Teaching fish new tricks: Repeated exposure to a velocity barrier improves passage performance

Rachel MB Crawford; Eleanor M. Gee; Brendan J. Hicks; Katherine A. Corn; Paul A. Franklin

doi:10.1371/journal.pone.0329371

Peer Review History

Original SubmissionNovember 20, 2024
24 Mar 2025 Decision Letter - Mizanur Rahman, Editor Dear Dr. Crawford, 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 May 08 2025 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. 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'. 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Please be assured that, once you have provided your new statement, the assessment of your exemption will not hold up the peer review process. [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? Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: Yes Reviewer #4: Partly ******** 2. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: Yes Reviewer #4: Yes ****** 3. Have the authors made all data underlying the findings in their manuscript fully available??> The PLOS Data policy Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: No Reviewer #4: Yes ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: Yes Reviewer #4: Yes ****** Reviewer #1: Comments on the manuscript Thank you for the opportunity to review this manuscript. The paper is well-written and structured, and it addresses an important topic: how repeated exposure to a high-velocity water barrier affects the ability of juvenile Galaxias maculatus to pass through it. The experiment involved subjecting individual fish to the same high-speed water conditions in a raceway over five consecutive days. They found that the proportion of fish successfully passing the barrier increased significantly from 40% on Day 1 to 63% on Day 5. Time-to-event analysis revealed that fish passed the barrier more quickly by Day 5 than Day 1 but did not significantly improve approach or entry rates into the raceway. The study suggests that cognition and spatial memory play a role in improving passage performance through velocity barriers, but other factors, such as attraction flows, are also important. However, there are a few points that could be strengthened: 1. A total of 40 fish were used in the experiment. Although this sample size may be adequate, a larger sample size could provide more robust results and increase the statistical power of the study. 2. The study focuses on one species (Galaxias maculatus), which may not fully represent cognitive responses in other fish species. 3. While the study discusses cognition and memory, it does not explicitly assess fish personality traits (e.g., boldness or exploratory behavior), which could influence passage success. 4. While water temperature was monitored, other environmental factors, such as dissolved oxygen and pH levels, were not explicitly addressed. Fluctuations in these factors could potentially influence fish behavior and passage performance. 5. The experimental raceway does not fully replicate natural stream conditions, which may affect generalizability. 6. The study does not assess whether repeated exposure induces stress or fatigue, which could influence fish behavior. Therefore, based on the concerns outlined above, I recommend that this manuscript be accepted for publication after major revision. Reviewer #2: The manuscript presents a well-designed and executed study with important implications for understanding fish passage through anthropogenic barriers. However, the ecological realism, exploration of behavioral mechanisms, and statistical reporting could be improved. Addressing these weaknesses would strengthen the manuscript and enhance its contribution to the field of freshwater ecology and conservation. Reviewer #3: 1. The manuscript presents a technically sound scientific investigation, supported by a detailed and rigorous methodology. It includes all the essential elements of a well-structured study, such as the description of the required permits and approvals for fish collection, experimental trials, setup and experimental protocol, as well as statistical analysis. The results are presented clearly and in alignment with the methodology, allowing the reader to assess whether the objectives were achieved. Additionally, the analyses are well-founded, providing a robust interpretation of the data while transparently acknowledging the study’s limitations. In particular, the article highlights the ability of fish to improve their passage success with repeated exposures but also recognizes that it remains uncertain whether this learning is transferable to new obstacles. A valuable aspect of the manuscript is that, in addition to addressing its research question, it provides relevant findings for the management of fish passage structures. It highlights challenges in fish attraction and entry, as well as the potential effect of shyness in some individuals, suggesting that management strategies should focus not only on the physical structure of passageways but also on improving fish attraction. Overall, this study significantly contributes to the understanding of fish passage efficiency and provides valuable information for both science and the management of aquatic ecosystems. Editorial Recommendations Some structural adjustments are necessary in the manuscript: a) In the Modelling Binary Success section, when mentioning p-values, the text should correctly direct the reader to Table 2. b) In line 278, "Table 2" should be changed to "Table 4." c) It is recommended to reorganize the order of the paragraphs to maintain the logical sequence of the results, placing Table 3 before Table 4. 