DNA barcoding echinoderms from the East Coast of South Africa. The challenge to maintain DNA data connected with taxonomy

Gontran Sonet; Nathalie Smitz; Carl Vangestel; Yves Samyn

doi:10.1371/journal.pone.0270321

Peer Review History

Original SubmissionJune 7, 2022
5 Jul 2022 Decision Letter - Tzen-Yuh Chiang, Editor PONE-D-22-16400DNA barcoding echinoderms from the East Coast of South Africa. The challenge to maintain DNA data connected with taxonomyPLOS ONE Dear Dr. Sonet, 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 19 2022 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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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: I Don't Know ****** 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: No ****** 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: Authors present quite standard procedures broadly utilized for barcoding diverse groups of animals. They also used four standard methods to delimit species based on acquired sequences, and compared them with classic morphological identifications. In Results and Discussion sections they discussed in details differences between those methods that predicted slightly different number of taxa. ?However, in my opinion the greatest weakened of the presented paper are illustrations. Authors discuss differences between algorithms, however, they didn't present results from each calculation, so it is impossible to compare them by a reader. These results should be at least attached as a supplementary materials. Moreover, on the Fig 3 authors wrote that trees were calculated using Neighbour Joining method. There is nothing about this method in M&M section. On the other hand there are no trees calculated using Bayes as mentioned i M&M. That should be definitely corrected or clarified. In general manuscript is well written, however, level of novelty of this research is limited. ****** 6. 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Revision 1
18 Aug 2022 Author Response Rebuttal letter (also attached in this submission as a doc file) PONE-D-22-16400 DNA barcoding echinoderms from the East Coast of South Africa. The challenge to maintain DNA data connected with taxonomy PLOS ONE N.B. All replies to the comments of the reviewers start with * Review from the editor 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 https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf We read again the PLOS ONE's style requirements and adapted our manuscript accordingly. 2. We note that the grant information you provided in the ‘Funding Information’ and ‘Financial Disclosure’ sections do not match. We adapted the ‘Funding Information’ section in order to match the Financial disclosure. 3. PLOS requires an ORCID iD for the corresponding author in Editorial Manager on papers submitted after December 6th, 2016. Please ensure that you have an ORCID iD and that it is validated in Editorial Manager. To do this, go to ‘Update my Information’ (in the upper left-hand corner of the main menu), and click on the Fetch/Validate link next to the ORCID field. This will take you to the ORCID site and allow you to create a new iD or authenticate a pre-existing iD in Editorial Manager. Please see the following video for instructions on linking an ORCID iD to your Editorial Manager account: https://www.youtube.com/watch?v=_xcclfuvtxQ ORCID ID was linked 4. Please include your full ethics statement in the ‘Methods’ section of your manuscript file. In your statement, please include the full name of the IRB or ethics committee who approved or waived your study, as well as whether or not you obtained informed written or verbal consent. If consent was waived for your study We added the ethic statement in the material and methods: “All specimens studied here are invertebrates and were collected legally with written permissions from the regional and national South African authorities. The permit number of the expedition of 2016 is RES 2016-02 and was granted by the Department of Agriculture, Forestry and Fisheries (DAFF) and the Department of Environmental Affairs (DEA) of South Africa to Yves Samyn., please include this information in your statement as well.” 5. We note that Figure 1 in your submission contain [map/satellite] images which may be copyrighted. We confirm that we have the permission to publish Figure 1 specifically under the CC BY 4.0 license. Indeed, the map was created using the software QGIS v. 3.22.6, the GEBCO Grid and Natural Earth. We added this information and the citation of all three sources in the caption of the figure and uploaded the terms of use of these tools as "Other"" file in the submission. 6. We note that Figure 3 in your submission contain copyrighted images. All PLOS content is published under the Creative Commons Attribution License (CC BY 4.0). We present a written permission from the copyright holder (a coauthor of this article) to publish these figures specifically under the CC BY 4.0 license (form uploaded as "Other"" file in the submission). Reviewer's Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? Reviewer #1: Yes ________________________________________ 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: I Don't Know ________________________________________ 3. Have the authors made all data underlying the findings in their manuscript fully available? Reviewer #1: No All data supporting the findings related to this manuscript were uploaded a public repository (BOLD). As stated in the original submission, data will be released directly upon acceptance to publish this article in PONE. Based on the additional comments of the reviewer, we added all phylogenetic trees as supporting information (see below). ________________________________________ 4. Is the manuscript presented in an intelligible fashion and written in standard English? Reviewer #1: Yes ________________________________________ 5. Review Comments to the Author Reviewer #1: Authors present quite standard procedures broadly utilized for barcoding diverse groups of animals. They also used four standard methods to delimit species based on acquired sequences, and compared them with classic morphological identifications. In Results and Discussion sections they discussed in details differences between those methods that predicted slightly different number of taxa. However, in