Substitution bias, rapid saturation, and the use of mtDNA for nematode systematics

Only relatively recently have researchers turned to molecular methods fornematode phylogeny reconstruction. Thus, we lack the extensive literatureon evolutionary patterns and phylogenetic usefulness of different DNAregions for nematodes that exists for other taxa. Here, we examine theusefulness of mtDNA for nematode phylogeny reconstruction and provide datathat can be used for a priori character weighting or for parameterspecification in models of sequence evolution. We estimated thesubstitution pattern for the mitochondrial ND4 gene from intraspecificcomparisons in four species of parasitic nematodes from the familyTrichostrongylidae (38-50 sequences per species). The resulting patternsuggests a strong mutational bias toward A and T, and a lowertransition/transversion ratio than is typically observed in other taxa. Wealso present information on the relative rates of substitution at first,second, and third codon positions and on relative rates of saturation ofdifferent types of substitutions in comparisons ranging from intraspecificto interordinal. Silent sites saturate extremely quickly, presumably owingto the substitution bias and, perhaps, to an accelerated mutation rate.Results emphasize the importance of using only the most closely relatedsequences in order to infer patterns of substitution accurately fornematodes or for other taxa having strongly composition-biased DNA. ND4also shows high amino acid polymorphism at both the intra- andinterspecific levels, and in higher level comparisons, there is evidence ofsaturation at variable amino acid sites. In general, we recommend usingmtDNA coding genes only for phylogenetics of relatively closely relatednematode species and, even then, using only nonsynonymous substitutions andthe more conserved mitochondrial genes (e.g., cytochrome oxidases). On theother hand, the high substitution rate in genes such as ND4 should makethem excellent for population genetics studies, identifying crypticspecies, and resolving relationships among closely related congeners whenother markers show insufficient variation.