Comparative mitogenomic analysis provides evolutionary insights into Formica (Hymenoptera: Formicidae)

Min Liu; Shi-Yun Hu; Min Li; Hao Sun; Ming-Long Yuan

doi:10.1371/journal.pone.0302371

Peer Review History

Original SubmissionJune 6, 2023
6 Feb 2024 Decision Letter - Yanbin Yin, Editor PONE-D-23-17435Comparative mitogenomic analysis provides evolutionary insights into Formica (Hymenoptera: Formicidae)PLOS ONE Dear Dr. Yuan, 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. ==============================Both reviewers have concerns on the presentation and writing, which should be improved in the new version.============================== Please submit your revised manuscript by Mar 22 2024 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. 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Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: “This study was funded by the Second Tibetan Plateau Scientific Expedition and Research (STEP) Program (2019QZKK0302), and the Key Project of Science and Technology Department of Xinjiang Autonomous Region, China [2020E0213, 2016A03006]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.” Please include your amended statements within your cover letter; we will change the online submission form on your behalf. 3. Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. 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Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: 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: The manuscript investigated two mt-genomes of the genus Formica and resconstructed the phylogenic relationship within the genus using those datasets. The results will be a potential reference for the understanding of insects mt-genome and their applification for the phlogeny within genus. Reviewer #2: The authors sequenced two Formica species and assembled the mitogenomes, then the authors did some analysis, such as coding genes, tRNAs, codon usage. I have some comments as follows: 1. I suggest the authors marked the ‘Line numbers’ throughout the manuscript, it would be easier to track the comments. 2. In the section ‘3.2. Nucleotide composition and codon usage’, keep the number ‘3274’ and ‘3712’ (be 3,712) the same style with previous content, please check with all the manuscript. 3. In the section ‘3.3. Intergenic spacers’, I suggest rephrase the intergenic spacers (IGSs), especially you don’t need to list all the 14 spacers in details, please emphasize most important results. 4. In the section ‘3.6. Mitochondrial phylogeny of Formica’, there is a typo error ‘group 2 including five species, with.’ 5. In the section ‘4.5. Formica Phylogeny and intergenic spacers’, the authors said ‘unstable phylogenetic relationships of Formica’, which phylogeny gives most confident their relationships? What’s the explanation? 6. Figure 9, I suggest the authors label all the nodes with bootstrap values. ****** 6. 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Revision 1
21 Mar 2024 Author Response For Reviewer #1 The manuscript investigated two mt-genomes of the genus Formica and resconstructed the phylogenic relationship within the genus using those datasets. The results will be a potential reference for the understanding of insects mt-genome and their applification for the phlogeny within genus. Response: We thank the reviewer’s positive comments on the manuscript. For Reviewer #2 1. I suggest the authors marked the ‘Line numbers’ throughout the manuscript, it would be easier to track the comments. Response: We have provided “Line numbers” throughout the revised manuscript, as suggested. 2. In the section ‘3.2. Nucleotide composition and codon usage’, keep the number ‘3274’ and ‘3712’ (be 3,712) the same style with previous content, please check with all the manuscript. Response: We have revised the manuscript, as suggested. 3. In the section ‘3.3. Intergenic spacers’, I suggest rephrase the intergenic spacers (IGSs), especially you don’t need to list all the 14 spacers in details, please emphasize most important results. Response: We have rephrased the intergenic spacers, by deleting some unnecessary descriptions of 14 IGSs to emphasize the most important results, as suggested. 4. In the section ‘3.6. Mitochondrial phylogeny of Formica’, there is a typo error ‘group 2 including five species, with.’ Response: We have changing “group 2 including five species, with” into “group 2 including five species”, as suggested. 5. In the section ‘4.5. Formica Phylogeny and intergenic spacers’, the authors said ‘unstable phylogenetic relationships of Formica’, which phylogeny gives most confident their relationships? What’s the explanation? Response: We thank the reviewer’s invaluable comments. The Formica phylogeny (Figure 9A) obtained from the P123 dataset may be most confident, as reported by Goropashnaya et al. (PLoS One, 2012). We discussed the unstable phylogenetic relationships of Formica in the Discussion section. 6. Figure 9, I suggest the authors label all the nodes with bootstrap values. Response: We thank the reviewer’s invaluable comments. Given the six Formica phylogenies have almost consistent phylogenetic relationships and most support values were more than 90 and 0.9, we integrated all phylogenetic results (Figure 3A) into a common phylogenetic backbone and used black dots to denote support values greater than 90 (RA x ML) and 0.9 (MrBayes and NJ), which did not affect the understanding of the phylogenies. We also provided all phylogenetic trees with specific support values for each node in Figure 3A. Attachments Attachment Submitted filename: Reply to Reviews Comments-Submission.docx https://doi.org/10.1371/journal.pone.0302371.r002
3 Apr 2024 Decision Letter - Yanbin Yin, Editor Comparative mitogenomic analysis provides evolutionary insights into Formica (Hymenoptera: Formicidae) PONE-D-23-17435R1 Dear Dr. Yuan, 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, Yanbin Yin Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0302371.r003
Formally Accepted
30 May 2024 Acceptance Letter - Yanbin Yin, Editor PONE-D-23-17435R1 PLOS ONE Dear Dr. Yuan, 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. Yanbin Yin Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0302371.r004

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