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

合作研究：原始龙的单源性--精细分类学水平上的全证据方法活的鸟类构成了一个广泛的、无疑是单源的脊椎动物组合。 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，鸟类是兽脚亚目恐龙的巢穴。其中一些化石已经被发现，显示了许多以前被认为是鸟类的特征（例如羽毛，育雏行为，叉）。 我们建议在非常精细的水平上使用全证据方法来检查兽脚亚目恐龙（包括鸟类）的关系。在形态学分析中，我们将在整个非鸟类兽脚亚目的多样性和鸟类内部的精细分类水平（即接近属的水平）上开发一个可评分特征矩阵。 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之前的线粒体测序; RAG-1外显子将被测序的大多数属的现存鸟类，和其他基因，如RAG-2，MC 3R，和cMOS将被测序的范例，以建立更深层次的关系。 对这些数据的分析将导致一个精细的系统发育假说的生活和化石鸟类和他们的近亲兽脚亚目。 这样的一个系统发育对于研究兽脚亚目动物中广泛的进化问题具有明显的重要性。 这项赠款的一个主要重点是开发一个“超级矩阵”。 我们设想这个矩阵是一个虚拟档案馆的所有字符信息，我们在这项研究中产生。 几种不同类型的数据将存储在这里。 标本的数字图像将允许在矩阵的上下文中检查特征条件。分子信息也将可用。 还将具备将特征矩阵开发和输出为系统发育分析常用格式的能力。随着这一信息的发布，它将在www.

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.