my opinion the greatest weakened of the presented paper are illustrations. Authors discuss differences between algorithms, however, they didn't present results from each calculation, so it is impossible to compare them by a reader. These results should be at least attached as a supplementary materials. We totally agree with this comment. Illustrations are difficult to make for large data sets, and other large scale DNA barcoding studies already published also lack illustrative figures. Our Fig. 2 (general appreciation of the distances between the new sequences and those preexisting) and Fig. 3 (illustrated cases) are there to compensate. The different partitions obtained using the different algorithms were indeed not presented as raw data (they were included in Table 2 but we agree that this is not easy to consult. Hence, we added the putative species ID in the Table S1, which provides all info about all specimens and which can be easily reused by other researchers. The legend of the table was adapted: “S1 Table. Specimen information. Columns ABGD, GMYC, bPTP and RESL provide the putative species identifications for each method”. Moreover, on the Fig 3 authors wrote that trees were calculated using Neighbour Joining method. There is nothing about this method in M&M section. Indeed, we forgot to mention that “Neighbour joining trees based on p-distances were constructed using MEGA v7.0.26 (41) in order to illustrate distance among putative species.” This sentence was added in the Materials and Methods. On the other hand there are no trees calculated using Bayes as mentioned i M&M. That should be definitely corrected or clarified. We thank the reviewer for this observation. The original Materials and Methods section was indeed misleading in this regard. Bayesian inferences were generated in order to use them as an input for 2 of the 4 species delimitation methods (GMYC and bPTP), whereas Neighbour joining trees were generated to visualise the distances among the DNA sequences. In addition to the correction described above (concerning the neighbour joining trees), we also modified one sentence in the M&M as follow: “Phylogenetic trees were reconstructed through Bayesian inference (BI) and were used as an input for both GMYC and bPTP” to avoid any confusion. We also provide all 5 phylogenetic trees as Files S1-5 (one tree for each Class). In general manuscript is well written, however, level of novelty of this research is limited. Thank you. “Level of novelty” is of course a relative appreciation. We agree that we do not provide a lot of firm conclusions, but we present data and analyses that will undoubtedly be useful for the taxonomy and systematics of echinoderms, and for future biodiversity inventories. ________________________________________ 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. 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 ________________________________________ 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. *All three figures passed the PACE quality control. Attachments Attachment Submitted filename: Rebuttal letter.docx* https://doi.org/10.1371/journal.pone.0270321.r002
14 Sep 2022 Decision Letter - Tzen-Yuh Chiang, Editor PONE-D-22-16400R1DNA barcoding echinoderms from the East Coast of South Africa. The challenge to maintain DNA data connected with taxonomyPLOS ONE Dear Dr. Sonet, 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 Oct 29 2022 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: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols. We look forward to receiving your revised manuscript. Kind regards, Tzen-Yuh Chiang Academic Editor PLOS ONE Journal Requirements: 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. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #2: All comments have been addressed ******** 2. 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 #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #2: Yes ****** 4. 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 #2: Yes ****** 5. 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 #2: Yes ****** 6. 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 #2: The authors appear to have addressed all of the matters raised by previous reviews. They have done a good job of analysing and presenting a complex mix of existing and new DNA barcode data in a poorly studied group. It is often very difficult to combine new barcode data with existing data which not infrequently contains sequences attributed to incorrect species. The authors point out the limitations in their dataset and highlight areas that need further clarification in future. I make only minor comments on the methods which the authors should address in the final version of the manuscript, nevertheless I reccomend the manuscript be accepted for publication: Lines 161-163: NJ trees were based on p-distances. Building trees based on uncorrected distances has not been acceptable practice since model-based distance corrections became commonplace in the 1980s. While Bayesian or ML trees would be vastly preferable, NJ trees are acceptable for barcode analyses if based on corrected distances. MEGA has many options for distance correction. BOLD uses K2P-distances by default so that would be a good choice. Regardless, if the NJ trees are never shown then what is their purpose? I suggest deleting all reference to NJ trees and using the Bayesian trees. Lines 163-164: On what date was the search function used on BOLD to retrieve sequences? This information is vital for reproducibility of methods. Lines 181-183: Although BOLD produces BINs based on the RESL algorithm, it is not correct to equate BINs to the results of RESL analysis because BOLD uses additional criteria to assign sequences to BINs, including data quality standards (sequence length, etc.). It is common to have only a subset of sequences in a dataset assigned to BINs. However, it is possible to perform RESL analysis on BOLD for all sequences in your dataset, regardless of whether BOLD assigns them to a BIN. Besides which, BINs are not assigned immediately but only periodically as BOLD analyses new sequences for BIN assignment. So, did the authors perform RESL analyses or not? Were all their sequences assigned to BINs? The authors need to clarify exactly what they did. ****** 7. 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 #2: Yes: Andrew Mitchell ******** [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. https://doi.org/10.1371/journal.pone.0270321.r003
