The impact of fossil data on annelid phylogeny inferred from discrete morphological characters

As a result of their plastic body plan, the relationships of the annelid worms and even the taxonomic makeup of the phylum have long been contentious. Morphological cladistic analyses have typically recovered a monophyletic Polychaeta, with the simple-bodied forms assigned to an early-diverging clade or grade. This is in stark contrast to molecular trees, in which polychaetes are paraphyletic and include clitellates, echiurans and sipunculans. Cambrian stem group annelid body fossils are complex-bodied polychaetes that possess well-developed parapodia and paired head appendages (palps), suggesting that the root of annelids is misplaced in morphological trees. We present a reinvestigation of the morphology of key fossil taxa and include them in a comprehensive phylogenetic analysis of annelids. Analyses using probabilistic methods and both equal- and implied-weights parsimony recover paraphyletic polychaetes and support the conclusion that echiurans and clitellates are derived polychaetes. Morphological trees including fossils depict two main clades of crown-group annelids that are similar, but not identical, to Errantia and Sedentaria, the fundamental groupings in transcriptomic analyses. Removing fossils yields trees that are often less resolved and/or root the tree in greater conflict with molecular topologies. While there are many topological similarities between the analyses herein and recent phylogenomic hypotheses, differences include the exclusion of Sipuncula from Annelida and the taxa forming the deepest crown-group divergences.

7. Segment 1 with notopodia onlyls 8. Anal chaetal ring. Present in Urechis [42] 9. Spermatozoon with acrosome. Coded as per [3], with the presence of an acrosomal tube (character 10) coded as a contingent character. 10. Spermatozoon with acrosomal tube [3] 11. Prototroch. Larval characters (11--22) follow [3], which in turn are adopted from [2,43,44] 12. Metatroch. Coded following [44] except for the capitellid Notomastus, in which a metatroch appears to be present [25] 13. Opposed band larval feeding 14 [9,10] was coded as possessing palps. Rather than coding the buccal tentacles of terebelliforms in a character complex with true palps, these structures were coded as a separate character due to substantial differences between the innervation and attachment of these structures when compared with true palps [9,10]. Although tentacles in the buccal cavity are present in Cossura, they are not considered homologous [18].  and Laonice (Spionidae) is coded as homologous with the median antenna of aciculate taxa with this character [8,9,12]. The median branchus of Cossura is attached and innervated differently and is not scored as homologous [18]. neurochaetae, as per Tilic, Lehrke [39]. Although Thompson and Johnson [48] considered Esconites zelus to have notochaetae, this is considered unlikely as although two distinct bundles are visible in some specimens,  [14]. New character.

128.
Jaws. Although jaws among aciculate polychaetes may not be homologous, we followed [54] and coded their presence as a single state.

139.
Proboscis terminal papillae, coded from family descriptions in [12]. New character.  [63]. Also coded as present in fossil taxa that preserve cuticle, such as those from the Burgess Shale.
New character.

174.
Body with trunk and introvert, coded as present in sipunculans.