Scientific progress made towards bridging the knowledge gap in the biology of Mediterranean marine fishes

Eva Daskalaki; Evangelos Koufalis; Donna Dimarchopoulou; Athanassios C. Tsikliras

doi:10.1371/journal.pone.0277383

Peer Review History

Original SubmissionAugust 3, 2022
12 Sep 2022 Decision Letter - Roberta Cimmaruta, Editor PONE-D-22-21777Scientific progress made towards bridging the knowledge gap in the biology of Mediterranean marine fishesPLOS ONE Dear Dr. Daskalaki, 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. In particular follow the requests of ref. n.2 about data valilability as an Appendix and about the details on methodology. Please submit your revised manuscript by Oct 27 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, Roberta Cimmaruta, PhD 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 https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. We note that the grant information you provided in the ‘Funding Information’ and ‘Financial Disclosure’ sections do not match. When you resubmit, please ensure that you provide the correct grant numbers for the awards you received for your study in the ‘Funding Information’ section. 3. Thank you for stating the following financial disclosure: "This research was partly funded by the European Union’s Horizon 2020 Research and Innovation Program (H2020-BG-10-2020-2), grant number No. 101000302 - EcoScope (Ecocentric management for sustainable fisheries and healthy marine ecosystems)." 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. 4. Thank you for stating the following in the Acknowledgments Section of your manuscript: "This research was partly funded by the European Union’s Horizon 2020 Research and Innovation Program (H2020-BG-10-2020-2), grant number No. 101000302 - EcoScope (Ecocentric management for sustainable fisheries and healthy marine ecosystems)." We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. 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 research was partly funded by the European Union’s Horizon 2020 Research and Innovation Program (H2020-BG-10-2020-2), grant number No. 101000302 - EcoScope (Ecocentric management for sustainable fisheries and healthy marine ecosystems)." Please include your amended statements within your cover letter; we will change the online submission form on your behalf. 5. 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. 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 Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: N/A ****** 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 Reviewer #2: 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 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: In the paper Scientific progress made towards bridging the knowledge gap in the biology of Mediterranean marine fishes, Daskalaki and colleagues provided an update of a previous analysis conducted in 2017, aimed to uncover gaps in the current knowledge on the biology of Mediterranean marine fishes. The authors used mainly data from FishBase and scientific literature, showing how the current knowledge in the last 5 years only shrunk by 6%. However, some interesting results emerge from a situation still far from being optimal. For instance, they found how 40 new species have at least one study on their biology and that scientific research has slightly shifted towards traditionally neglected species, as for instance sharks, rays and chimaeras. Overall, their findings suggest an increasing awareness in the study of fish biology in the Mediterranean Sea not exclusively devoted to commercial fishes. I did not find major concerns in this paper, as it is well written, concise and goes straight to the focus of their main questions. However, I am wonder if the Authors are aware of the paper of Albouy and collegues, FishMed: traits, phylogeny, current and projected species distribution of Mediterranean fishes, and environmental data, Ecology 96(8) 2312, were the authors provided an updated overview (and datasets) of traits, phylogeny and current and projected spatial distribution of 635 Mediterranean fish species, “compiled from a published expert knowledge atlas of fishes of the northern Atlantic and the Mediterranean (FNAM) edited between 1984 and 1986 and from an updated exotic fish species list”. I understand that the final aim of this paper is to update the actual knowledge following the same procedure used in a recently published paper from the authors. At the same time, I am aware how FishBase still represents one (if not the most) complete and up-to-date global biodiversity information system on finfishes. Anyway, it would be interesting to understand if and how the data provided in this dataset (including the literature sources) are able or not to add information on the gap analysis of Mediterranean fish biology. When working with non-proprietary data, as for instance in meta-analysis, one should be aware of the multiple and often different sources of information that, sometimes, help filling the gap of knowledge. For instance, Courtney et al. (2011) Errors in Length-weight Parameters at FishBase.org. Nature Precedings (2011). https://doi.org/10.1038/npre.2011.5927.1, cast doubts on how specific parameters (as for instance one used in the current ms, that is, length-weight) are not generally reliable. Of course, the above-mentioned paper mainly used non-marine fish species, but the results obtained still cast serious doubts on the reliability of some parameters for other species. Such reflection applies, obviously, for those parameters shared in both databases. Besides my comments above, which I hope can stimulate a deep discussion about the use of different (and often fragmented) information available on different databases that might influence the knowledge gap in the biology of Mediterranean marine fishes I did not find major issues on the ms. Reviewer #2: This study is an updated version of a previous study (Dimarchopoulou et al. 2017) aiming to quantify knowledge gaps about the traits of Mediterranean fishes. This study is quite similar to the original one but given the time passes since the original publication is still useful information that needs to be put out there. The manuscript is generally well written and I have few comments. The two major ones are: 1. To make this a truly useful paper, it is important to actually add the data on the traits collected as a (appendix) table. This will be a tremendously useful resource for marine scientists in the region and I feel is well worth the effort. 