Peer Review History
| Original SubmissionOctober 10, 2024 |
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PONE-D-24-45532A deep dive into the coelacanth phylogenyPLOS ONE Dear Dr. Cavin, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by Jan 18 2025 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised manuscript:
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Kind regards, Giorgio Carnevale, Ph.D Academic Editor PLOS ONE Journal requirements: When submitting your revision, we need you to address these additional requirements. 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and 2. Thank you for stating the following financial disclosure: “Swiss National Science Foundation (200021-172700) ‘Evolutionary pace in the coelacanth clade: New evidence from the Triassic of Switzerland’ Please state what role the funders took in the study. If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. 3. Please amend either the abstract on the online submission form (via Edit Submission) or the abstract in the manuscript so that they are identical. Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes ********** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes ********** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes ********** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: Dear Editor and Authors, Thanks for allowing me to review this excellent and comprehensive study revising the phylogeny of coelacanths based on morphological characters. I am of the opinion that the study is acceptable pending some major revisions. First, I want to congratulate the authors on what has clearly been a lot of work. The illustrations and thorough description are excellent. There are, however, a few issues that need to be addressed before publication. 1) There are some omissions in the comprehensive review of extinct coelacanth phylogenetic diversity and phylogenetic studies that need to be addressed. A recently published revision of Diplurus newarki from 2022 (https://bmcecolevol.biomedcentral.com/articles/10.1186/s12862-022-02043-4) was not cited or discussed, and the species erected in that contribution ("D. enigmaticus") and in a second study by one of the authors ("Whiteia giganteus" https://palaeo-electronica.org/content/2023/3804-big-dockum-group-coelacanth) were not included in your comprehensive review without comment. These studies provide phylogenies that place these species. Even if you disagree with the erection of these new taxa (and indeed, the authors of those studies split them based on few characters), the goal of your manuscript is clearly to provide a much-needed service by reviewing extinct coelacanth diversity in the context of their phylogeny. So, you need note why you do not consider these species valid and for what reasons if you exclude them from your list (especially since they are recently published). Secondly, the first study indicates that some features considered in your paper to be intraspecific variation (e.g., ridge counts on the opercle) are suggested to correspond to different species by the first paper. Also note that the first paper documented teeth from Diplurus newarki, which is important insofar as you note that this character coding was one you needed to review. This excellent paper is a service to the literature and these corrections will only further that service. 2) The introduction and discussion need to be expanded. Although I understand that this paper is primarily a follow-up to the other recent work by the authors, it needs to be better set in the context of the literature on coelacanths and similarly old groups of 'fishes' (lungfishes, sturgeons and paddlefishes, gars and bowfin, bichirs). Additional discussion of the 'living fossilhood' of coelacanths is needed, for example, because this is essential to your point on stability. Some key studies that should be cited include Casane and Laurenti (2013) on coelacanth 'living fossilhood' (you cite the response paper to this but not the original, and it is always good scholarship to review both particularly since the response is by one of the authors of the current manuscript) as well as a couple of recent papers that have looked at morphological and molecular evolution in living fossils: Meyer et al. (2021), Nature : the Neoceratodus genome Schartl et al. (2024), Nature : the Lepidosiren genome Wang et al. (2021), Cell: the Protopterus genome Brownstein et al. (2024), Evolution showing molecular stasis in gars and sturgeons but not coelacanths and lungfishes As it is, the discussion makes it seem like only a handful of authors have considered the evolutionary history of coelacanths (both timescale and morphology-based relationships). A lot more has been done than that, simply put. For example, the timescale of coelacanth evolution is something you figure in this study but do not discuss at any length in the introduction or discussion. The results of Clement et al. (2024) in Nature Communications for example should be discussed at greater length than a short paragraph at the end of the discussion, especially since you all produce somewhat different hypotheses of the timescale of coelacanth evolution. From the last paragraph, it seems like this paper was rapidly worked after the publication of that paper, which is understandable, but in a revision I would like to see some additional engagement with that paper. Particularly, your phylogeny appears to support a very rapid diversification of coelacanths at the Permian-Triassic mass extinction. This is super interesting and definitely matches expectations from the authors' previous work on the Triassic coelacanths of Switzerland. I would like some more text to focus on the time tree and its implications for our understanding of coelacanth evolution, and this is one detail I would definitely appreciate more information about given that Clement et al. (2024) do not recover anywhere near as pronounced a signature of Permo-Triassic diversification. Would this support coelacanths as Elvis Taxa? The abstract, introduction, and discussion are also worded oddly in places. For example, the abstract ends like this: "For the first time, a set of Palaeozoic coelacanth genera are found gathered within a monophyletic family, namely the Diplocerciidae. All Mesozoic coelacanths, including the extant Latimeria, are solved as member of the order Coelacanthiformes, a group that originated in the Permian with Coelacanthus as the basal most genus. We also found that most Mesozoic coelacanths are gathered into a monophyletic group, the Latimerioidei, itself divided into the Latimeriidae and the Mawsoniidae, themselves each divided into two subfamilies. Although these important changes, the new phylogeny of the Actinistia shows no significant alteration, and it remains relatively similar compared to previous studies. This demonstrates that the understanding of coelacanth phylogeny is now rather stable despite the weak support for most nodes in the phylogeny, and despite the difficulty of defining relevant morphological characters to score in this relatively slowly evolving lineage." -monophyletic family/clade is oxymoronic. A clade is by definition monophyletic, so please fix this here and throughout. -basalmost doesn't really mean anything/communicate anything in phylogenetics. Please use something like "the first to diverge." -"itself divided into ... themselves divided into" creates a run-on sentence. -"the understanding of coelacanth phylogeny" can be edited to "coelacanth phylogeny." Similar issues of clunkiness are found throughout the introduction and discussion. I recommend a hard edit of both these sections. 3) Figure 72 is entirely illegible as submitted and needs to be remade at higher resolution. I also recommend changing the brightness values in several of the real color images of textures; as it is these are difficult to see. 4) It is perhaps almost cliché to ask for this, but I would like the authors to expand the reportoire of phylogenetic analytical protocols employed in this manuscript to include Bayesian methods. Bayesian analyses are commonplace now in phylogenetics and are widely applied to morphological datasets. One can also jointly infer a timescale of evolution and relationships in some programs (e.g., BEAST2). The authors should at the very least run an uncalibrated Bayesian analysis (say, in MrBayes or RevBayes) to see whether the phylogeny that they present in this study is found using different methodologies. Indeed, one of the pushes of the current study is that the stability of coelacanth phylogeny might be due to the repeated use of the same dataset. An analogous issue is the repeated use of one criterion (parsimony) as the method of inference. Clement et al. (2022) and Brownstein and Bissell (2022) both conducted Bayesian tip-dating analyses on the modified Forey dataset and resolved different trees than they did when they used parsimony. In order to be able to pronounce coelacanth phylogeny stable, the authors really should be exploring multiple methods of inference. Thanks again for allowing me to review this paper, and I look forward to reading the manuscript when it is published! ********** 6. 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| Revision 1 |
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A deep dive into the coelacanth phylogeny PONE-D-24-45532R1 Dear Dr. Cavin, We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Giorgio Carnevale, Ph.D Academic Editor PLOS ONE Additional Editor Comments (optional): All the issues (except one) raised by the referee have been properly addressed and the manuscript is now suitable of publication in PLOS One. |
| Formally Accepted |
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PONE-D-24-45532R1 PLOS ONE Dear Dr. Cavin, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks to review your paper and let you know the next and final steps. Lastly, if your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. If we can help with anything else, please email us at customercare@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Giorgio Carnevale Academic Editor PLOS ONE |
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