The importance of making testable predictions: A cautionary tale

Emma S. Choi; Erik Saberski; Tom Lorimer; Cameron Smith; Unduwap Kandage-don; Ronald S. Burton; George Sugihara

doi:10.1371/journal.pone.0236541

Peer Review History

Original SubmissionJuly 8, 2020
6 Aug 2020 Decision Letter - Andrea Belgrano, Editor PONE-D-20-21189 Temperature triggers provide quantitative predictions of multi-species fish spawning peaks PLOS ONE Dear Dr. Sugihara, 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 your revision please address all the comments and suggestions made by reviewer #1. In particular also make sure that the data are freely available and that the link provided to access the data works, thank you. Please submit your revised manuscript by Sep 20 2020 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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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 [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 ******** 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: 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: This is an interesting analysis. It was a pleasure to read it. I favor publication. I am left with few questions, and a suggestion, which I hope the authors can address in a review. 1. What is the species composition of the egg catch? I am unsure with the statement that eggs are buoyant. Many are not, and it depends on the species. 2. Somewhat related to my previous question, Fig S2 is interesting and it shows decline of egg diversity in relation to peak eggs abundance. This is presumably driven by an increase of dominance of few or a single species. Can you elaborate on the species that dominate the samples, especially when egg abundance increases? At the end of the methods the authors indicate that the morphologically distinct anchovy and sardine eggs were removed, and the rest of the eggs were counted and identified to species using DNA barcoding. Would be great to see the species list. 5. This is a comment/suggestion. I suggest redirecting the focus of the research question toward a more mechanistic relationship between temperature and egg abundance. The author ask whether 'finer-timescale temperature dynamics provide information about finer-timescale fish egg abundance dynamics.' However, the striking relationships that they have uncovered between STT and peak egg abundance, in my view, is still an integrated measure rather than an examination of a finer scale relationship between temperature and eggs. There is still value in this relationship of course, but not of the same type suggested by the author. This analyses reveals potential mechanisms, pointing to the fact that large variations of water temperature during spring, may trigger massive spawning events during summer. ****** 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: Yes:** Lorenzo Ciannelli [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.0236541.r001
Revision 1
22 Oct 2020 Author Response Response to Reveiwer 1 Reviewer’s comment: What is the species composition of the egg catch? I am unsure with the statement that eggs are buoyant. Many are not, and it depends on the species. The Reviewer raises an important point, and we’re sure many people will be interested in the composition of the samples. To address this, we have included two new supplemental tables. The first of these two tables, Table S2: Scripps Pier Species Abundance 2013–2019, lists all 46 of the species identified from the sampling at Scripps Pier from 2013 to 2019 and the number of eggs identified as each of these species within each year. The second of these two tables, Table S3: Scripps Pier Species Frequency 2013–2019, lists all 46 of the species and the proportion of samples (out of the yearly sampling effort) in which eggs from the species were observed within each year. With regard to buoyancy, we have added a statement to the manuscript that our methods only effectively sample eggs suspended in the water column; we found very few eggs from species with demersal eggs – those were presumably stirred off the bottom by the net. Reviewer’s comment: Somewhat related to my previous question, Fig S2 is interesting and it shows decline of egg diversity in relation to peak eggs abundance. This is presumably driven by an increase of dominance of few or a single species. Can you elaborate on the species that dominate the samples, especially when egg abundance increases? At the end of the methods the authors indicate that the morphologically distinct anchovy and sardine eggs were removed, and the rest of the eggs were counted and identified to species using DNA barcoding. Would be great to see the species list. We thank the Reviewer for highlighting this opportunity for clarification. We have now included a new supplemental table, Table S1: Species composition of the peak summer egg abundance samples, that lists the proportion of the annual summer peak eggs that were identified as each species. This table highlights which species dominate the peak summer egg abundance samples. We have slightly expanded the main text in the discussion of synchrony to accommodate the addition of this table. Reviewer’s comment: This is a comment/suggestion. I suggest redirecting the focus of the research question toward a more mechanistic relationship between temperature and egg abundance. The author ask whether 'finer-timescale temperature dynamics provide information about finer-timescale fish egg abundance dynamics.' However, the striking relationships that they have uncovered between STT and peak egg abundance, in my view, is still an integrated measure rather than an examination of a finer scale relationship between temperature and eggs. There is still value in this relationship of course, but not of the same type suggested by the author. This analyses reveals potential mechanisms, pointing to the fact that large variations of water temperature during spring, may trigger massive spawning events during summer. While we greatly appreciate this suggestion, and would like to be able to pursue it, it is not currently possible to redirect our research question to address the finely resolved details of the mechanistic relationship between temperature and egg abundance. This is because we did not specifically measure a variable to demonstrate how temperature is acting to influence fish reproduction. Given that we are measuring a macroscopic output variable, egg abundance, it is difficult to determine whether the STT is having a direct physiological effect on the fish or whether it is related to other more proximate factors that drive increases in egg abundance. These are questions perhaps best answered by experimental manipulation; in the current experimental design of our study we could not discern the finer-scale details of the mechanism at play. The causality detection method (CCM), however, does verify (within these data) that there is a causal link here between temperature and egg abundance insofar as changes in temperature propagate to changes in egg abundance. Moreover, we show that the strength of the relationship identified here is dependent upon fine time scale measurements – both the STT and the peak summer egg abundance are captured through frequent measurements, daily in the case of STT and weekly in the case of peak summer egg abundance. In Figure 3A we showed that in smoothing the daily temperature datum, we lose the signal between the STT and peak summer egg abundance. Therefore, we focused our research question on fine time scale dynamics that are shown to be essential to this analysis, rather than a mechanistic relationship that we are unable to speak to, given the output variable we measured. Attachments Attachment Submitted filename: Response to Reviewers_9.01.2020.pdf https://doi.org/10.1371/journal.pone.0236541.r002
2 Nov 2020 Decision Letter - Andrea Belgrano, Editor The importance of making testable predictions: a cautionary tale PONE-D-20-21189R1 Dear Dr. Sugihara, 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, Andrea Belgrano, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): The revised manuscript addresses All the comments/suggestions made by reviewer #1 including the availability/access to All the data that you have now nicely provided via the GitHub repository. The manuscript makes an interesting and transparent "tale" that I believe will be of great interest to the broad readership of PLOS ONE. https://doi.org/10.1371/journal.pone.0236541.r003
Formally Accepted
26 Nov 2020 Acceptance Letter - Andrea Belgrano, Editor PONE-D-20-21189R1 The importance of making testable predictions: a cautionary tale Dear Dr. Sugihara: 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. Andrea Belgrano Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0236541.r004

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