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

合作研究：祖龙系统发育——精细分类水平上的全面证据方法现生鸟类形成了一个广泛的、无疑是单系的脊椎动物群落。 然而，即使经过 150 多年的深入研究，人们对现存鸟类的目、科和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亚目恐龙的体内筑巢的。其中一些类群的化石被发现具有许多以前被认为是鸟类的特征（例如羽毛、孵卵行为、分叉）。 我们建议使用非常精细的全面证据方法来研究兽脚亚目恐龙（包括鸟类）的关系。在形态学分析中，我们将开发一个可评分特征矩阵，涵盖非鸟类兽脚亚目动物的整个多样性以及鸟类的精细分类水平（即接近属水平）。 分子分析将使用高通量测序技术来产生鸟类和外类群的分子序列。 核基因将主要用于补充之前的线粒体测序；将对大多数现存鸟类属的 RAG-1 外显子进行测序，并对范例的 RAG-2、MC3R 和 CMOS 等其他基因进行测序，以建立更深层次的关系。 对这些数据的分析将得出现存鸟类和化石鸟类及其近亲兽脚类恐龙的细粒度系统发育假说。 这样的系统发育对于研究兽脚类动物的广泛进化问题具有明显的重要性。 这笔赠款的一个主要重点是“超级矩阵”的开发。 我们设想这个矩阵成为我们在本研究中生成的所有角色信息的虚拟档案。 这里将存储几种不同类型的数据。 样本的数字图像将允许在矩阵的背景下检查特征条件。分子信息也将可用。 还将提供将特征矩阵开发并导出为系统发育分析常用格式的功能。此信息发布后，将通过 www 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.