Peer Review History
| Original SubmissionJuly 19, 2023 |
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PONE-D-23-22016The influence of freshwater inflow and seascape context on occurrence of juvenile Spotted seatrout Cynoscion nebulosus across a temperate estuaryPLOS ONE Dear Dr. Whaley, 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 Sep 30 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. Please include the following items when submitting your revised manuscript:
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Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. 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 If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references.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 If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. Additional Editor Comments: We received comments from three reviewers, who are experts on the subjects (species, ecology, and/or methodology). All of the comments are very positive. It is consistent with my assessment as well. I agree with Reviewer 1 that some clarifications are needed. From my experience, when clarifications are needed, we might discover some problems after revisions. For now, I expect minor revisions for clarifications are sufficient. However, I will read a revised version carefully and if necessary, I will send it for reviews again. [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: Partly Reviewer #2: Yes Reviewer #3: Yes ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: 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: Yes Reviewer #2: Yes Reviewer #3: 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 Reviewer #3: 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 manuscript describes the effects of freshwater inflow on the habitat use patterns of juvenile spotted seatrout across four distinct life stages. The authors found that habitat use patterns were influenced by freshwater inflow (primarily during the 3-months prior to recruitment) for the smallest size classes, but less so for the larger juveniles. I found the methods to be sound, but encountered some confusion about how the freshwater inflow variables were determined and incorporated into the models. The time lag component was a bit unclear, and didn’t come across well in the figures. The authors also make some statements and conclusions regarding the effect of freshwater inflow on presence probability, but from what I understand the results only show the effect of freshwater inflow on spatial distribution of seatrout and their use of biogenic habitats. This wording needs to be clarified throughout the manuscript and possibly visually clarified via figures. The figures could benefit from some reworking, since I found that they didn’t clearly visualize some of the patterns the authors discuss (especially habitat richness). I also wonder if more detailed figures would help alleviate confusion regarding the freshwater inflow variables. I am supportive of this manuscript for publishing following revisions. Specific comments below: Abstract: - Line 23: suggest “recreational sportfish” - Line 26: “We used” - Lines 34-35: I'm not sure how we can determine a positive relationship between presence and inflow based on the figures provided. From what I can gather based on the figures, the models assess the effect of inflow on habitat use patterns, not the effect of inflow on presence probability. Reconsider this wording. - Line 43: suggest changing “larger sized fishes” to “larger juveniles” Introduction: - Lines 57-63: Could be informative to add some text here linking freshwater inflow patterns with these habitats. Habitat-forming plants and animals also respond to changes in freshwater inflow, meaning the two concepts (freshwater flow/salinity and availability of structured habitat) are inherently linked. Furthermore, the results suggest use of different habitats depends on inflow conditions, so the two ideas should be more cohesive instead of separate (as written). - Lines 63-65: With the addition of text above, this could become a new paragraph about habitat richness. - Line 79: “popular recreational fishery species” - Line 80: “live out life” is odd wording, suggest something like “spend their lifespan” or “are resident within” - Line 85: I suggest staying consistent as possible with “juvenile spotted seatrout” throughout the manuscript. (Here it says juveniles of seatrout, but later says juvenile spotted seatrout). - Line 120-121: Maybe give context here for peak recruitment – which months/time of year? Methods: - Lines 177-184: Has there been any change in saltmarsh/seagrass/oyster coverage across the study period (2001-2018), and do you think the coverage you have is reasonably close to the coverage across that timescale? I would suggest adding a justification for the mismatch between habitat and fish data. I appreciate the challenges with getting high res habitat data, so I assume you did the best you could, but a quick discussion of potential caveats would be good to include. - Line 187: Add a little more detail about QA/QC – not sure what standard means - Lines 194-198: Could do this same calculation for distance from the major freshwater inflow source. Looking at Fig 1 there are collection points way out East in the bay that are far from the river, and others that are immediately adjacent to the river. I would expect that those locations would not experience the same magnitude of influence of inflow, right? Giving all locations the same inflow value seems like you might be missing some important spatial patterns of inflow effect. - Lines 206-208: This sentence is confusing - please clarify wording and provide a more specific citation - Lines 209-211: Would be helpful to add a marker for the stream gauge location on Fig 2 to