2. I consider that the statistical analysis in the manuscript has been conducted appropriately and rigorously. The authors applied a solid approach using generalized binomial generalized linear mixed models (GLMM) to model binary success in approach, entry, and successful passage, incorporating random effects to capture individual variability in fish. Additionally, they employed Cox regression to assess event rates (approach rate, entry rate, and passage rate), allowing for the interpretation of the effects of repeated exposure over time and generating Hazard Ratios (HR) to measure the instantaneous probability of success at each threshold of the experimental channel. However, I found an inconsistency in the application of the Hosmer-Lemeshow goodness-of-fit test. In the methodology, it is stated that this test was used to evaluate model fit in the GLMM for all three events (approach, entry, and successful passage), but in the results, its use is only reported for the entry model. This raises questions about whether it was also applied to the other two events or if its reporting was omitted. Furthermore, I consider that the Hosmer-Lemeshow test is not the most appropriate for evaluating the fit of GLMM models, as it does not account for the random effects characteristic of these models. I suggest using more suitable methods, such as residual inspection, AIC/BIC comparison, or the simulation of predicted versus observed values. If a new model fit method is adopted, I recommend applying it uniformly across all events and including the corresponding results in the results section to ensure consistency with what is described in the methodology. Despite this observation, I believe that the analyses used in the study are appropriate for addressing the research question and allow for well-supported conclusions. 3. In the manuscript, the authors indicate that the data will be available through the Zenodo digital repository and provide the corresponding doi: 10.5281/zenodo.14194951. However, I was unable to access this DOI or find an active link. I suggest that the authors verify the availability of the link and confirm that the data are correctly deposited in the repository to ensure open access and transparency in the publication. 4. The manuscript is written clearly, without ambiguities, and in a comprehensible level of English. During my review, I did not identify any typographical or grammatical errors that would affect the understanding of the content. However, since English is not my native language, my assessment of full compliance with linguistic standards is limited. Reviewer #4: L105� Were the juveniles caught before they had completed their upstream migration to their habitat? Or was the capture location their habitat? This may be considered one of the reasons why "fish failed to enter the raceway each day." L117� Did they reuse the waterway described in (39), or did they use the features of (39)? I would like you to add a little more explanation about the introduction of the waterway so that it can be understood without reading (39). If PVC is an abbreviation for something, I would like an explanation for that. L130� If the subject of the paper is "velocity barrier," I think there should be some experiments or discussion on "rush speed" as well as "critical swimming speed." L134� It would be good if the design concept of the "40° angle" was described. I would like to see the concept of the water flow not starting from a single point in the center, but evenly flowing from a 0.5m width or from multiple outlets described. L137� It is suggested that the "starting pool" refers to the space between (D) and (E) on the right, but a more specific description would be needed. If there was an elevation drawing, it would be easier to understand the following points: - "with a consistent water depth of 0.2 m maintained throughout all trials." - "Measurements were taken at three heights: 20%, 60%, and 80% of the water column above the raceway floor." - The height at which the starting water flow occurs Does "successful "passage" of the fishway" mean the passage of the entire fish body? L165� Please state in the caption of the image that the water depth is 50 cm or give a specific water depth. L180� I would like to know if "Fish weight and condition factor were not included in any of the statistical models due to high correlation with length (0.85 and 0.76 respectively)." is a general statement or a result calculated this time. L182� Does "in the downstream pool" refer to the "starting pool"? L212� Regarding "the end of the 30 min trial," I was unable to find an explanation for why the maximum trial time was set at 30 minutes. Please describe how the juvenile fish were managed between experiments (23 hours?). L220� It seems to me that this equation only applies to fish where the relationship between body length and weight is constant, such as "young Plecoglossus