From NematodeGenomes

Systematics of Nematoda - a molecular revision

The molecular phylogenetic revision of the systematics of phylum Nematoda that has taken place since 1998 (Blaxter et al 1998) has resulted in a new system that is relatively stable. This stability may be real, or may be an artefact of the use of a single gene (nuclear small subunit ribosomal RNA) for analyses.

While the major clades identified in 1998 (using only 53 species) have been affirmed, the subsequent addition of many missing major taxa and renanalyses have refined and revised the picture (Holterman et al 2006, Meldal et al 2007, van Mengen et al 2009).

De Ley and Blaxter attempted to turn the numbered clades into a systematics in 2002-2004 (De Ley, P. and M. Blaxter (2004). A new system for Nematoda: combining morphological characters with molecular trees, and translating clades into ranks and taxa. Nematology Monographs and Perspectives. R. Cook and D. J. Hunt. Leiden, E.J. Brill. 2: 633-653; De Ley, P. and M. L. Blaxter (2002). Systematic position and phylogeny. The Biology of Nematodes. D. Lee. London, Taylor & Francis: 1-30) and many other workers have revised local subsections of the phylum.

We have chosen to annotate species with

(a) the 'accepted' taxonomy as enshrined in the NCBI Taxonomy database (ENTREZ Taxonomy for Nematoda [1]). All species of Nematoda with representation in NCBI as of 04/2010 (except "environmental" samples) have been preloaded, along with their relationships.

(b) the Major Clades of Blaxter et al 1998 ("Bclades") [2], as systematised by De Ley and Blaxter 2002-2004. These are labeled I, II, III, IV, V and 'C'. Note that 'C' includes III, IV and V, but is used here to indicate the paraphyletic assemblage not contained in III, IV and V. 'C' is thus NOT a monophyletic clade.

(c) the Minor Clades of Holterman and van Mengen (2006-2009) ("Hclades") [3] [4]. These have Arabic numeral identifiers (1 to 12). We have also included the subclades defined by Hans Helder's group (e.g. 9A, 9B, etc.).

In some cases Bclades correspond to a single Hclade (e.g. Bclade III == Hclade 8), while others correspond ~nearly~ to a taxon in the NCBI heirarchy (eg Bclade I == Hclade 2 ~= NCBI Dorylaimida + Trichocephalida + Mermithida + others).

The systematics of Rhabditida ss (Bclade V == Hclade 9) are not well resolved in our systematisation here, and will be revised in the near future.

This should be regarded as an interim solution and we welcome clarification and correction.