2. Methodologically, more information is needed on how the trait were searched in Scopus (for those that were not found in FishBase). What were the search words exactly? How many results were retrieved and screened? How much data was added on top of that presented in FishBase? If these comments are addressed I feel the manuscript should be accepted to this journal. Other minor comments: In “The lack of data regarding basic biological characteristics of many deep-sea species”…… I would replace “almost impossible” with a more moderate word. Explain what is meant exactly for absolute and relative number of oocytes. Explain what the diet categories were and how gut content analyses was matched to these categories. “However, a recently developed method [56], with which LWR can be estimated even from single fish records, based on a Bayesian hierarchical method,” Bayesian mthods are related to statistics. Please explain in a few words what this method is based on in terms of data, not stats. No matter how fancy the stats, you cannot infer LWR from a single point. The grammar is off in the first sentence of the conclusions. Conclusions: “dreaded” conveys too much emotions. I would use a less emotional phrase. I would add another figure showing the cumulative number of traits with records (as Fig. 5 in Dimarchopoulou et al. 2017) to help assess if the rate has changed since the last assessment. ****** 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 Reviewer #2: Yes: Jonathan Belmaker ******** [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.0277383.r001
Revision 1
14 Oct 2022 Author Response Response letter of Daskalaki et al. (PONE-D-22-21777) The authors would like to thank the two reviewers for their comments and suggestions that really improved this manuscript. Reviewer #1 In the paper Scientific progress made towards bridging the knowledge gap in the biology of Mediterranean marine fishes, Daskalaki and colleagues provided an update of a previous analysis conducted in 2017, aimed to uncover gaps in the current knowledge on the biology of Mediterranean marine fishes. The authors used mainly data from FishBase and scientific literature, showing how the current knowledge in the last 5 years only shrunk by 6%. However, some interesting results emerge from a situation still far from being optimal. For instance, they found how 40 new species have at least one study on their biology and that scientific research has slightly shifted towards traditionally neglected species, as for instance sharks, rays and chimaeras. Overall, their findings suggest an increasing awareness in the study of fish biology in the Mediterranean Sea not exclusively devoted to commercial fishes. I did not find major concerns in this paper, as it is well written, concise and goes straight to the focus of their main questions. Comment 1 However, I am wonder if the Authors are aware of the paper of Albouy and collegues, FishMed: traits, phylogeny, current and projected species distribution of Mediterranean fishes, and environmental data, Ecology 96(8) 2312, were the authors provided an updated overview (and datasets) of traits, phylogeny and current and projected spatial distribution of 635 Mediterranean fish species, “compiled from a published expert knowledge atlas of fishes of the northern Atlantic and the Mediterranean (FNAM) edited between 1984 and 1986 and from an updated exotic fish species list”. I understand that the final aim of this paper is to update the actual knowledge following the same procedure used in a recently published paper from the authors. At the same time, I am aware how FishBase still represents one (if not the most) complete and up-to-date global biodiversity information system on finfishes. Anyway, it would be interesting to understand if and how the data provided in this dataset (including the literature sources) are able or not to add information on the gap analysis of Mediterranean fish biology. Reply Indeed, this is a very good point. We are familiar with the FishMed database, which we believe is a valuable source of information on Mediterranean fishes and an important tool for researchers. However, as the reviewer acknowledges, the scope of the present work was to include only published scientific output and update a previous review using the same methodology. Thus, we have not used raw biological data available in stock assessments (such as GFCM and STECF) and databases (e.g., FishMed, Med&BS RDBFIS, Ormef). We have now included a reference to FishMed to improve data availability to the readers and to provide a better description of the most complete datasets that may be used to examine hypotheses by scientists and complement their publications. Comment 2 When working with non-proprietary data, as for instance in meta-analysis, one should be aware of the multiple and often different sources of information that, sometimes, help filling the gap of knowledge. For instance, Courtney et al. (2011) Errors in Length-weight Parameters at FishBase.org. Nature Precedings (2011). https://doi.org/10.1038/npre.2011.5927.1, cast doubts on how specific parameters (as for instance one used in the current ms, that is, length-weight) are not generally reliable. Of course, the