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

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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.