Conflicting signal within a single gene confounds syllid phylogeny (Syllidae, Annelida).

The phylogenetic relationships within the family Syllidae have been analyzed previous to this study and a new subfamily (Anoplosyllinae) defined. However, the monophyly of the family Syllidae was not well-supported. A conflict between the different molecular data sets combined in previous preceding molecular analyses is studied herein treating the genes 18S and 16S independently using different alignment parameters, algorithms, methodologies and secondary structure considerations. The lack of support for the monophyly of Syllidae relates to a fragment of the 18S gene, the variable region V4, which demonstrates a conflicting signal when compared to the remaining 18S sequence data. A discussion regarding the phylogenetic information contained in the secondary structure of 18S is provided. In the light of these results, the implications of including/excluding ambiguous regions in the alignments are evaluated, and finally a systematic proposal for the classification of syllids is put forward. 2010 Elsevier Inc. All rights reserved.