Phylogeny of the phylum nematoda based on small subunit ribosomal DNA sequences

On the basis of full-length SSU rDNA sequences (e¨ 1700 bp), the phylogeny of the phylum Nematoda was reconstructed. The majority of nematode sequences were collected at the Laboratory of Nematology (Wageningen University). Sequences obtained from GenBank were added to these. In order to obtain a SSU rDNA sequence, we isolated DNA from a single individual nematode, which had been identified and photographed beforehand. The SSU rDNA was PCR amplified, cloned into vectors and sequenced. A number of nematode species were sequenced multiple times to assess intraspecific variation and sequence errors. For these species a consensus sequence was constructed. This resulted in an alignment, which included the SSU sequences of 355 nematode species. Ten members of the phyla Arthropoda, Priapulida, Tardigrada, Nematomorpha and Kinorhyncha represented the outgroup. The alignment was constructed with the ClustalW algorithm and checked manually. Two regions of the SSU (99 and 76 bp), which were difficult to align, were omitted from the analysis. Trees were constructed using Neighbour-Joining, Maximum Parsimony, Maximum Likelihood and Bayesian inference of phylogeny. All methods showed consensus in that they revealed five major clades. Our results suggest that the classic division of the nematodes into the Adenophorea and Secernentea is invalid: the Adenophorea are paraphyletic with respect to the Secernentea. This is in correspondence with earlier molecular phylogenetic analyses.