-->PONE-D-25-52212-->-->Long-term Changes in the Juvenile Sockeye Salmon Rearing Capacity of the Chignik Lakes Watershed-->-->PLOS ONE

Dear Dr. Gammelin,

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.-->--> -->-->Specifically, the reviewers have provided generally positive comments on the manuscript; however, some criticisms have been made on some minor points which have to be thoroughly addressed in a revised version of the ms before it can be further considered for publication in PLOS ONE.-->--> -->-->Please submit your revised manuscript by Jan 08 2026 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

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We look forward to receiving your revised manuscript.

Kind regards,

Giorgio Mancinelli, Ph.D.

Academic Editor

PLOS ONE

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When submitting your revision, we need you to address these additional requirements.

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2. Thank you for stating the following financial disclosure:

“Funding was provided by the Gordon and Betty Moore Foundation (CG,DS), the Chignik Regional Aquaculture Association (DS), the Fishery Disaster Relief Program of the Pacific States Marine Fisheries Commission (DS), and the School of Aquatic and Fishery Sciences at the University of Washington (CG, DS).”

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3. Thank you for stating the following in the Acknowledgments Section of your manuscript:

“Funding was provided by the Gordon and Betty Moore Foundation, the Chignik Regional Aquaculture Association, the Fishery Disaster Relief Program of the Pacific States Marine Fisheries Commission, and the School of Aquatic and Fishery Sciences at the University of Washington.”

We note that you have provided additional information within the Acknowledgements Section that is not currently declared in your Funding Statement. Please note that 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:

“Funding was provided by the Gordon and Betty Moore Foundation (CG,DS), the Chignik Regional Aquaculture Association (DS), the Fishery Disaster Relief Program of the Pacific States Marine Fisheries Commission (DS), and the School of Aquatic and Fishery Sciences at the University of Washington (CG, DS).”

Please include your amended statements within your cover letter; we will change the online submission form on your behalf.

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Additional Editor Comments (if provided):

The reviewers have provided on the manuscript generally positive comments, even though criticisms have been made on some minor points which have to be thoroughly addressed before the ms can be further considered for publication in PLOS ONE

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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: Partly

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-->2. Has the statistical analysis been performed appropriately and rigorously? -->

Reviewer #1: Yes

Reviewer #2: Yes

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-->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

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-->4. Is the manuscript presented in an intelligible fashion and written in standard English?

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Reviewer #1: Yes

Reviewer #2: Yes

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-->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 a well-written manuscript that uses several multi-decal datasets to determine if Sockeye salmon rearing capacity in the Chignik Lakes watershed has declined. The authors have done an excellent job at utilizing existing long-term data and assessing whether the physical and biological conditions in Black Lake and Chignik lakes have changed to indicate a loss in rearing capacity preceding the 2018–2021 stock collapse. I appreciate the authors well-organized and crafted paragraphs as well as the numerous figures to display the results. The manuscript is suitable for publication in PLOS ONE and I strongly recommend acceptance for publication.

Please see my minor comments, suggestions, and questions attached to the PDF. Also, figure 3 appears to be missing from my PDF. Could this be a technical issue caused by the manuscript submission page? Is there a figure or upload limit?

Reviewer #2: Thank you for the opportunity to review this manuscript. I thoroughly enjoyed reading it and believe that with revision it will make a valuable contribution to understanding factors contributing to Pacific salmon declines.

My overarching comments relate mainly to how the research is presented to ensure the data support the conclusions presented (publication criteria #4) and clear presentation of ideas and the broader context of the work (publication criteria #5).

Overall, the manuscript is well-written in an intelligible fashion. However, as someone with a general knowledge of Pacific salmon fisheries but not specific knowledge of the Chignik region, I found the work could be better placed in the broader context of sockeye salmon fishery declines in the region, including both freshwater and marine factors that could contribute to declines. For example, the potential role of harvest and interactions with species that prey on sockeye salmon eggs/juveniles are not currently discussed. The manuscript appears to make a case for the hypothesis that warmer temperatures in Black Lake led individuals in poor condition to emigrate downstream early to Chignik Lake, where littoral rearing habitat is limited, leading to high early life stage mortality. However, assessing emigration/origins of individuals is not possible. Other hypothesis such as failed spawning, low egg maturation and survival are mentioned (mainly later in the conclusion) and the data presented don’t support the hypothesis that declines in rearing habitat quality primarily caused the 2018 collapse. I recommend the authors revise to provide a broader background on the Chignik sockeye fishery collapse and potential contributing factors before narrowing in on the impacts of climate on rearing habitat. I further recommend aligning how findings are presented in the manuscript text with how they are presented in the abstract, which does so more objectively. The discussion would benefit from leading with main, overarching findings and not following the same structure as the results to convey relationships between indicators more clearly and concisely.

Unfortunately, they dryad link provided did not work and therefore I was unable to confirm whether all data underlying findings are fully available. I was curious what spawner and recruit data were used to estimate recruits/spawner and how these data were collected. The figures appear out of order/mislabeled and I believe that Fig. 3 might be missing? Lastly, I recommend a thorough read to screen for typos (e.g., lines 318, 351, 575, 594).

Attached are specific comments in a pdf. I hope the authors find these comments helpful for improving their manuscript.

