Insight into phylogenetic relationships among nematodes based on a phylumwide molecular framework of ~2500 full-length small subunit ribosomal DNA sequences

For decades nematodes systematics has been unstable. This can in part be attributed the limited number of informative morphological characters. Another major factor underlying the volatility of nematode systematics is the extensiveness of convergent evolution; it is hard to find any characteristic that has not evolved at least twice during evolution. These issues can in part be solved when a switch is made towards molecular data; this gives access to sheer inexhaustible number of characters. Most likely, nematodes arose during the Cambrian explosion about 530 MYA. Keeping the ancient nature of the nematodes as a group in mind, a relatively conserved gene should be selected for phylogenetic reconstruction. Two of the ribosomal DNA genes, the small and large subunit (SSU and LSU) rDNA, could be considered for phylum-wide analysis. However, the LSU rDNA (D1-D3) was shown to be too diverse for this purpose; it was almost impossible to align partial LSU rDNA sequences from Tylenchida (Clade 12) and Dorylaimida (Clade 2) (Helder, unpublished results). So far, the SSU rDNA gene is the only target gene that can be amplified easily with standard universal and nematode specific primers, and properly aligned. Over the last few years, we’ve collected, identified and sequenced a large number of mainly terrestrial and freshwater nematode species. This data set was supplemented with all publicly available animal parasitic and marine nematode sequences, and the results and implications of an overall phylogenetic analysis will be presented. Special attention will be paid to Clade 1, the most basal nematode clade harboring mainly representatives of the orders Enoplida and Triplonchida, and the most distal Clade 12, a clade that includes the most of the economically relevant plant-parasitic nematode species