altivelis" or "young Oncorhynchus masou" but will this be considered? L251� If there were a clear explanation somewhere that larger fish are easier to approach, this statement would be easier to understand, and it could also be used in discussions about small fish. L260� Although Figure 3 appears before Table 2 in the text, why are they listed in the opposite order? L264� Considering the development of the discussion in this study, if the "effect of day" could be rephrased somewhere with the intention of "effect of frequency," mutual understanding would advance. L265� Considering this case in which the fish's body length has a significant effect, it would be helpful to clarify the relationship between the fish's body length and their charging speed. L268� Does "this increase appeared to asymptote and even decrease after Day 4," indicate that while repeated attempts increase the probability of success, repeated attempts also cause some individuals to give up on the upstream migration? L276� I would like to know which values in Table 2 are used and how the calculation results in "HR = 1.0." I did not understand how Figure 4 should be interpreted to support this statement. L279� Although Figure 4 appears before Table 3 in the text, why are they presented in the opposite order? L314� I felt that this was not an argument about attempting to overcome a single barrier multiple times, but rather about the need to overcome multiple barriers to reach a habitat. Because this is an important argument, I feel it would be better to make this point of view the purpose of the paper and make it a bit clearer. ****** 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: Md. Fakhrul Islam Reviewer #2: Yes: Syed Shafat Hussain Reviewer #3: No Reviewer #4: No ******** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/ . PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org . Please note that Supporting Information files do not need this step. Attachments Attachment Submitted filename: Review report.docx Attachment Submitted filename: Reviewer Comments.docx Attachment Submitted filename: renamed_3f713.pdf https://doi.org/10.1371/journal.pone.0329371.r001
Revision 1
4 Jun 2025 Author Response Manuscript ID: PONE-D-24-53465 Dear Editor Dr Mizanur Rahman, Thank you for the opportunity to revise our manuscript “Teaching fish new tricks: Repeated exposure to a velocity barrier improves passage performance ” (Manuscript ID PONE-D-24-53465) for consideration for publication in PLOS ONE. We appreciate the constructive comments provided by the two peer reviewers. We hope that our revision has suitably addressed all identified concerns. Please see below for a point-by-point summary of changes as raised by reviewers (in RED). We have also provided both a tracked change and clean copy of the revised manuscript for your consideration. Any references to line numbers in our response to the reviewers are based on the tracked change version. On behalf of the full authorship, Yours sincerely, Rachel Crawford National Institute of Water and Atmospheric Research, Hamilton, New Zealand rachelmbcrawford@gmail.com Reviewer 1: Thank you for the opportunity to review this manuscript. The paper is well-written and structured, and it addresses an important topic: how repeated exposure to a high-velocity water barrier affects the ability of juvenile Galaxias maculatus to pass through it. The experiment involved subjecting individual fish to the same high-speed water conditions in a raceway over five consecutive days. They found that the proportion of fish successfully passing the barrier increased significantly from 40% on Day 1 to 63% on Day 5. Time-to-event analysis revealed that fish passed the barrier more quickly by Day 5 than Day 1 but did not significantly improve approach or entry rates into the raceway. The study suggests that cognition and spatial memory play a role in improving passage performance through velocity barriers, but other factors, such as attraction flows, are also important. However, there are a few points that could be strengthened: Thank you for your feedback. We have made revisions in response to your comments as described below. 1. A total of 40 fish were used in the experiment. Although this sample size may be adequate, a larger sample size could provide more robust results and increase the statistical power of the study. While a larger sample size would produce more robust results, we were limited logistically, in terms of seasonal availability and amount of time it takes to conduct trials, which limited the number of fish we could use in this study. 2. The study focuses on one species (Galaxias maculatus), which may not fully represent cognitive responses in other fish species. This is correct that Galaxias maculatus may not fully represent cognitive responses in other fishes. We hope to use this as a foundation for future work to look at cognitive abilities across more species in the future. We have also added in some discussion around this limitation (Lines 413-415). 3. While the study discusses cognition and memory, it does not explicitly assess fish personality traits (e.g., boldness or exploratory behavior), which could influence passage success. In hindsight, individual fish personality is something we wish we had assessed. We have included some theories on how fish personality may have influenced passage success in our experimental raceway rather than just cognitive ability alone (Lines 443-453). 