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.