AToL: Building the Dipteran Tree: Cooperative Research in Phylogenetics and Bioinformatics of True Flies (Insecta: Diptera)

据估计，被描述的物种有15万种，双翅目昆虫(真正的苍蝇)是生命树上最多样化的分支之一。苍蝇树主要树枝之间的进化关系在很大程度上仍然未知或有争议。了解苍蝇的历史在生物学和医学上至关重要，因为苍蝇是在基因组学、发育、神经生物学和行为方面进行比较研究的模式生物(例如，果蝇、蚊子、家蝇、麦德蝇)。对苍蝇的比较研究取决于对它们的系统发育树有一个可靠的估计。我们将从史无前例的大量比较遗传学和解剖学数据样本中重建苍蝇树。我们还将整合来自双翅目特殊化石记录、新兴基因组和发育数据库、新的和现有的标本数据以及以前发表的系统发育树的信息。该项目涉及一个大型国际团队的合作努力，该团队在苍蝇生物多样性、遗传学和行为方面拥有广泛的研究专长。研究小组还将开发基于网络的生物信息学工具，以获取有关苍蝇的自然历史信息、它们的生物学信息以及对其他研究领域的影响。这项任务将通过三级方法来掌握。在第一层，我们基于第一个全面的形态特征矩阵和大的基因组数据集重建了42个物种的骨干树，这些物种代表了所有主要的双翅目谱系，并包含了重要的模式生物。第二级分析将使用更全面的物种样本，包括所有苍蝇科的至少一个物种，更多的形态特征，以及更少的分子数据。在这一层，我们还将纳入保存完好的化石物种的特征。第三层将依靠在前两层中重建的主干树，为1500-2000个物种建立基于荟萃分析的超树。在项目的每一层中使用这些数据，我们探索了多种比较分析方法和采样策略，以重建巨型多样性类群的系统发育。一个更具体的双翅目生命树将为苍蝇惊人的多样性提供一个主要的组织框架，并指导其他生物多样性领域的研究。这个项目中探索的分子和形态特征系统和基因应该对解决其他昆虫类群中的类似问题非常有用。最终，一个全面的新的双翅目系统发生学将为检验进化假说提供一个有价值的框架，这些假说在双翅目昆虫发育、行为、基因组和神经生物学的比较研究中至关重要。研究团队包括K-12、本科生和研究生的教育和研究培训经验，以及几名博士后研究人员的广泛研究和职业发展机会。为了有效地传达我们的结果，我们将建立“双翅目昆虫网站”。该网站将成为有关双翅目昆虫信息的中心枢纽，并展示我们的树木，包含重要的电子目录、基因组数据库、全面的解剖图集、交互式检索表和收藏主页的链接。这一资源将极大地扩大研究界、教育工作者和公众对苍蝇的基本信息的可及性。

With an estimated 150,000 described species, the insect order Diptera (the true flies) is one of the most diverse branches on the Tree of Life. The evolutionary relationships between the main branches of the fly tree are still largely unknown or controversial. Understanding the history of flies is critically important in biology and medicine because flies are model organisms for comparative research in genomics, development, neurobiology, and behavior (e.g., fruit flies, mosquitoes, house flies, medfly). Comparative research on flies depends on having a reliable estimate of their phylogenetic tree. We will reconstruct the fly tree in detail from an unprecedentedly large sample of comparative genetic and anatomical data. We will also integrate information from the exceptional fossil record of Diptera, from emerging genomic and developmental databases, from new and existing specimen data, and from previously published phylogenetic trees. The project involves a collaborative effort among a large, international team with extensive research expertise in fly biodiversity, genetics, and behaviour. The research team will also develop web-based bioinformatics tools for natural history information about flies, their biology, and impact on other fields of research. The task will be mastered in a three-tier approach. In the first tier, we reconstruct a backbone tree based on the first comprehensive morphological character matrix and large genomic data set for 42 species representing all major dipteran lineages and incorporating important model organisms. The second-tier analysis will use a more comprehensive species sample comprising at least one species for all fly families, more morphological characters, and a reduced amount of molecular data. In this tier we will also incorporate characters from well-preserved fossil species. The third tier will rely on the backbone trees reconstructed in the first two tiers for building a meta-analysis-based supertree for 1500-2000 species. Using these data within each tier of the project, we explore multiple comparative analytical approaches and sampling strategies for reconstructing the phylogenies of megadiverse taxa. A more exactly specified Tree of Life for Diptera will provide a major organizing framework for the astounding diversity of flies and guide research in other areas of biodiversity. Molecular and morphological character systems and genes explored in this project should be extremely useful in resolving similar questions in other insect groups. Ultimately a comprehensive new phylogeny for all of Diptera will provide a valuable framework for testing evolutionary hypotheses critical in comparative studies of dipteran development, behavior, genomics, and neurobiology. The research team includes educational and research training experiences for K-12, undergraduate, and graduate students, as well as extensive research and career-building opportunities for several postdoctoral researchers. In order to efficiently communicate our results, we will build the 'Diptera Web.' This website will be the central hub for information on Diptera and present our trees, contain important electronic catalogs, genomic databases, a comprehensive anatomy atlas, interactive keys, and links to collection homepages. This resource will greatly expand the accessibility of primary information on flies to the research community, educators, and the public.