above-mentioned paper mainly used non-marine fish species, but the results obtained still cast serious doubts on the reliability of some parameters for other species. Such reflection applies, obviously, for those parameters shared in both databases. Reply Agreed and thanks for pointing this out. Indeed, some of the parameters that are routinely determined in scientific papers are based on non-realistic assumptions and result in errors. FishBase performs a quality check on most of the parameters listed in the database based on sample size, range of lengths/weights included in the sample, statistical tests and/or common practices in fisheries biology. When a parameter or a method violates any of the standards or deviates a lot from what it is expected then it is marked as questionable in the corresponding “Tables” of FishBase. For example, when growth parameters are to be included, they are considered questionable if t0 is lower than -1.5 y or if Linf deviates a lot from Lmax. We had already excluded questionable records from the first version of our analysis and we have now stated so in material and methods by adding the text: “…leaving out all growth records of “questionable” status in FishBase [42].”. Reviewer #2 This study is an updated version of a previous study (Dimarchopoulou et al. 2017) aiming to quantify knowledge gaps about the traits of Mediterranean fishes. This study is quite similar to the original one but given the time passes since the original publication is still useful information that needs to be put out there. The manuscript is generally well written and I have few comments. The two major ones are: Major Comment 1 To make this a truly useful paper, it is important to actually add the data on the traits collected as a (appendix) table. This will be a tremendously useful resource for marine scientists in the region and I feel is well worth the effort. Reply Agreed. A new Appendix was added (Appendix S1), containing the number of records per characteristic per species gathered from literature published between 2015-2021 as well as the total number of records per characteristic per species up to 2021. Major Comment 2 Methodologically, more information is needed on how the trait were searched in Scopus (for those that were not found in FishBase). What were the search words exactly? How many results were retrieved and screened? How much data was added on top of that presented in FishBase? Reply Agreed. More information was added in Methods that now describes in detail the search process in SCOPUS. In addition, we added another appendix (Appendix S2) containing the papers extracted from FishBase and SCOPUS, that have been screened for this study. Minor comment 1 In “The lack of data regarding basic biological characteristics of many deep-sea species”…… I would replace “almost impossible” with a more moderate word. Reply Agreed and rephrased. Minor comment 2 Explain what is meant exactly for absolute and relative number of oocytes. Reply Agreed. The definitions on absolute and relative fecundity were added with references. Minor comment 3 Explain what the diet categories were and how gut content analyses was matched to these categories. Reply Within the scope of this gap analysis we recorded the number of papers per biological characteristic per species -as it is shown in the newly added Appendix S1-. So, we did not divide diet preferences and gut content into categories. In order to clarify this we have added the following text in the manuscript: “Specifically, we recorded the existence (or not) of papers containing information on eight biological characteristics for every species in the list.”. Minor comment 4 “However, a recently developed method [56], with which LWR can be estimated even from single fish records, based on a Bayesian hierarchical method,” Bayesian methods are related to statistics. Please explain in a few words what this method is based on in terms of data, not stats. No matter how fancy the stats, you cannot infer LWR from a single point. Reply Agreed and elaborated as proposed. Minor comment 5 The grammar is off in the first sentence of the conclusions. Reply Agreed and corrected. Minor comment 6 Conclusions: “dreaded” conveys too much emotions. I would use a less emotional phrase. Reply Agreed and rephrased. Minor comment 7 I would add another figure showing the cumulative number of traits with records (as Fig. 5 in Dimarchopoulou et al. 2017) to help assess if the rate has changed since the last assessment. Reply Although it is a good addition to the study and valuable as information, unfortunately it cannot be done because Figure 5 in Dimarchopoulou et al. (2017) was a count of articles on specific characteristics of species, as they appeared in SCOPUS (i.e., articles on spawning of Mediterranean fishes per year) and does not include any information on which (new) species records had been published each year. Additional note Two references were added in the reference list [43, 80] in line with the reviewers’ comments. The Qadri et al. (2015) paper was added as reference to the definitions on absolute and relative fecundity. The Albouy et al. (2015) paper was added after the first comment of reviewer #1. Attachments Attachment Submitted filename: Response to Reviewers_Daskalaki et al.docx https://doi.org/10.1371/journal.pone.0277383.r002
26 Oct 2022 Decision Letter - Roberta Cimmaruta, Editor Scientific progress made towards bridging the knowledge gap in the biology of Mediterranean marine fishes PONE-D-22-21777R1 Dear Dr. Daskalaki, 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, Roberta Cimmaruta, PhD Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0277383.r003

Open letter on the publication of peer review reports

PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.

We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.

Learn more at ASAPbio .