a Rapid, Mega-Diverse Radiation of Insect Herbivores

这个项目旨在提高我们对食草性昆虫中最大的一类之一鳞翅目的进化和分类的了解，鳞翅目由蝴蝶和飞蛾组成(所描述的物种有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，它们扮演着重要的角色，如草食动物、传粉者和鸟类和其他物种的猎物。它们还包括许多破坏性的农业害虫，但一些物种提供了一种有商业价值的纤维，丝虫和毛虫在许多文化中是重要的食物。鳞翅目的一些物种是用于发现遗传学、生理学、发育、生态学和其他生命科学领域基本原理的模式研究物种。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。准确的家谱是了解鳞翅目昆虫多样性和特征的过去和潜在未来进化的重要基础，包括那些与害虫管理相关的进化，以及预测以前未被研究的物种的特征。最近利用DNA序列数据进行的研究在弄清鳞翅目目前被划分为的大约125个科之间的系谱关系方面取得了重大进展。然而，事实证明，一些关系，特别是包含大多数物种的科的子组内的关系，尤其难以推断。这个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，这种方法提供的每个物种的数据是以前方法的100多倍。新的结果有望在许多领域得到应用，既包括基础领域，也包括应用领域。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，结果将被纳入新的教材，以推广到K-12儿童和广大公众。大多数早期分化的鳞翅目昆虫谱系之间的关系，以及几乎所有主要超家族之间的关系已经得到很好的解决。然而，在包含绝大多数鳞翅目物种的高级分支Apoditrysia中，超级家族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，将通过转录组RNA-Seq将160个样本物种的基因样本增加到2200kb。由此产生的系统发育将用于分析鳞翅目物种多样性的分化日期和速度，试图确定导致其物种丰富的主要因素。Leptree计划从91%的科的900个物种中产生了大约10000个碱基的DNA序列。为了测试RNA-Seq是否能够解决Leptree留下的不确定的关系，我们获得了来自38个样本物种的1579个基因(2.2+mb)的DNA序列，这些基因代表了Apoditrysia的主要谱系。在最初的最大似然系统发育分析中，去除了所有显示出同源关系的基因后剩下的741个基因(764mb)，在树上联合两个或更多超级家族的13个组中，有10个组的引导支持率超过85%，其中7个具有100%的引导支持，而只有14.8kb的0/13。因此，计划中的转录组采样的扩大似乎很可能为Apoditrysia提供极大的系统发育分辨率。新的结果将成为有史以来第一个全面的、得到有力支持的鳞翅目生物学研究系统发育框架的顶峰。

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.