Figure 1

Maximum likelihood (ML) analysis of 18S ribosomal RNA from 25 nematode species. The ML calculation assumes a molecular clock; thus, the tips of the tree are all equidistant, in branch length, from its root. This model of base substitution allows the expected frequencies of the four bases to be unequal, and different rates of evolution at different sites are allowed. The numbers indicate reconstruction of percentage changes in overall codon usage on this phylogenetic topology (see Codon usage patterns and relationships to sampling method, nematode phylogeny, and GC content [under Results]). A distance matrix of D values corrected for non-additivity [1 - antilog(-D)] × 100 was partitioned on the topology using the cyclic neighbor-joining algorithm, as illustrated by Avise [82]. Approximate percentage change in overall codon usage is indicated for five branches inferred to have undergone 5% or more divergence from an ancestral nematode pattern. This analysis identified genera Globodera, Meloidogyne, Pristionchus, and Strongyloides as having the most highly derived patterns of codon usage, and the remaining species as having relatively little net divergence from an ancestral nematode pattern. Definitions of species two letter codes are provided in Table 1; GenBank accession numbers are listed on right. Clades V are shown in red, IVa in blue, IVb in green, III in yellow, and I in brown.