The phylogeny of meiofaunal polychaetes based on morphological data is controversially discussed due to their great simplicity. These species often lack characters typical of larger polychaetes, such as parapodia and head appendages, and exhibit an overall similarity to juveniles. This group comprises the former archiannelids (e.g. Dinophilidae, Protodrilida and Polygordiidae) as well as the clitellate-like polychaetes Aeolosomatidae, Parergodrilidae, Hrabeiella periglandulata, Rheomorpha neiswestonovae and Potamodrilus fluviatilis.
To infer the phylogeny of these taxa the sequences of the 18S-rDNA of different species of Dinophilidae, Protodrilida, Polygordiidae, Aeolosomatidae, Parergodrilidae and other polychaete taxa as well as of R. neiswestonovae and P. fluviatilis were determined. The data matrix was extended by sequences of H. periglandulata and species of Annelida and other invertebrate taxa from GeneBank. Finally, the taxon sampling comprised about 150 polychaete species. Generalised parsimony and maximum likelihood methods were performed.
Monophyly of Parergodrilidae and Dinophilidae is confirmed. H. periglandulata is not related to Parergodrilidae. A close relationship of Parergodrilidae, Orbiniidae and Questidae is weakly favoured. These analyses significantly support the hypothesis that R. neiswestonovae and P. fluviatilis are Aeolosomatidae. A close relationship of Aeolosomatidae to Clitellata can neither be substantiated nor be rejected by the data at hand. A sistergroup relationship of Dinophilidae and Eunicida is declined. Monophyly of Protodrilida is rejected and, surprisingly, Saccocirridae is closely related to the Polygordiidae.