Diagnostic and Phylogenetic Utility of the rDNA Internal Transcribed Spacer Sequences of Steinernema.

The ITS regions of 10 species of Steinernema were PCR amplified and directly sequenced. Restriction mapping of these sequences revealed diagnostic variation such that the number of cuts and the length of the resulting fragments can be used to diagnose Steinernema species. Nevertheless, identical fragment sizes produced by non-homologous restriction sites also were identified. Pronounced variation in sequence length and nucleotide composition resulted in optimized alignments containing extensive regions of dubious homology. Significant shifts in nucleotide base composition exist among taxa and appear to mirror evolutionary history. These shifts do not have an observable influence on phylogenetic reconstruction and are probably due to descent as opposed to convergence. Alignment instability and the presence of alignment-ambiguous regions had the greatest effect on phylogeny reconstruction. Our results support the taxonomic utility of the ITS region to diagnose nematode species of the genus Steinernema, and all sampled taxa show evidence (in the form of numerous autapomorphic characters) of lineage independence. However, the ITS region appears to be phylogenetically informative only for closely related sister species. High variability among more distantly related taxa preclude its use for confidently resolving relationships among all members of the genus.