A Phylogenomic Backbone for Acoelomorpha Inferred from Transcriptomic Data

Xenacoelomorpha are mostly microscopic, morphologically simple worms, lacking many structures typical of other bilaterians. Xenacoelomorphs –which include three main groups: Acoela, Nemertodermatida, and Xenoturbella– have been proposed to be an early diverging Bilateria, sister to protostomes and deuterostomes, but other 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. Given that Xenoturbella includes only six species whose relationships are well understood, we decided to focus on the most speciose Acoelomorpha (Acoela + Nemertodermatida). Here, we have sequenced 29 transcriptomes, doubling the number of sequenced species, to infer a backbone tree for Acoelomorpha based on genomic data. The recovered topology is mostly congruent with previous studies. The most important difference is the recovery of Paratomella as the first off-shoot within Acoela, dramatically changing the reconstruction of the ancestral acoel. Besides, we have detected incongruence between the gene trees and the species tree, likely linked to incomplete lineage sorting, and some signal of introgression between the families Dakuidae and Mecynostomidae, which hampers inferring the correct placement of this family and, particularly, of the genus Notocelis. We have also used this dataset to infer for the first time diversification times within Acoelomorpha, which coincide with known bilaterian diversification and extinction events. Given the importance of morphological data in acoelomorph phylogenetics, we tested several partitions and models. Although morphological data failed to recover a robust phylogeny, phylogenetic placement has proven to be a suitable alternative when a reference phylogeny is available.