give spatial context - Lines 211-212: This is essentially a time lag, right? This determines whether recent or past conditions affect the fish more or less? Please clarify the wording of this. - Lines 213-215: How is this incorporated into the analyses? I'm having a hard time understanding what the freshwater inflow predictor variables actually look like. I would think that for each seine data point, there would be a classification of wet, dry, or normal during the month prior, and 3, 6, and 12 months prior - is that correct? I think there needs to be a clearer explanation of how these variables truly operate within the models. - Lines 272-273: This wording is confusing - the sentences above make it sound like AUC and Brier scores were calculated for each model (without testing vs. training datasets). Consider changing the order of how this process is presented, starting with the splitting of data into testing and training, followed by AUC and Brier score calculations, and ending with how you summarized the performance results. - Lines 282-283: Does this refer to calculated predictions of encounter probabilities across the range of values for each predictor variable? The wording in this section is hard to follow - Lines 285-287: Don't the models already include values for the habitat variables around each sample location? Wouldn't the range of those values be used for prediction? This makes it sound like it’s predicting spatially, but I'm not sure why that would be necessary here (since it occurs in the prediction maps section) - Lines 287-290: I assume this is what we're seeing in Figs 3 and 6, but it isn't super clear. Predicted encounter probabilities were calculated across the possible range of each predictor variable for each inflow condition, correct? - Line 293: How does the above paragraph describing model prediction link to these maps. I see here that you've exported a spatial map of predictions, but then it's later stated (last sentence of this paragraph) that you only used the top model for this. Aren't the predictions coming from the weighted/averaged models above? Please clarify this section and the previous paragraph to clearly state what models and predictions relate to each figure (effects vs. maps) Results: - Line 329: This isn't something I can easily distinguish from the figures - There's no figure that shows the relationship between habitat richness and spotted seatrout presence - Line 330: Same here, no visualization of the oyster reef trend - Lines 330-332: I suggest adding figure labels (including panel labels) here to distinguish exactly what fig the reader should look at to see these patterns - Line 334: What does prolonged mean in this context? This word is used throughout the results but in relation to all time lags (1,3,6,12 months), which doesn't make sense to me. Define what "prolonged" means in the context of the freshwater flow variables Discussion - Lines 414-416: Add a figure(s) for this! It's an interesting result but I don't see it visually - Line 433: “estuarine biogenic habitats” - Lines 445-447: Consider looking into literature on edge effects and how fragmentation in seagrass beds influences predator-prey dynamics. - Line 455: Again, since this is a major point of discussion there should be a clear visualization of these trends. - Lines 529-531: From what I understand based on figure 3, juvenile spotted seatrout were found more frequently in areas with a high proportion of saltmarsh during dry conditions. Isn't this the opposite of what's being stated here? - Line 536: Are you only referring to biogenic habitat use here? What about distance from the inlet (fig 3 C,F)? - Lines 540-541: I'm not seeing this result in figure 3. I see high probability of presence in seagrass habitat during wet AND dry conditions for the smallest size class (panel A), and lower presence in seagrass during dry conditions for the next size class (panel D). - Lines 547-550: Develop this idea a bit more - they seemed to move down-estuary (closer to inlet) under wet conditions, and there appears to be less saltmarsh present near the inlets. Make that link to the spatial arrangement of habitat. Also, why would they move down-estuary under high inflow? Is it physiological (salinity stress)? Physical transport? Figures: - Fig 1 could add stream gauge location - I like the predictive maps! - Figures 3 and 4 are well done, but I think we’re missing some important results like the habitat richness. Consider adding to these figures or creating additional figures to clearly show the habitat richness effects. - In figures 3 and 4, what freshwater inflow variable are we looking at? 1,3,6,12 month? The methods section is not super clear in describing how the figures were created (see comments in that section) Reviewer #2: This paper presents a detailed analysis of a long-term dataset to describe drivers of variation in juvenile seatrout distribution in Apalachicola Bay, Florida. The paper is well written, clear, and concise. Although focused on one species in one large estuary, I think the paper is of wide interest to coastal ecologists, and provides a framework for this type of long-term data analysis. I think it is a solid paper and I have just a few comments for the authors to consider. General comments No mention of direct effects of salinity on juvenile trout distribution. At some level of FW inflow, salinities may become too low for small juveniles. I think this should be at least mentioned. E.g. the results at L333-336 suggest during high flows, small juveniles were not found up the bay far from the inlets, presumably in areas where salinity would be depressed. Perhaps this simply reflects salinity being too low for them at those times? Similarly the results at L337-339. Context used here is not quite the same as defined by Bradley