4. While water temperature was monitored, other environmental factors, such as dissolved oxygen and pH levels, were not explicitly addressed. Fluctuations in these factors could potentially influence fish behavior and passage performance. While other environmental variables were not monitored, such as dissolved oxygen and pH levels, we expected the variability in these variables to be relatively minimal. The flume was open to the air and had highly turbulent flow (Reynolds number = 220, 588). Any differences in dissolved oxygen would be minimal and strongly correlated with temperature. For pH, the fish were very small relative to the volume of the experimental setup, and no other factors were present that would influence pH, as the system used raw, dechlorinated water. See lines 143-148. 5. The experimental raceway does not fully replicate natural stream conditions, which may affect generalizability. This limitation has been discussed in the Discussion section (Lines 407-413). However, the controlled environment of the laboratory flume offers several advantages, including the ability to control for confounding factors. This allows us to more accurately isolate learning effects from other influences, such as variation in group size, as well as ensuring consistent flow conditions and water speeds across all trials. In the first instance we need to have a controlled experimental setup which can then inform field tests in the future. 6. The study does not assess whether repeated exposure induces stress or fatigue, which could influence fish behavior. This is a valid point—measuring blood chemistry as a proxy for stress would be a valuable addition in future experiments. Therefore, based on the concerns outlined above, I recommend that this manuscript be accepted for publication after major revision. It is not feasible to repeat these experiments with a greater number of individuals or with additional species at this stage. If the editor considers these additions essential for publication in this journal, we are prepared to withdraw the manuscript. While we acknowledge that including additional species or increasing the sample size would strengthen the study, we believe the current work offers a valuable contribution to the literature and provides a solid foundation for future research. Reviewer 2: The study addresses an important ecological issue: the impact of anthropogenic barriers on fish migration. The findings have implications for conservation and management of freshwater ecosystems, particularly for small-bodied, non-salmonid species. The focus on Galaxias maculatus, an obligate migratory species, adds ecological relevance, as this species is widely distributed in the Southern Hemisphere and faces challenges from human-altered environments. Following points need to be addressed for improvement in manuscript. Thank you for your suggestions and recommendations for the improvement of our manuscript. 1. At line 109, Elaborate reason why authors kept fish in 6 ppt salinity. Does it match the source of procurement? Give reason. The use of 6 ppt salinity in quarantine tanks is to help prevent disease and kill any potential disease the fish may bring with them from the river. This is explained at line 125. 2. Expand the sample size and replicate the experiment across multiple groups or populations to improve the robustness of the findings. While a larger sample size would produce more robust results, we were limited logistically, in terms of seasonal availability and amount of time it takes to conduct trials, which limited the number of fish we could use in this study. 3. Consider reusing individual fish in follow-up experiments to assess individual variability in learning and performance. In hindsight, this would be a good suggestion, however, it was not feasible given the seasonality and timing constraints of this experiment. As suggested to Reviewer 1, in the future we would like to assess individual fish personality and take that into account in our experiments. 4. Isn't it better to consider reusing individual fish in follow-up experiments to assess individual variability in learning and performance. This appears to make the same point as item 3, and as noted it was unfortunately not feasible to conduct further trials in the current study. 5. Provide specific recommendations for conservation and management based on the findings, such as how to improve fishway design or mitigate the impacts of barriers on fish migration. We have added some additional discussion around this topic, please see lines 421-430. 6. The experimental setup, while controlled, may not fully replicate real-world conditions. For example, the raceway's simplified structure and uniform flow conditions do not account for the sample size (40 fish) is relatively small, and the study does not mention whether the experiment was replicated across multiple groups or populations. Replication would strengthen the robustness of the findings. Similar to Reviewer 1’s comments, while a larger sample size would produce more robust results, we were limited logistically, in terms of seasonal availability and amount of time it takes to conduct trials, which limited the number of fish we could use in this study. Additionally, while only juvenile Galaxias maculatus were used in this study, care should be taken not to over-extrapolate findings to other populations or other fish species (Lines 413-415). We have discussed limitations to this study in the discussion section, lines 407-415. 