Reviewer 1's Review (Tim Littlewood)

“What are the main claims of the paper?
• the title says it all

Are the claims properly placed in the context of the previous literature?
• yes, the scene is set with a concise history of the molecular phylogenetics of flatworms and Metazoa showing how acoels have 'enjoyed' a turbulent history in attempts to place them accurately in the animal evolutionary tree
• the advantages of a phylogenomic approach and the use of improved models aimed at buffering the effects of LBA are introduced

Do the experimental data support the claims? If not, what other evidence is required?
• there's not much more one can ask for in a phylogenomic assessment (except the usual call for greater taxonomic sampling), and this paper reports on the first phylogenomic assessment of acoel relationships among the Metazoa. The gene and taxon sampling is excellent as an initial foray into the use of this technique in placing the acoels away from the Platyhelminthes. Curiously though, there is still sufficient ambiguity at the basal nodes to allow a number of hypotheses to remain concerning the exact placement of this group. Perhaps most tantalizing is the prospect that Xenoturbella and Convoluta might yet still share a close common ancestry. The authors are wise not interpret this possible deuterostome affinity with too much gusto, at least until new dat become available. Certainly, the contents of the paper well fit the title and this is another important nail in the coffin against Platyhelminthes (sensu lato); ie excluding acoels.

Who would find this paper of interest? And why?
• Animal evolutionary biologists, developmental biologists, taxonomists, systematists, bioinformaticians. The placement of the Acoela has very important implications for the understanding of the early radiation of bilaterally symmetrical animals. If they are associated with deuterostomes the implications are even more shocking. All systematists (including botanists and palaeontologists) would be interested in the means used to reconcile such deep branches in the tree of life, and the implications for the results found; given the volume of data so far accumulated it is clear that problems remain although other problems (as dictated by the title) are clearly resolved.
• Those interested in the secondary loss of complex morphologies, as opposed to the perceived basal nature of (secondarily) simplified organisms would be interested in this paper, regardless of specific taxonomic interest

In what further directions would it be useful to take the current research?
• greater taxon sampling is critical (e.g. Paratomella, a nemertodermatid etc) as suggested by the authors themselves; in spite of the use of the CAT model the final trees clearly include long branching taxa. Also of us would be the search for rare genomic changes/synapomorphies in this data set (c.f. the gene present/absent in Deuterostomes and acoels). Care must be taken in interpreting a lot of the data that falls into the problems of 'absence of evidence is not evidence of absence', when dealing with some of the molecular data that fails to appear in the EST approach associated with phylogenomics.

Is the manuscript written clearly enough that it is understandable to non-specialists? If not, how could it be improved?
• the manuscript is well written and clear; see list of typos/errors/suggested changes at end

Have the authors provided adequate proof for their claims without overselling them?
• yes

Have the authors treated the previous literature fairly?
• I think so

Does the paper offer enough details of its methodology that its experiments could be reproduced?
• yes”

N.B. These are the general comments made by the reviewer when reviewing this paper in light of which the manuscript was revised. Specific points addressed during revision of the paper are not shown.