Phylogeny of Anseriformes and Galliformes Using mtDNAs: The Role of Rate Heterogeneity and Alignment Strategies

系统科学家在研究DNA时面临的主要挑战 序列特征是区分多源发生的 从更大的字符变化集的信息变化 测定 序列信息量因变量而异 核苷酸内部和核苷酸之间的进化变化率 序列的 因此，迎接上述挑战需要 系统主义者了解变量的性质和速率 DNA序列特征的变化。 现存鸟类谱系的早期历史仍然很差 已知的，与矛盾的假设表明缺乏 信息字符。 解决鸟类之间的关系 订单是关于可靠性的更大辩论的核心 和替代系统发育方法的优点。 为了解决分子系统学的问题 方法和鸟类繁殖学在一起， 建议的研究是：1）确定系统发育 雁形目和鸡形目的关系， 以及它们相对于古颚类（平胸类和 tinamous）和Neognathae（所有其他现存鸟类）; 2）到 确定DNA序列特征的相对变化率， 并评估其在系统发育分析中的应用; 3） 评估不同比对策略对系统发育的影响 分析。 线粒体DNA将从组织中提取，12 S 核糖体RNA和细胞色素氧化酶I基因将被扩增 通过聚合酶链反应，并使用标准的 双脱氧链终止技术。 拟议的研究有望大幅改善 我们对早期分化物种间系统发育关系的了解 鸟类谱系，并提供有关的基本信息 系统发育方法广泛适用于 分类学

The primary challenge facing systematists working with DNA sequence characters is to distinguish plylogenetically informative change from the larger set of character change determined. Sequence informativeness varies due to variable rates of evolutionary change within and among nucleotide sequences. Meeting the challenge stated above, thus, requires systematists to learn about the variable nature and rate of change for DNA sequence characters. The early history of extant avian lineages remains poorly known, with conflicting hypotheses denoting a shortage of informative characters. Resolution of relationships among avian orders is central to a larger debate concerning the reliability and merits of alternative phylogenetic methods. In seeking to address issues of molecular systematics methods and avian phylogeny together, the objectives of the proposed research are: 1) to determine phylogenetic relationships for the avian orders Anseriformes and Galliformes, and their placement relative to Paleognathae (ratites and tinamous) and Neognathae (all other extant birds); 2) to determine relative rates of change for DNA sequence characters, and assess their application to phylogenetic analyses; and 3) to assess effects of different alignment strategies in phylogenetic analyses. Mitochondrial DNA will be extracted from tissues, and 12S ribosomal RNA and cytochrome oxidase I genes will be amplified via the polymerase chain reaction and sequenced using standard dideoxy chain termination techniques. The proposed research is expected to improve significantly our knowledge of phylogenetic relationships among early diverging avian lineages, and to provide fundamental information regarding phylogenetic methods broadly applicable within the field of systematics.