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

合作研究：祖龙系统发育——在精细分类学水平上的全面证据方法——现存的鸟类形成了广泛的、毫无疑问的脊椎动物单系组合。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。最近有确凿的证据表明，鸟类是在兽脚亚目恐龙中筑巢的。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、孵蛋行为、毛囊）。我们建议在非常精细的水平上使用全证据方法来研究兽脚亚目恐龙（包括鸟类）之间的关系。在形态学分析中，我们将在非鸟类兽脚亚目的整个多样性和鸟类的精细分类水平（即接近属水平）上建立一个可评分的特征矩阵。分子分析将使用高通量测序技术从鸟类和外类群中产生分子序列。核基因将主要用于补充先前的线粒体测序；rag1外显子将对大多数现存鸟类进行测序，其他基因如rag2、MC3R和cmo将进行测序，以建立更深层次的关系。对这些数据的分析将产生一个精细的现存和化石鸟类及其近亲兽脚亚目动物的系统发育假说。这种系统发育对于研究兽脚亚目动物的广泛进化问题具有明显的重要性。这项拨款的一个主要焦点是“超矩阵”的发展。我们设想这个矩阵是我们在研究过程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。标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。还将提供将字符矩阵开发和导出为通常用于系统发育分析的格式的能力。随着这些信息的发布，它将在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 information is published it will be made available over the www.