Conflicting Phylogenetic Patterns Caused by Molecular Mechanisms in Mitochondrial DNA Sequences

Abstract

patterns from the noise (Farris, 1983). Even with transition or compositional bias, the directionality and phylogenetic distribution of mutations may remain largely random. However, the existence of deterministic mutation processes could cause serious complications in phylogenetic analyses by skewing the distribution of homoplastic characters to suggest spurious hypotheses of relationships. Recent reports have re? vealed nonrandom patterns of mutation in eukaryotic nuclear (Selker, 1990; Kricker et al., 1992) and bacteriophage (Cunningham et al., 1997) genomes. Here we analyze a peculiar distribution of riucleotide varia? tion in mitochondrial DNA (mtDNA) of a cyprinid fish and suggest that nonrandom homoplasy in molecular data may be more widespread than is currently recognized. Sequence duplications are a common fea? ture of animal mtDNAs (Rand, 1993), par? ticularly in the control region. Duplicated se-