Revision 2
19 Sep 2022 Author Response Rebuttal letter Nota bene: Responses to the reviewer are in bold and follow the signs “>>>”. Actions taken in the manuscript follow the signs “->”. Reviewers' comments: Reviewer's Responses to Questions Comments to the Author Reviewer #2: All comments have been addressed ________________________________________ 2. Is the manuscript technically sound, and do the data support the conclusions? Reviewer #2: Yes ________________________________________ 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #2: Yes ________________________________________ 4. Have the authors made all data underlying the findings in their manuscript fully available? Reviewer #2: Yes ________________________________________ 5. Is the manuscript presented in an intelligible fashion and written in standard English? Reviewer #2: Yes ________________________________________ 6. Review Comments to the Author Reviewer #2: The authors appear to have addressed all of the matters raised by previous reviews. They have done a good job of analysing and presenting a complex mix of existing and new DNA barcode data in a poorly studied group. It is often very difficult to combine new barcode data with existing data which not infrequently contains sequences attributed to incorrect species. >>> Thank you. Yes, we agree that it represented a major part of the effort involved in this manuscript The authors point out the limitations in their dataset and highlight areas that need further clarification in future. >>> Yes, this is important of course I make only minor comments on the methods which the authors should address in the final version of the manuscript, nevertheless I reccomend the manuscript be accepted for publication: Lines 161-163: NJ trees were based on p-distances. Building trees based on uncorrected distances has not been acceptable practice since model-based distance corrections became commonplace in the 1980s. While Bayesian or ML trees would be vastly preferable, NJ trees are acceptable for barcode analyses if based on corrected distances. MEGA has many options for distance correction. BOLD uses K2P-distances by default so that would be a good choice. Regardless, if the NJ trees are never shown then what is their purpose? I suggest deleting all reference to NJ trees and using the Bayesian trees. >>> We totally agree that uncorrected distances are not recommended for phylogenetic tree reconstructions. That is why we used Bayesian inference to reconstruct the ultrametric phylogenetic trees that were used for tree-based species delimitations. Here we simply used uncorrected distances to illustrate the proportion of substitutions observed among some putative species in Fig. 3. In our opinion, these trees are good for illustration (because they are without any a priori model-based distances) if they are introduced correctly to avoid risks of misinterpretation. We understand that this is debatable and apply the changes suggested by the reviewer. --> We remove the reference to the NJ tree and Fig. 3. which are only there to illustrate a content, which is already fully described in the main text and in the tables. Lines 163-164: On what date was the search function used on BOLD to retrieve sequences? This information is vital for reproducibility of methods. >>> We agree that it is of primary importance and the information was already in reference ‘25’ cited on line 163. --> To make it more visible, we repeat it in the main text by adding “(…) on the 24 May 2022”. Lines 181-183: Although BOLD produces BINs based on the RESL algorithm, it is not correct to equate BINs to the results of RESL analysis because BOLD uses additional criteria to assign sequences to BINs, including data quality standards (sequence length, etc.). It is common to have only a subset of sequences in a dataset assigned to BINs. However, it is possible to perform RESL analysis on BOLD for all sequences in your dataset, regardless of whether BOLD assigns them to a BIN. Besides which, BINs are not assigned immediately but only periodically as BOLD analyses new sequences for BIN assignment. So, did the authors perform RESL analyses or not? Were all their sequences assigned to BINs? The authors need to clarify exactly what they did. >>> We thank the reviewer for these precisions. We did not perform RESL analyses ourselves. We indeed used the BIN IDs when they became available on BOLD. For a few sequences without a BIN, we followed the advice of the support team of BOLD (email of 12 June 2020) who advised to use the “Cluster Sequences tool” in the workbench to group COI sequences into OTUs. If the other sequences in the OTU have a BIN, it is likely that those without a BIN belong to that same one, but may not be included in it for some quality check reasons, otherwise they would have been assigned to that BIN. --> In the text, we replaced “RESL” by “BIN”. The way we obtained the BINs was already clarified in lines 182-187 (but the “RESL” abbreviation was inded wrongly used). It reads now: “The BINs were obtained on BOLD. (…). When the sequence overlap with the BOLD sequences was lower than 300 bp and a BIN was not attributed directly by BOLD, the BIN of the best match above 99% similarity was assigned to the record.” Attachments Attachment Submitted filename: Rebuttal letter rev2.docx https://doi.org/10.1371/journal.pone.0270321.r004
23 Sep 2022 Decision Letter - Tzen-Yuh Chiang, Editor DNA barcoding echinoderms from the East Coast of South Africa. The challenge to maintain DNA data connected with taxonomy PONE-D-22-16400R2 Dear Dr. Sonet, 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, Tzen-Yuh Chiang Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0270321.r005
Formally Accepted
30 Sep 2022 Acceptance Letter - Tzen-Yuh Chiang, Editor PONE-D-22-16400R2 DNA barcoding echinoderms from the East Coast of South Africa. The challenge to maintain DNA data connected with taxonomy Dear Dr. Sonet: 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 plosone@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. Tzen-Yuh Chiang Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0270321.r006

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