Molecular phylogenetics of finches and sparrows: Consequences of characterstate removal in cytochrome b sequences

The complete mitochondrial cytochrome b genes of 53 genera of oscine passer ine birds representing the major groups of finches and some allies were com pared. Phylogenetic trees resulting from three levels of character partitio n removal (no data removed, transitions at third positions of codons remove d, and all transitions removed [transversion parsimonyl) were generally con cordant, and all supported several basic statements regarding relationships of finches and finch-like birds, including: (1) larks (Alaudidae) show no close relationship to any finch group; (2) Peucedramus (olive warbler) is p hylogenetically far removed from true wood warblers; (3) a clade consisting of fringillids, passerids, motacillids, and emberizids is supported, and t his clade is characterized by evolution of a vestigial 10th wing primary; a nd (4) Hawaiian honeycreepers are derived from within the cardueline finche s. Excluding transition substitutions at third positions of codons resulted in phylogenetic trees similar to, but with greater bootstrap nodal support than, trees derived using either all data (equally weighted) or transversi on parsimony. Relative to the shortest trees obtained using all data, the t opologies obtained after elimination of third-position transitions showed o nly slight increases in realized tree-length and homoplasy. These increases were negligable compared to increases in overall nodal support; therefore, this partition removal scheme may enhance recovery of deep phylogenetic si gnal in protein-coding DNA datasets. (C) 1998 Academic Press.