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The evolutionary history of the mitochondrial COX2 locus has been used to infer the phylogenetic relationships among 15 peronosporomycete and a hyphochytriomycete species. This molecular phylogenetic analysis at both the ordinal and generic levels provides strong evidence for the recognition of the Saprolegniomycetidae and the Peronosporomycetidae as natural groups, and for the monophyly of the Saprolegniales, Leptomitales and Pythiales. A three amino acid insertion/deletion event (indel) has been identified as a putative synapomorphy for the Saprolegniales. Parsimony mapping of 12 morphological and biochemical characters on the COX2 molecular phylogeny yields an hypothesis for peronosporomycete ancestral states and shared-derived features.

Ascaridoid nematodes parasitize the gastrointestinal tract of vertebrate definitive hosts and are represented by more than 50 described genera. We used 582 nucleotides (83% of the coding sequence) of the mitochondrial gene cytochrome oxidase subunit 2, in combination with published small- and large-subunit nuclear rDNA sequences (2,557 characters) and morphological data (20 characters), to produce a phylogenetic hypothesis for representatives of this superfamily. This combined evidence phylogeny strongly supported clades that, with 1 exception, were consistent with Fagerholm's 1991 classification. Parsimony mapping of character states on the combined evidence tree was used to develop hypotheses for the evolution of morphological, life history, and amino acid characters. This analysis of character evolution revealed that certain key features that have been used by previous workers for developing taxonomic and evolutionary hypotheses represent plesiomorphic states. Cytochrome oxidase subunit 2 nucleotides show a strong compositional bias to A+T and a substitution bias to thymine. These biases are most apparent at third positions of codons and 4-fold degenerate sites, which is consistent with the nonrandom substitution pattern of A+T pressure. Despite nucleotide bias, cytochrome oxidase amino acid sequences show conservation and retention of critical functional residues, as inferred from comparisons to other organisms.

The evolutionary history of the mitochondrial COX2 locus has been used to infer the phylogenetic relationships among 15 peronosporomycete and a hyphochytriomycete species. This molecular phylogenetic analysis at both the ordinal and generic levels provides strong evidence for the recognition of the Saprolegniomycetidae and the Peronosporomycetidae as natural groups, and for the monophyly of the Saprolegniales, Leptomitales and Pythiales. A three amino acid insertion/deletion event (indel) has been identified as a putative synapomorphy for the Saprolegniales. Parsimony mapping of 12 morphological and biochemical characters on the COX2 molecular phylogeny yields an hypothesis for peronosporomycete ancestral states and shared-derived features.