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

研究DNA序列性状的系统学家所面临的主要挑战是如何从更大范围的性状变化中区分出多聚性信息变化。序列信息性因核苷酸序列内部和序列之间的进化变化率不同而不同。因此，为了应对上述挑战，系统学家需要了解DNA序列特征的可变性质和变化率。现存鸟类谱系的早期历史仍然知之甚少，相互矛盾的假设表明缺乏翔实的特征。解决鸟类目之间的关系是一个更大的争论的核心，关于可靠性和优点的替代系统发育方法。在寻求解决分子系统学方法和鸟类系统发育问题的同时，提出的研究目标是：1)确定鸟类目anserformes和Galliformes的系统发育关系，以及它们相对于Paleognathae （ratites和tinamous）和Neognathae（所有其他现存鸟类）的位置；2)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)评价不同比对策略在系统发育分析中的作用。将从组织中提取线粒体DNA，通过聚合酶链反应扩增12S核糖体RNA和细胞色素氧化酶I基因，并使用标准的双脱氧链终止技术进行测序。本文的研究成果将有助于提高我们对鸟类早期分化谱系系统发育关系的认识，并为系统系统学领域广泛应用的系统发育方法提供基础信息。

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.