7. Consider conducting follow-up experiments in more complex environments or with different types of barriers to assess the generalizability of the findings. Incorporate variability in flow conditions or barrier design to better mimic real-world scenarios. Include direct measures of spatial learning, memory, and behavioral traits (e.g., boldness, exploration) to strengthen the interpretation of results. As suggested to Reviewer 1, this limitation has been discussed in the Discussion section (Lines 443-453). However, the controlled environment of the laboratory flume offers several advantages, including the ability to control for confounding factors. This allows us to more accurately isolate learning effects from other influences, such as variation in group size, as well as ensuring consistent flow conditions and water speeds across all trials. In the first instance we need to have a controlled experimental setup which can then inform field tests in the future. The manuscript presents a well-designed and executed study with important implications for understanding fish passage through anthropogenic barriers. However, the ecological realism, exploration of behavioral mechanisms, and statistical reporting could be improved. Addressing these weaknesses would strengthen the manuscript and enhance its contribution to the field of freshwater ecology and conservation. In lieu of any specific statistical comments from this reviewer, we are using Reviewer 3’s comments and have made changes in line with their recommendations. Reviewer 3: The manuscript presents a technically sound scientific investigation, supported by a detailed and rigorous methodology. It includes all the essential elements of a well-structured study, such as the description of the required permits and approvals for fish collection, experimental trials, setup and experimental protocol, as well as statistical analysis. The results are presented clearly and in alignment with the methodology, allowing the reader to assess whether the objectives were achieved. Additionally, the analyses are well-founded, providing a robust interpretation of the data while transparently acknowledging the study’s limitations. In particular, the article highlights the ability of fish to improve their passage success with repeated exposures but also recognizes that it remains uncertain whether this learning is transferable to new obstacles. A valuable aspect of the manuscript is that, in addition to addressing its research question, it provides relevant findings for the management of fish passage structures. It highlights challenges in fish attraction and entry, as well as the potential effect of shyness in some individuals, suggesting that management strategies should focus not only on the physical structure of passageways but also on improving fish attraction. Overall, this study significantly contributes to the understanding of fish passage efficiency and provides valuable information for both science and the management of aquatic ecosystems. Thank you very much for your feedback and your suggestions. Editorial Recommendations Some structural adjustments are necessary in the manuscript: a) In the Modelling Binary Success section, when mentioning p-values, the text should correctly direct the reader to Table 2. Thank you for pointing this out, this has now been corrected. b) In line 278, "Table 2" should be changed to "Table 4." Thank you for pointing this out, this has now been corrected. c) It is recommended to reorganize the order of the paragraphs to maintain the logical sequence of the results, placing Table 3 before Table 4. Thank you for pointing this out, this has now been corrected. 2. I consider that the statistical analysis in the manuscript has been conducted appropriately and rigorously. The authors applied a solid approach using generalized binomial generalized linear mixed models (GLMM) to model binary success in approach, entry, and successful passage, incorporating random effects to capture individual variability in fish. Additionally, they employed Cox regression to assess event rates (approach rate, entry rate, and passage rate), allowing for the interpretation of the effects of repeated exposure over time and generating Hazard Ratios (HR) to measure the instantaneous probability of success at each threshold of the experimental channel. However, I found an inconsistency in the application of the Hosmer-Lemeshow goodness-of-fit test. In the methodology, it is stated that this test was used to evaluate model fit in the GLMM for all three events (approach, entry, and successful passage), but in the results, its use is only reported for the entry model. This raises questions about whether it was also applied to the other two events or if its reporting was omitted. Furthermore, I consider that the Hosmer-Lemeshow test is not the