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

Only relatively recently have researchers turned to molecular methods for n ematode phylogeny reconstruction. Thus, we lack the extensive literature on evolutionary patterns and phylogenetic usefulness of different DNA regions for nematodes that exists for other taxa. Here, we examine the usefulness of mtDNA for nematode phylogeny reconstruction and provide data that can be used for a priori character weighting or for parameter specification in mo dels of sequence evolution. We estimated the substitution pattern for the m itochondrial ND4 gene from intraspecific comparisons in four species of par asitic nematodes from the family Trichostrongylidae (38-50 sequences per sp ecies). The resulting pattern suggests a strong mutational bias toward A an d T, and a lower transition/transversion ratio than is typically observed i n other taxa. We also present information on the relative rates of substitu tion at first, second, and third codon positions and on relative rates of s aturation of different types of substitutions in comparisons ranging from i ntraspecific to interordinal. Silent sites saturate extremely quickly, pres umably owing to the substitution bias and, perhaps, to an accelerated mutat ion rate. Results emphasize the importance of using only the most closely r elated sequences in order to infer patterns of substitution accurately for nematodes or for other taxa having strongly composition-biased DNA. ND4 als o shows high amino acid polymorphism at both the intra- and interspecific l evels, and in higher level comparisons, there is evidence of saturation at variable amino acid sites. In general, we recommend using mtDNA coding gene s only for phylogenetics of relatively closely related nematode species and , even then, using only nonsynonymous substitutions and the more conserved mitochondrial genes (e.g., cytochrome oxidases). On the other hand, the hig h substitution rate in genes such as ND4 should make them excellent for pop ulation genetics studies, identifying cryptic species, and resolving relati onships among closely related congeners when other markers show insufficien t variation.