Environmental DNA reveals patterns of biological invasion in an inland sea

Joe Duprey; Ramón Gallego; Terrie Klinger; Ryan P. Kelly

doi:10.1371/journal.pone.0281525

Peer Review History

Original SubmissionJanuary 24, 2023
11 Jul 2023 Decision Letter - Hideyuki Doi, Editor PONE-D-23-02132Environmental DNA reveals patterns of biological invasion in an inland seaPLOS ONE Dear Dr. Duprey, 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 Aug 25 2023 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. 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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: The study entitled “Environmental DNA reveals patterns of biological invasion in an inland sea” study which habitat types are most prone to biological invasion and what are the vector that drive those invasions. I am not an expert on environmental DNA but I think that the paper is written in a clear manner and it is easy to follow the flow of the research article. Beside that, I’ve made some suggestion that, in my opinion, can strength the paper. I think that in some part this paper can be improve with some work on the images. In the detailed comments I have made different advice. To strengthen the paper, I suggest: 1. To Improve the method part as suggested in the detailed comments. 2. To improve the readability of the figure created. DETAILED COMMENTS: • L123-125 repetition of concept, I suggest rewrite the sentence to make it clearer. • L186-188 Is there any reference on this approach used? Any previous work? • L202 you should cite both R and the R package used. • L211 cite the vegan package. • Figure 1 is missing the scale and the northern arrow. I also suggest using different symbol instead of colors to point the study sites. • Figure 5 is it possible to have symbols instead of colors? The graph with color is pretty hard to read. • Figure 6 if you use color to define the study site you can’t change the color you assigned to another figure. For example, at TW is assigned red but in the fig 5 is the blue one. That make the readability of the graph lower. ****** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No ******** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. Attachments Attachment Submitted filename: comments.docx https://doi.org/10.1371/journal.pone.0281525.r001
Revision 1
14 Nov 2023 Author Response also see attached response_to_reviewers.docx: We appreciate the comments made by the reviewer and have addressed them as described below. L123-125 repetition of concept, I suggest rewrite the sentence to make it clearer. I’ve eliminated the repeated concept from the previous paragraph L114-115. I’ve also clarified the comparison of abiotic habitat factors between sites L124-L126. L186-188 Is there any reference on this approach used? Any previous work? To our knowledge no previously published work has taken this exact approach to classifying species as native, non-native or cryptogenic. Previously published invasive species research often reports similar approaches, or does not explicitly report their classification process. We offer examples from two of the non-native species metabarcoding studies cited in our manuscript: Lacoursiere-Roussel et al (2018) state that they identified potential “NIS invaders” based on previously published risk assessments, and monitoring studies of their study region – an approach similar to our own. They also highlight that “focal taxa [potential NIS invaders] vary among surveys”, an observation that highlights the challenges of this classification process in general. Holmen et al (2019) do not explicitly state how they classify species as non-native to their study region. “In total 18 NIS to the study region and 24 species documented as NIS in other regions were detected across the four sites (see Supplementary Table 2 for full list). Out of the detected NIS, eight were present in the list of 21 NIS previously detected in rapid assessment (RA) surveys at the sampling sites”. We note that in the context of the broader non-native species literature our approach to classifying species is conservative – relying on multiple databases sourced from peer reviewed literature, and requiring multiple peer-reviewed sources to have already classified a species as non-native. L202 you should cite both R and the R package used. Citations added for both. L211 cite the vegan package. Citation added. Figure 1 is missing the scale and the northern arrow. I also suggest using different symbol instead of colors to point the study sites. Fig1: I have added a scale bar and a north arrow. I have made the study sites different symbols in addition to different colors to represent that different substrate types. Figure 5 is it possible to have symbols instead of colors? The graph with color is pretty hard to read. Fig5: I think symbols for each site distract from the main take-away of this scatter plot which is the relationship between temperature and relative non-native richness. I have increased the size of each data-point to make the color more legible. Figure 6 if you use color to define the study site you can’t change the color you assigned to another figure. For example, at TW is assigned red but in the fig 5 is the blue one. That make the readability of the graph lower. Fig 6: I have changed the colors on Figure 6 so that each site has the same color on both Figure 5 and Figure 6. Attachments Attachment Submitted filename: response_to_reviewers.docx https://doi.org/10.1371/journal.pone.0281525.r002
29 Nov 2023 Decision Letter - Hideyuki Doi, Editor Environmental DNA reveals patterns of biological invasion in an inland sea PONE-D-23-02132R1 Dear Dr. Duprey, 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 for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, 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, Hideyuki Doi Academic Editor PLOS ONE Additional Editor Comments (optional): I carefully checked the revised manuscript as well as the response letter. I agree with the revisions and now can recommend publishing the paper. Reviewers' comments: https://doi.org/10.1371/journal.pone.0281525.r003
Formally Accepted
6 Dec 2023 Acceptance Letter - Hideyuki Doi, Editor PONE-D-23-02132R1 Environmental DNA reveals patterns of biological invasion in an inland sea Dear Dr. Duprey: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. 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. Hideyuki Doi Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0281525.r004

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