most appropriate for evaluating the fit of GLMM models, as it does not account for the random effects characteristic of these models. I suggest using more suitable methods, such as residual inspection, AIC/BIC comparison, or the simulation of predicted versus observed values. If a new model fit method is adopted, I recommend applying it uniformly across all events and including the corresponding results in the results section to ensure consistency with what is described in the methodology. Despite this observation, I believe that the analyses used in the study are appropriate for addressing the research question and allow for well-supported conclusions. Thank you for pointing this out. After doing more research, we found that you are correct and the AIC comparison is more appropriate for GLMM models with random effects. Using the AIC comparison, the GLMM model chosen for each threshold meets the AIC selection criteria (Lines 247-251). 3. In the manuscript, the authors indicate that the data will be available through the Zenodo digital repository and provide the corresponding doi: 10.5281/zenodo.14194951. However, I was unable to access this DOI or find an active link. I suggest that the authors verify the availability of the link and confirm that the data are correctly deposited in the repository to ensure open access and transparency in the publication. The data are now available via the Zenodo digital repository: https://doi.org/10.5281/zenodo.14194951 4. The manuscript is written clearly, without ambiguities, and in a comprehensible level of English. During my review, I did not identify any typographical or grammatical errors that would affect the understanding of the content. However, since English is not my native language, my assessment of full compliance with linguistic standards is limited. Reviewer 4: Were the juveniles caught before they had completed their upstream migration to their habitat? Or was the capture location their habitat? This may be considered one of the reasons why "fish failed to enter the raceway each day." Juvenile fish were captured at the beginning of their upstream migration to control for migratory urge across individuals (Lines 120-122). L117� Did they reuse the waterway described in (39), or did they use the features of (39)? I would like you to add a little more explanation about the introduction of the waterway so that it can be understood without reading (39). We have clarified in text that this study used the same flume and same setup as described in (39). If PVC is an abbreviation for something Attachments Attachment Submitted filename: Response_to_reviewers.docx https://doi.org/10.1371/journal.pone.0329371.r002
22 Jun 2025 Decision Letter - Mizanur Rahman, Editor Dear Dr.Crawford, 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. 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. 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 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, Mizanur Rahman, Ph.D. 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 Reviewer #1: All comments have been addressed Reviewer #2: All comments have been addressed Reviewer #3: (No Response) ******** 2. Is the manuscript technically sound, and do the data support the conclusions??> Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: Partly ****** 3. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: I Don't Know ****** 4. Have the authors made all data underlying the findings in their manuscript fully available??> The PLOS Data policy Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: Yes ****** 5. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: Yes ****** Reviewer #1: I appreciate the efforts made by the authors to provide a more concise version that better highlights the important findings. However, the author addresses the comments very carefully, and I gladly recommend that this manuscript be accepted for publication. Reviewer #2: (No Response) Reviewer #3: 1. Although I initially assumed that the authors had implemented the requested corrections regarding model fitting, as the methods section explicitly mentions the use of the Akaike Information Criterion (AIC) to select the most appropriate models for the three thresholds (approach, entry, and passage success), upon reviewing the results section, it is unclear whether the models presented were actually selected based on this criterion. Instead, the Hosmer-Lemeshow test is mentioned, despite not being previously referenced, which introduces a methodological inconsistency. This lack of alignment between the methods and results sections prevents verification that the reported models truly represent the best fit according to AIC. Clarification of this issue in the results section is recommended. That said, the authors have adequately addressed all editorial recommendations. Table and figure references are now accurate and consistent with the narrative. The paragraph order has been corrected for logical flow, and all statistical results are clearly linked to the corresponding tables. No inconsistencies remain in that regard. 