Why one-kilobase sequences from mitochondrial DNA fail to solve the Hoatzin phylogenetic enigma.

To address the suitability of mitochondrial DNA sequence data for higher avian systematics, cytochrome b sequences for nine species of Cuculiformes and Galliformes were gathered and compared to those of the Hoatzin, a specialized bird whose phylogenetic affinities have long puzzled ornithologists. Additional avian cytochrome b sequences from GenBank also were incorporated into the comparisons. Various phenetic and parsimony analyses applied to the molecular data coded in four formats (nucleotide sequences, purines versus pyrimidines, first and second positions of codons, and translated amino acid sequences) yielded several consistent phylogenetic arrangements, including the distinction of Galliformes from Cuculiformes, a clade composed of the Guira Cuckoo and Groove-billed Ani (Crotophagidae) to the exclusion of the other assayed cuculiforms (Cuculidae and Coccyzidae), and a clade composed of the New World quail (Odontophoridae, in the Sibley-Ahlquist classification) as a sister group to most or all Old World galliforms assayed (Phasianidae and Numididae). The latter result is of particular interest because it supports a controversial systematic realignment of the Galliformes based on DNA-DNA hybridization data. With regard to the phylogenetic position of the Hoatzin, the analysis differed in face-value outcome, although alternative clades were in all cases poorly supported by bootstrapping, and internodal distances were small relative to the range of genetic separations within either Cuculiformes or Galliformes. These uncertainties in phylogenetic resolution of the Hoatzin appear to be attributable to shallow slopes in the regressions relating cytochrome b sequence differences to evolutionary time, in conjunction with homoplasy in the data, sampling error in the estimation of genetic differences, and the relatively close temporal placements of relevant evolutionary nodes.