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

研究DNA序列特征的系统学家面临的主要挑战是从已确定的更大的一组特征变化中区分多基因信息性变化。由于核苷酸序列内和核苷酸序列之间进化变化的速率不同，序列信息量也不同。因此，要应对上述挑战，需要系统学家了解DNA序列特征的变量性质和变化率。现存鸟类谱系的早期历史仍然鲜为人知，相互矛盾的假设表明缺乏信息特征。解决鸟类目之间的关系是关于替代系统发育方法的可靠性和优点的更大辩论的核心。为了解决分子系统学方法和鸟类系统发育的问题，本研究的目的是：1)确定雀形目和雀形目鸟类的系统发育关系，以及它们相对于古颌目(有翅目和有翅目)和新喙目(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；以及3)评估不同比对策略在系统发育分析中的效果。线粒体DNA将从组织中提取，12S核糖体RNA和细胞色素氧化酶I基因将通过聚合酶链式反应进行扩增，并使用标准的双脱氧链终止技术进行测序。这项拟议的研究有望显著提高我们对早期分化的鸟类谱系之间的系统发育关系的了解，并提供广泛应用于系统学领域的系统发育方法的基本信息。

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.