et al. 2020. Here the authors refer to “seascape context” when discussing the number and extent of other habitats in the surrounding seascape. This is a component of context described by Bradley et al. but context also includes other factors such as tide range, climate, general rainfall regime, geomorphology. Of course, in the current study, many of these other factors are constant, since the whole study is in one large estuary. In the current study, all factors considered in aim 2 (L 125-127) would be part of the “context” of each sampling location. It’s a pretty minor point. Minor comments: L56: should “represent” be “support”? L181: how stable are the seagrass beds in the bay? How much might they have changed since 2010, or over the sampling period? I think 2010 is a good time point to use, since it is in the middle of the time period of nekton sampling, but some mention of the stability of seagrass in the bay would be helpful. L197: can you describe what least-cost distance is? Is it the shortest distance via water from a point to the nearest inlet? The modeling approach is quite complex, but the authors have done a good job describing it, and it seems appropriate for the data. Reviewer #3: This paper analyzes the relationship between estuarine habitat, freshwater inflow, and juvenile spotted seatrout occurrence in Apalachicola Bay, FL. The study uses a seascape approach to quantify habitat surrounding sampling sties from a long term fisheries independent monitoring program and river flow at various time lags in a GLM framework. The main findings were that occurrence of small juveniles is positively correlated with seagrass area and river flow 3 months prior; and occurrence of large juvenile is related to availability of nearby habitats. The paper is well written, and the methods are clear and technically sound. I recommend it for publication after addressing my concerns and comments below. Introduction Line 80 Provide reference for recreational importance statement, and some values for amount of effort or landings from recreational fishing survey (MRIP) Line 112 A recent study by Nehemiah et al (2022, 10.1002/mcf2.10201) found that temperature and adult abundance during the spawning season were the best predictors of year class strength, but they did not find a relationship with river flow. The contrasting results of various studies highlights the challenges with understanding this relationship. Methods Line 170 When is the spawning season? That should be stated somewhere, for context. Line 174 Provide some information on samples sizes from this dataset. Line 183 Habitat has changed drastically over this time period. Oysters in particular have declined rapidly over the last few years. It’s unlikely the habitat maps would ground truth very well with the FIM samples at fine spatial scales. Did the authors attempt to compare the reported habitat types at each FIM sample location with the maps? This is probably the biggest issue with the analysis, yet the assumption made here of static habitat layers is not addressed, in discussion and/or sensitivity analyses. Line 214 Is the proportion of months in each flow stage treated as a continuous variable in the models? It seems to be an odd way to characterize flow, and the variable can take a limited number of values based on number of months. Line 230 How did you decide which of the correlated variables to omit? Line 233 So if it’s binary wet or dry, how are normal conditions represented, a zero for both? Results Line 330 What is meant by prolonged? Line 332 Is it possible that seatrout are moving to optimal salinity conditions. Can you distinguish between preference for marsh habitat or preference for certain salinity ranges during dry years? Discussion Line 410 I don’t think the first two paragraphs are necessary, as they seem to reiterate the results. Line 443 Perhaps this paper is relevant here: Barry SC, Hyman AC, Jacoby CA, Reynolds LK, Kowalewski M, Frazer TK. Variation in seagrass-associated macroinvertebrate communities along the Gulf Coast of Peninsular Florida: an exploration of patterns and ecological consequences. Frontiers in Marine Science. 2021 Mar 4;8:596966. Line 447 The word vulnerable is not the best choice. Maybe ‘responsive’ is better. Line 493 See Sinnickson et al. (https://doi.org/10.1007/s10021-023-00845-1) for some thoughts on time lags between flow and biomass at different trophic levels. Line 522 Sinnickson et al (2023) showed a slightly longer lag from phytoplankton to benthic inverts than phyto to zoo under simulated top-down forcing. Line 529 This statement seems contradictive to the finding that seatrout occurrence is higher in marsh habitat during dry conditions. Table 1 How are normal flows represented in the models? That wasn’t clear in the methods. Is it implicit, as 1-(Wet+Dry)? Fig 4 Missing letter A in caption. ********** 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: Mariah Livernois Reviewer #2: No Reviewer #3: 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. |
| Revision 1 |
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The influence of freshwater inflow and seascape context on occurrence of juvenile Spotted seatrout Cynoscion nebulosus across a temperate estuary PONE-D-23-22016R1 Dear Dr. Whaley, 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, Masami Fujiwara, PhD Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: |
| Formally Accepted |
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PONE-D-23-22016R1 The influence of freshwater inflow and seascape context on occurrence of juvenile Spotted seatrout Cynoscion nebulosus across a temperate estuary Dear Dr. Whaley: 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. Masami Fujiwara Academic Editor PLOS ONE |
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