Despite several unquestionably homologous characters with Annelida, the Echiura have generally been considered to form a distinct taxon due to apparent lack of segmentation: neither in the body cavity nor in any other structures of the adult animals have clear signs of a metameric organization been observed. However, it must be considered that this lack of segmentation could represent a secondary condition and that Echiura are derived from segmented ancestors. An immunohistochemical analysis visualized with confocal laser-scanning microscopy (cLSM) shows the development of serially repeated units in the nervous system of Bonellia viridis. This organization corresponds to the metameric ganglia typical of Annelida. Antibodies against the neurotransmitters serotonin (5-hydroxytryptamine) and FMRFamide label distinct subsets of neurons. Their perikarya are arranged in discrete repetitive units in the ventral nerve cord of different larval stages. Labeling of neurotubuli using antibodies against different tubulin isoforms provides additional support for the metameric character of the nervous system. Contrary to previous descriptions, the peripheral nerves extending from the ventral nerve cord into the body wall musculature are paired and are evenly distributed; their arrangement corresponds to that of the serotoninergic perikarya. Morphological and neurochemical differentiation of the nervous system clearly proceeds from anterior to posterior, indicating the occurrence of a posterior growth zone. The serial ganglionic organization of the nervous system of Articulata is generally regarded as having evolved in conjunction with repetitive muscular units, in particular with the formation of typical annelid segments. Therefore, these results are interpreted as an indication that Echiura are derived from segmented ancestors and thus support the systematic inclusion of the Echiura within the Annelida.

The phylogenetic position of Echiura is still in continuous debate. The commonly accepted view regards Echiura as a distinct taxon, often classified as phylum, which forms the sister group of the Articulata. The alternative view considers Echiura to be a subtaxon of Annelida, which is supported by numerous shared characters. The correct systematic position of Echiura is inevitably linked to the presence or absence of true segmentation. The apparent lack of segmentation in Echiura is considered to be either primary, thereby supporting their exclusion from Annelida, or alternatively to be the result of reduction. The latter would clearly substantiate their classification as a subtaxon of Annelida. Immunohistochemical methods and confocal laser-scanning microscopy clearly demonstrate a metameric organisation of the nervous system in different larval stages of Urechis caupo, which corresponds to the segmental arrangement of ganglia in "typical" Annelida. This segmental pattern is reflected in the serially repetitive distribution of neurons containing the neurotransmitter serotonin (5-hydroxytryptamine) and also in the corresponding distribution of strictly paired peripheral nerves. Precisely two pairs of peripheral nerves are associated with each of the repetitive units. This metameric pattern also corresponds to the transient annulation of the trunk, which is found in late larval stages. Other characters of the nervous system including the paired origin of the ventral nerve cord, the anterior-posterior development gradient and the presence of a distinct suboesophageal ganglion are also found accordingly in typical Annelida. These results are interpreted as an indication that Echiura are derived from formerly segmented ancestors, and thus support their systematic inclusion within Annelida.

Absent characters (negative characters) are difficult to assess and their correct interpretation as symplesiomorphies, synapomorphies or convergencies (homoplasies) is one of the greatest challenges in phylogenetic systematics. Different phylogenetic assessments often result in contradictory phylogenetic hypotheses, in which the direction of evolutionary changes is diametrically opposed. Especially in deciding between primary (plesiomorphic) and secondary (apomorphic) absence, false conclusions may be reached if only the outgroup comparison and the principle of parsimony are employed without attempting any biological evaluation or interpretation of characters. For example, in the higher‐level systematization of the Annelida and related taxa different assessments of absent characters have led to conflicting hypotheses about the phylogenetic relationships and the ground pattern of the annelid stem species. Varying phylogenetic interpretations regarding the absence of the chemosensory nuchal organs in the clitellates and their presence in polychaetes initiated a controversy that produced two alternative phylogenetic hypotheses: (1) the Clitellata are highly derived Annelida related to a subtaxon within the, in this case, paraphyletic ‘Polychaeta’ or (2) the Clitellata are comparatively primitive Annelida representing the sister group of a monophyletic taxon Polychaeta. In the former, the absence of nuchal organs in the Clitellata is regarded as a secondary character, in the latter as primary. As most Clitellata are either limnetic or terrestrial, we must ask which characters are plesiomorphies, taken from their marine stem species without changes. In addition to a thorough investigation and evaluation of clitellate characters, a promising approach to these questions is to look for such characters in limnetic and terrestrial annelids clearly not belonging to the Clitellata. A similar problem applies to the evaluation of the position of the Echiura, which lack both segmentation and nuchal organs. Evidence is presented that in both taxa these absent characters represent derived, apomorphic character states. The consequences for their phylogenetic position and the questionable monophyly of the Polychaeta are discussed. The conclusion drawn from morphological character assessments is in accordance with recently published hypotheses based on molecular data.

The Aeolosomatidae and the Parergodrilidae are meiofaunal Annelida showing different combinations of clitellate‐like and non‐clitellate character states. Their phylogenetic positions and their systematic status within the Annelida are still in debate. Here we attempt to infer their systematic position using 18S rDNA sequences of the aeolosomatid Aeolosoma sp. and the parergodrilid Stygocapitella subterranea and several other meiofaunal taxa such as the Dinophilidae, Polygordiidae and Saccocirridae. The data matrix was complemented by sequences from several annelid, arthropod and molluscan species. After evaluation of the phylogenetic signal the data set was analysed with maximum‐parsimony, distance and maximum‐likelihood algorithms. Sequences from selected arthropods or molluscs were chosen for outgroup comparison. The resolution of the resulting phylogenies is discussed in comparison to previous studies. The results do not unequivocally support a sister‐group relationship of Aeolosoma sp. and the Clitellata. Instead, depending on the algorithms applied, Aeolosoma clusters in various clades within the polychaetes, for instance, together with eunicidan species, the Dinophilidae, Harmothoë impar or Nereis limbata. The position of Aeolosoma sp. thus cannot be resolved on the basis of the data available. S. subterranea always falls close to a cluster comprising Scoloplos armiger, Questa paucibranchiata and Magelona mirabilis, all of which were resolved as not closely related to both Aeolosoma sp. and the Clitellata. Therefore, convergent evolution of clitellate‐like characters in S. subterranea and hence in the Parergodrilidae is suggested by our phylogenetic analysis. Moreover, the Clitellata form a monophyletic clade within the paraphyletic polychaetes.

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