2. I marked "partially" because, although the study presents a clear structure and a solid experimental design, there remains an unresolved methodological issue that limits a more positive evaluation. As previously noted to the authors, the application of the model selection criterion (AIC) has not been adequately clarified, leading to a lack of coherence between the methodology and the results sections. This omission prevents confirmation that the reported statistical models indeed reflect the best-fitting ones. While the results are well-articulated and the study provides valuable insights for fish passage management, the authors must address this methodological inconsistency in order for the manuscript to be considered technically complete. 3. I select “Don’t know” because, although the statistical approach is appropriate for the research question, there remains a methodological inconsistency between the model selection criterion described in the methods section (AIC) and the one reported in the results (Hosmer-Lemeshow test). This discrepancy prevents a clear confirmation that the statistical analysis was applied rigorously and consistently. 4. In this revised version of the manuscript, the link provided to access the data through the Zenodo digital repository (DOI: https://doi.org/10.5281/zenodo.14194951) is active and allows full download of the dataset. This correction ensures open access and enhances the transparency and reproducibility of the results presented in the study. I would like to encourage the authors to make the necessary adjustments so that their study can be shared with the scientific community and contribute to guiding and managing fish passage in rivers impacted by dams and reservoirs. ****** 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: Syed Shafat Hussain 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 https://doi.org/10.1371/journal.pone.0329371.r003
Revision 2
26 Jun 2025 Author Response Manuscript ID: PONE-D-24-53465 Dear Editor Dr Mizanur Rahman, Thank you for the opportunity to revise our manuscript “Teaching fish new tricks: Repeated exposure to a velocity barrier improves passage performance ” (Manuscript ID PONE-D-24-53465) for consideration for publication in PLOS ONE. We appreciate the constructive comments provided by the two peer reviewers. We hope that our revision has suitably addressed all identified concerns. Please see below for a point-by-point summary of changes as raised by reviewers (in RED). We have also provided both a tracked change and clean copy of the revised manuscript for your consideration. Any references to line numbers in our response to the reviewers are based on the tracked change version. On behalf of the full authorship, Yours sincerely, Rachel Crawford National Institute of Water and Atmospheric Research, Hamilton, New Zealand rachelmbcrawford@gmail.com Response to Reviewers: Reviewer 1: I appreciate the efforts made by the authors to provide a more concise version that better highlights the important findings. However, the author addresses the comments very carefully, and I gladly recommend that this manuscript be accepted for publication. Thank you very much for your feedback throughout this process, we appreciate the time that was put into it. Reviewer 2: (No Response) Reviewer 3: 1. Although I initially assumed that the authors had implemented the requested corrections regarding model fitting, as the methods section explicitly mentions the use of the Akaike Information Criterion (AIC) to select the most appropriate models for the three thresholds (approach, entry, and passage success), upon reviewing the results section, it is unclear whether the models presented were actually selected based on this criterion. Instead, the Hosmer-Lemeshow test is mentioned, despite not being previously referenced, which introduces a methodological inconsistency. This lack of alignment between the methods and results sections prevents verification that the reported models truly represent the best fit according to AIC. Clarification of this issue in the results section is recommended. That said, the authors have adequately addressed all editorial recommendations. Table and figure references are now accurate and consistent with the narrative. The paragraph order has been corrected for logical flow, and all statistical results are clearly linked to the corresponding tables. No inconsistencies remain in that regard. We apologize for the lack of clarity in the manuscript regarding our switch to using AIC for model selection. In the revised version, we did adopt AIC as our primary model selection criterion; however, we overlooked removing previous references to the Hosmer-Lemeshow test. We have now corrected this by removing all mentions of the Hosmer-Lemeshow test and have added a table (lines 247–257) outlining our model selection process along with the associated AIC scores for transparency. 2. I marked "partially" because, although the study presents a clear structure and a solid experimental design, there remains an unresolved methodological issue that limits a more positive evaluation. As previously noted to the authors, the application of the model selection criterion (AIC) has not been adequately clarified, leading to a lack of coherence between the methodology and the results sections. This omission prevents confirmation that the reported statistical models indeed reflect the best-fitting ones. While the results are well-articulated and the study provides valuable insights for fish passage management, the authors must address this methodological inconsistency in order for the manuscript to be considered technically complete. We apologize for the inconsistency, and hope that our changes to the manuscript have made this clearer. Please see lines 247-257 for a description of our AIC model selection process, along with a table summarizing the AIC scores. 