Data from: 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 specious 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 tres 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.