Data from: Xenacoelomorpha is the sister group to Nephrozoa

The position of Xenacoelomorpha in the tree of life remains a major
unresolved question in the study of deep animal relationships.
Xenacoelomorpha, comprising Acoela, Nemertodermatida, and Xenoturbella,
are bilaterally symmetrical marine worms that lack several features common
to most other bilaterians, for example an anus, nephridia, and a
circulatory system. Two conflicting hypotheses are under debate:
Xenacoelomorpha is the sister group to all remaining Bilateria
(= Nephrozoa, namely protostomes and deuterostomes) or is a clade inside
Deuterostomia. Thus, determining the phylogenetic position of this clade
is pivotal for understanding the early evolution of bilaterian features,
or as a case of drastic secondary loss of complexity. Here we show robust
phylogenomic support for Xenacoelomorpha as the sister taxon of Nephrozoa.
Our phylogenetic analyses, based on 11 novel xenacoelomorph transcriptomes
and using different models of evolution under maximum likelihood and
Bayesian inference analyses, strongly corroborate this result. Rigorous
testing of 25 experimental data sets designed to exclude data partitions
and taxa potentially prone to reconstruction biases indicates that
long-branch attraction, saturation, and missing data do not influence
these results. The sister group relationship between Nephrozoa and
Xenacoelomorpha supported by our phylogenomic analyses implies that the
last common ancestor of bilaterians was probably a benthic, ciliated
acoelomate worm with a single opening into an epithelial gut, and that
excretory organs, coelomic cavities, and nerve cords evolved after
xenacoelomorphs separated from the stem lineage of Nephrozoa.