3. I select “Don’t know” because, although the statistical approach is appropriate for the research question, there remains a methodological inconsistency between the model selection criterion described in the methods section (AIC) and the one reported in the results (Hosmer-Lemeshow test). This discrepancy prevents a clear confirmation that the statistical analysis was applied rigorously and consistently. We apologize for the inconsistency, and hope that our changes to the manuscript have made this clearer. Please see lines 247-257. 4. In this revised version of the manuscript, the link provided to access the data through the Zenodo digital repository (DOI: https://doi.org/10.5281/zenodo.14194951) is active and allows full download of the dataset. This correction ensures open access and enhances the transparency and reproducibility of the results presented in the study. Thank you very much for your feedback throughout this process, we greatly appreciate the time that was put into it. Attachments Attachment Submitted filename: Response_to_reviewers_auresp_2.docx https://doi.org/10.1371/journal.pone.0329371.r004
16 Jul 2025 Decision Letter - Mizanur Rahman, Editor Teaching fish new tricks: Repeated exposure to a velocity barrier improves passage performance PONE-D-24-53465R2 Dear Dr. Crawford, 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 will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, 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, Mizanur Rahman, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: Reviewer's Responses to Questions Comments to the Author Reviewer #3: All comments have been addressed ******** 2. Is the manuscript technically sound, and do the data support the conclusions??> Reviewer #3: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #3: Yes ****** 4. Have the authors made all data underlying the findings in their manuscript fully available??> The PLOS Data policy Reviewer #3: Yes ****** 5. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #3: Yes ****** Reviewer #3: The authors have adequately addressed a key concern raised in the previous round regarding the methodological coherence between the description of model selection using AIC and the presentation of results. In the revised version, they clearly indicate that model selection for binary success outcomes was based on the corrected Akaike Information Criterion (AICc), and this is now consistent across the Methods, Results (Tables 1 and 3), and Discussion sections. The selected models are appropriate for the research questions posed, and their use of GLMMs and Cox mixed-effects models aligns well with the binary and time-to-event data structure. The statistical analyses have been performed rigorously, with thoughtful inclusion of random effects to account for individual variability, and proper handling of censored data. The consistency between the methodological framework and the statistical outputs strengthens the reliability of the conclusions. Additionally, the conclusions are appropriately drawn from the data and analyses. The authors maintain a balanced interpretation, acknowledging both the statistically significant effects and the limitations of the observed trends, particularly in the context of real-world fish passage structures. Their findings contribute valuable insights into how cognitive and physical traits may interact with hydraulic barriers, which is highly relevant for future design and assessment of fishways. Therefore, I can now state that the manuscript is technically sound and methodologically coherent, and I commend the authors for the thoughtful revisions that enhance the clarity and scientific robustness of the work. ****** 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 #3: No ******** https://doi.org/10.1371/journal.pone.0329371.r005
Formally Accepted
Acceptance Letter - Mizanur Rahman, Editor PONE-D-24-53465R2 PLOS ONE Dear Dr. Crawford, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset You will receive further instructions from the production team, including instructions on how to review your proof when it is ready. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few days to review your paper and let you know the next and final steps. Lastly, 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. You will receive an invoice from PLOS for your publication fee after your manuscript has reached the completed accept phase. If you receive an email requesting payment before acceptance or for any other service, this may be a phishing scheme. Learn how to identify phishing emails and protect your accounts at https://explore.plos.org/phishing. 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. Mizanur Rahman Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0329371.r006

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