Best,

Jenilee Gobin

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Reviewer #1: Yes: Jason C. Leppi

Reviewer #2: Yes: Jenilee Gobin

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Attachments

Attachment

Submitted filename: PONE-D-25-52212_JL.pdf

-->PONE-D-25-52212R1-->-->Long-term Changes in the Juvenile Sockeye Salmon Rearing Capacity of the Chignik Lakes Watershed-->-->PLOS One

Dear Dr. Gammelin,

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 Apr 24 2026 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 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,

Giorgio Mancinelli, Ph.D.

Academic Editor

PLOS One

Journal Requirements:

If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise.

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:

The authors made a successful attempt to incorporate the comments of the reviewers in the revised version of the manuscript, to the point that one of the reviewer consider it acceptable for publication. However, the second reviewer highlighted some additonal minor points to be addressed in an additional revision round before the ms can be further considered for publication in PLOS One

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Reviewers' comments:

Reviewer's Responses to Questions

-->Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.-->

Reviewer #1: All comments have been addressed

Reviewer #2: (No Response)

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-->2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. -->

Reviewer #1: Yes

Reviewer #2: Partly

**********

-->3. Has the statistical analysis been performed appropriately and rigorously? -->

Reviewer #1: Yes

Reviewer #2: Yes

**********

-->4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.-->

Reviewer #1: Yes

Reviewer #2: Yes

**********

-->5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.-->

Reviewer #1: Yes

Reviewer #2: Yes

**********

-->6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)-->

Reviewer #1: (No Response)

Reviewer #2: Thank you for the opportunity to review this revised manuscript. The authors have incorporated line by line feedback well. However, I suspect they might have missed a comment related to providing readers with a broader background on potential factors contributing to the Chignick sockeye fishery in the introduction before focusing on the potential role of changes in rearing habitat. Just 1-2 lines could be added in the paragraph starting on line 82 to address this, where the potential role of floods could also be mentioned briefly. Additionally, some details (e.g., reporting statistics) and typos/grammatical errors appear to have been overlooked. The implications of the study’s findings for management and future research needed for management summarized in the conclusion could also be more specific and clearly articulated.

I hope the authors find these additional comments helpful to continue improving their manuscript.

Best,

JL

Line by line comments:

- some typos/grammatical errors remain in the manuscript (e.g., line 71 missing comma between ‘degraded’ and ‘juvenile’, line 86 missing the word ‘of’ between ‘years’ and ‘painful’)

- year 2020 on x-axis cut off in Fig 1c

- year intervals in lines 186-187 don’t align with Fig 3

- linear regression analyses should report additional statistics beyond p values (e.g., test statistics, correlation coefficient)

- line 352 (previously 340) referring to defining abbreviations in caption was in reference to the abbreviated prey species depicted in the figure (i.e., listing prey species in the caption is more explicit and helps the figure ‘standalone’)

- paragraph starting line 461 (previously 433) – lack of clarity stemmed from paragraph structure. The message the reader is intended to take away is not immediately clear. What is the main point this paragraph aims to convey?

- lines 521-530 (previously 493-502) – suggest ‘couching’ text in this paragraph as was done in the response provided; present as a possible indication of top down effects as the authors clearly stated in their response that the data needed to determine mechanisms driving trends in zooplankton communities are not available. I don’t necessarily disagree with your claim that changes in zooplankton could reflect a release from predation; I’m simply suggesting you present it as a possibility rather than suggesting the evidence presented is sufficiently strong to infer mechanistic/causal relationships.

- line 585 (previously 555-557) – do not see additional sentenced referenced in the author’s response in the revised text

Conclusion:

- The current study does not suggest a decline in rearing habitat based on patterns in juvenile growth, temperature, zooplankton, and fish communities. This study assessed proxies for habitat but was unable to quantify rearing habitat directly – it remains possible that habitat features that support spawning and juveniles underwent changes that could not be measured in this study that contributed to failed spawning/low juvenile survival.

- The hypothesis that floods in 2013 could have contributed to the 2018 collapse does not emerge from the current study. I understand the authors focused on the question of potential declines in rearing habitat as a potential factor contributing to declines. They could nonetheless introduce this alternate hypothesis earlier. The alternative hypotheses presented in the conclusion should be moved into the introduction so that the conclusion can highlight the specific study implications and the questions it raises. It would be more useful to readers (and managers specifically) to present the broader context at the outset and situate the question of the role of rearing habitat within this.

- The introduction frames the study in the specific context of providing a comprehensive analysis to support effective management thus warranting more specific conclusions/recommendations for management in its conclusion. In light of your findings, is the proposed/current management strategy supported or not? It would help to inform the readers of what management actions are currently being taken and identify specific research is needs for adaptive management based on the current findings.

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-->7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.-->

Reviewer #1: Yes: Jason C. Leppi

Reviewer #2: Yes: Jenilee Gobin

**********

[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.]

To ensure your figures meet our technical requirements, please review our figure guidelines: https://journals.plos.org/plosone/s/figures

You may also use PLOS’s free figure tool, NAAS, to help you prepare publication quality figures: https://journals.plos.org/plosone/s/figures#loc-tools-for-figure-preparation

NAAS will assess whether your figures meet our technical requirements by comparing each figure against our figure specifications.

-->

Long-term Changes in the Juvenile Sockeye Salmon Rearing Capacity of the Chignik Lakes Watershed

PONE-D-25-52212R2

Dear Dr. Gammelin,

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.

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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,

Giorgio Mancinelli, Ph.D.

Academic Editor

PLOS One

Additional Editor Comments (optional):

In this second revision of the manuscript, all the minor points raised by the reviewers have been successfully addressed, making the ms acceptable for publication in PLOS One

Reviewers' comments: