A new phylogenomic backbone for Acoelomorpha inferred from transcriptomic data

Xenacoelomorpha, including Xenoturbella, Acoela, and Nemertodermatida, are mostly microscopic, morphologically simple worms, lacking many structures typical of other bilaterians. Xenacoelomorphs have been proposed to be an early diverging Bilateria, sister to protostomes and deuterostomes, but recent phylogenomic analyses have recovered this clade nested within the deuterostomes, as sister to Ambulacraria. The position of Xenacoelomorpha within the metazoan tree has understandably attracted a lot of attention, overshadowing the study of phylogenetic relationships within this group. To date, knowledge of suprafamilial relationships within Acoelomorpha, the clade formed by Acoela and Nemertodermatida, is based on two phylogenies inferred from three genes. Here, we have sequenced 29 transcriptomes, doubling the number of sequenced species, to infer a backbone tree for Acoelomorpha based on genomic data. In doing so, we not only generated a robust phylogeny but also explored the data to identify potential sources of incongruence that generate topological instability. We then used this new phylogenomic hypothesis to (1) date major cladogenetic events within Acoelomorpha, (2) evaluate the performance of available morphological characters when reconstructing acoelomorph phylogeny and in phylogenetic placement of new species, and (3) study morphological evolution in this group.