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Thanks for your revised manuscript - I am happy to move it forward into production.
[# PeerJ Staff Note - this decision was reviewed and approved by Patricia Gandini, a PeerJ Section Editor covering this Section #]
I have now heard back from both our previous expert referees and they are satisfied with your revisions and feel that the paper is now acceptable for publication. However there are a couple of small issues that need to be resolved before final acceptance. The first referee points our an error in the text that should be corrected prior to publication, and the second referee asks that the manuscript follow the journal guidelines for transparency and provide the methods in sufficient detail that the results could be reproduced. In accordance with the journal policies, the source code and/or relevant software components required to reproduce the reported results should be included in the manuscript or supplementary materials. I do not expect either of these revisions should be an obstacle for you, and I do not expect to send the paper out to referees again at this point. I look forward to seeing your final manuscript.
The paper is much improved, but contains one glaring error. Lines 340-342, states that balanomorph taxa listed are basal and close to the ibliformes. this is not true - they are highly derived.
Other than this, I recommend publication.
The new version addresses most of my concerns with the first submission, including providing the tree files, removing the section on additional molecular-based analyses, and including GBIF and GenBank data.
I would prefer to see enough information in the methods sections or the supplemental materials to fully describe and / or reproduce the synthesis results. The manuscript simply says 'trees were assembled into a synthesis tree using the propinquity pipeline' and the files provided in peerj-33472-Barnacle_synthesis_original_files.zip are the output files from the last step of the pipeline. What about the parameters used for synthesis, and version of software packages? This is simple to do - propinquity provides all of the output needed. For example, see the 'All pipeline outputs' link under Downloads on https://tree.opentreeoflife.org/about/synthesis-release/v10.4.
Sorry for the delay in getting this back to you - one referee ended up never responding and a second was unable to get this back to us sooner, so the process took longer than usual.
As you will see, both referees are supportive of the work and see the value of your submission, but each also has a number of suggestions for improvement. In particular, the second referee recommends a major revision to add important methodological details and make the data open and accessible for future work. Given the journal policy on data and sharing is quite clear in this regard (https://peerj.com/about/policies-and-procedures/#data-materials-sharing ), I find myself in agreement with the referees that this information should be added to the manuscript before publication.
Beyond the data and analyses sharing issue, which I consider a major revision requirement, I do not expect you should have any difficulty in responding to the referee suggestions, and I look forward to seeing your revised manuscript.
English fine, but a number of complex terms are used, of which the meaning is not clear to me, anyway.
not sure what this means precisely.
Negative results (i.e. phylogenetically unresolved thoracican taxa) needs discussion and explanation
Reading this MS, I first wondered that any success has been achieved in unraveling the barnacle tree of life! However, the reverse seems to be true, insofar as the sessile barnacles and some stalked groups is concerned, for which molecular phylogenies largely congruent with morphological data have been published. I think the paper should emphasise these positive and important findings, and also clearly explain why a mass of thoracican taxa included in fig. 3 (scalpellids, balanomorphs etc) have unresolved relationships.
I am not entirely sure what “little integration across taxonomic levels” actually means, or “lack of significant overlap in taxonomic entities” or “lack of overlap of characters” or indeed “overlap in represented taxa”. I suspect that some other readers are also unsure. Please explain clearly.
I can also see that there are difficulties in getting consistent results with basal relationships of groups, and that this needs much further study.
Fig. 3 clearly incorporates a lot of data, and indicates a number of significant relationships but is almost impossible to use, because if one zooms in to see names, the relationships are no longer visible. Why not also use colour for individual thoracican clades (e.g. balanomorphs) and add names down to family or superfamily level, as appropriate? This would then emphasise what we do know. The other question is one of support for clades, which is pretty essential really. An alternative would be to add a standard cladogram with support for individual nodes.
OK, so there’s a vast arc (NNE-SWS) of unresolved thoracicans, including scalpellids, balanomorphs etc. amongst which Ibliformes reside. Is there not some difference in the data available (quality, amount?) for these taxa? It seems bizarre, that their close relatives should yield phylogenetically important information, yet they do not. This needs explanation, surely.
A list of what we do know about barnacle evolution from molecules would help. This might include:
- Basal position of Ibla
- Monophyletic Sessilia, divided into clades of balanomorphs and verrucomorphs
- a highly resolved tree for the balanomorphs (Perez-Losada et al. 2014), with considerable detail
- a detailed tree for the Scalpellidae, which is congruent with morphology (e.g. Lin et al. 2015)
and other points as appropriate.
The language throughout is clear and the manuscript easy to read. The data publication is insufficient. The phylogeny is presented only as an image in a pdf file (despite the authors noting in the Methods the difficulties caused when phylogenies are not deposited in electronic repositories). The only link in the data section is the list of trees included as input to synthesis. Other ata I would expect to see:
* the genebank accessions used to reconstruct the additional tree
* the full output of the propinquity pipeline (including the synthesis tree)
* the occurrence data from GBIF
In general, there is not nearly enough detail in the methods section to understand the results being presented, and it would be impossible to reproduce the results.
The methods sections refers to the combination of the tree alignment graph method of Smith et al 2013 with the propinquity pipeline of Redelings and Holder. I am not sure this is accurate. The OpenTree project switched from the Smith et al method to the Redelings and Holder method in 2016 (see this blog post; https://blog.opentreeoflife.org/2016/04/08/new-version-of-tree-apis/). I am not aware of any workflows that combine the two synthesis methods, so the manuscript definitely needs clarification here.
If the synthesis was done using the propinquity method, then including the output from the propinquity pipeline would provide enough information to understand and reproduce the results (including the version of software packages, the exact inputs, and parameters used for synthesis). If propinquity was not the method used, the steps used to synthesize the trees needs to be much more clearly described.
The authors also describe using molecular data to “reconstruct an additional tree following the approach of Owen et al. (2015)”. Again, there is not enough detail here to understand the inference of this tree. The Owen paper is itself a synthesis phylogeny. Is the additional tree inferred directly from sequences and added to the synthesis method, or is the additional tree a synthesis tree? Is this one of the 27 trees included in the collection at https://tree.opentreeoflife.org/curator/collections/kcranston/barnacles?
In general, the lack of detail in the methods make it difficult to assess the findings.
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