ATOL: Collaborative Research: Archosaur Phylogeny- A Total Evidence Approach at Fine Taxonomic Levels

合作研究：始祖龙系统发育--细微分类水平的总体证据方法活着的鸟类形成了广泛的、毫无疑问的单系脊椎动物组合。然而，即使经过150多年的深入研究，现存鸟类的目、科、属之间的相互关系仍然知之甚少。最近有确凿证据表明，鸟类是在兽脚类恐龙体内筑巢的。其中一些类群的化石已经被发现显示出许多以前被认为是鸟类的特征(例如羽毛、孵化行为、毛囊)。我们建议在非常精细的水平上使用完全证据的方法来研究兽脚类恐龙(包括鸟类)的关系。在形态分析中，我们将建立一个可记分特征矩阵，涵盖非鸟类兽脚类的全部多样性，并在鸟类内部的精细分类水平上(即接近属级水平)。分子分析将使用高通量测序技术来产生鸟类和外类群分类群的分子序列。核基因将主要用于补充先前的线粒体测序；将对大多数现存鸟类的RAG-1外显子进行测序，并将为样本测序其他基因，如RAG-2、MC3R和cmos，以建立更深层次的关系。对这些数据的分析将得出活的和化石的鸟类及其近亲兽脚类动物的细粒度系统发育假说。这样的系统发育对于研究兽脚亚目动物中广泛的进化问题将具有明显的重要性。这笔赠款的一个主要重点是发展一个“超级矩阵”。我们设想这个矩阵将成为我们在这项研究中生成的所有字符信息的虚拟档案。这里将存储几种不同类型的数据。样品的数字图像将允许在矩阵的上下文中检查字符条件。分子信息也将可用。还将提供将字符矩阵开发和输出为通常用于系统发育分析的格式的能力。此信息发布后，将在WWW上提供。

Collaboartive Research: Archosaur phylogeny-a total evidence approach at fine taxonomic levelLiving birds form an extensive, undoubtedly monophyletic assemblage of vertebrates. Yet even after over 150 years of intense study the interrelationships of the orders, families, and genera of extant birds are still poorly understood. Recently it has beenconclusively demonstrated that birds are nested within theropod dinosaurs. Fossils of some of these groups have been found that display a number of features that have previously been thought of as avian (e.g. feathers, brooding behavior, furculae). We propose to examine the relationships of theropod dinosaurs (including birds) using a total evidence approach at very fine levels. In the morphological analysis we will develop a matrix of scoreable characters across the entire diversity of non-avian theropods andat fine taxonomic levels within birds (I.e. near the generic level). Molecular analyses will use high-throughput sequencing techniques to produce molecular sequences from birds and outgroup taxa. Nuclear genes will be used predominantly to complement prior mitochondrial sequencing; the RAG-1 exon will be sequenced for most genera of extant birds, and additional genes such as RAG-2, MC3R, and cMOS will be sequenced for exemplars to establish deeper level relationships. Analysis of these data will result in a fine-grained phylogenetic hypothesis of living and fossil birds and their close theropod relatives. Such a phylogeny will have obvious importance for the study of a broad range of evolutionary questions within theropods. A major focus of this grant is the development of a 'supermatrix'. We envision this matrix to be a virtual archive for all the character information that we generate during this study. Several different kinds of data will be stored here. Digital images of specimens will allow character conditions to be examined within the context of the matrix. Molecular information will be available as well. Capabilities for the development and export of character matrices into formats conventionally used for phylogenetic analysis will also be available. As this informationis published it will be made available over the www.