PCLM-D-21-00040

Tracking and forecasting community responses to climate perturbations in the California Current Ecosystem

PLOS Climate

Dear Dr. Hunsicker,

Thank you for submitting your manuscript to PLOS Climate. After careful consideration, we feel that it has merit but does not fully meet PLOS Climate’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.

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We look forward to receiving your revised manuscript.

Kind regards,

Wei Yu

Academic Editor

PLOS Climate

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Additional Editor Comments (if provided):

Two reviewers thought that this manuscript was interesting, well written and logically presented. Both provided some minor concerns on the present version. Thus, I invited the authors made some minor changes on this manuscript based on the comments and suggestions.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Does this manuscript meet PLOS Climate’s publication criteria? Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe methodologically and ethically rigorous research with conclusions that are appropriately drawn based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

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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 (please refer to the Data Availability Statement at the start of the manuscript PDF file)?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception. 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

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

PLOS Climate 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

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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: Climate-induced community responses are highly concerned as the urgent need of ecosystem-based and climate-ready fisheries management. Especially, marine heatwaves such extreme events have largely affected marine organisms and further the communities, and will lead to community reorganizations and the so-called regime shifts, results in great economic and social effects. This study focuses on the California Current Ecosystem (CCE), a famous upwelling ecosystem, using the newly developed Bayesian Dynamic Factor Analysis (DFA) to track the community’s response to climatic drivers and to forecast future changes in the community state. There are some insightful results to benefit understanding the biological responses to the unparalleled marine heatwave in 2014-2016 in the CCE. The forecasting ability and its effectiveness of this methods are proved by this study. Hence the methods can be extended to other areas in future works. The manuscript is well-structured and well-writing. I only have some minor comments for the authors to make corresponding revisions.

Minor comments

1 Lines 62. A simple definition on marine heatwave is recommended.

2 Lines 74-77. It is better to clarify that the thermal shifts that from a cold to a warm regime happened in the northeast Pacific.

3 Lines 79-85. Providing the exact numbers of SST or heat content anomalies would be helpful for readers to understanding the unparalleled marine heatwave.

4 Lines 120-129. The authors describe the DFA and the Bayesian DFA that both are useful replacements of the traditional PCA. However, the superiority of the Bayesian DFA to the DFA should be further clarified.

5 Lines 151-152. I wonder why the authors use the same climate variables from two regions. Are they distinguished from each other in the long-term scale?

6 Lines 166-169 There should be literatures to support that the ESNO is the dominant mode of interannual variability influencing the CCE. In addition, why do not the authors consider the effects of decadal-scale climatic variability modes such as the PDO (as mentioned in the introduction that the PDO is important for the northeast Pacific) and use winter averages?

7 Lines 190-191. How do the authors deal with the unequal time span in biological variables? Will it cause or not cause problems in the Bayesian DFA?

8 Lines 249-250. Similar to question 5, as biological variables are pooled together, is there any need to use climate variables with spatial differences (e.g. SST in the central and southern regions)?

9 Lines 253-257. Are they the same between LOO-CV and k-fold cross validation in which the k is equal to the number of years?

10 Lines 253-277. The LOO-CV, k-fold cross validation and LFO-CV confuse me. To my knowledge, the authors use LFO-CV to firstly identify parameters of (1), (2), (3) and (4), secondly identify the most appropriate error structure for the climate dataset. If it is, the authors should describe more on the LFO-CV rather than introduce other types of information criteria in this part.

11 Lines 291-293. It should be number of the regimes instead of trends.

12 Lines 306. The biology-climate model has only one climate covariate which I think may be incomplete. In my opinion, it would be better to include all the climate variable into the model and then conduct a variable selection procedure to identify the best model, or just use the climate trend (from the climate Bayesian DFA) as the climate covariate as it represents the shared variability of all the climate variable.

13 Line 353. It should be S2 Fig.

14 Lines 383-386. According to the “90%” criterion, Pacific sardine is not or weakly associated with the trend. Therefore, there is less need to focus on these species that were not or weakly captured by the trend as their dynamics are not well reflected by the trend.

15 Lines 395-398. Similar to question 7, as different span of time series will cause uncertainty, why do not the authors unify spans of all the time series.

16 Lines 405-409. I wonder if there is any similarity in these species as they show synchronous increases.

17 Line 412. It should be S3 Fig.

18 Line 429. The term B matrix is better to appear in the materials and methods.

19 Line 437 It should be S4 Fig.

20 Lines 436-437. The result of biology-CUTI model is similar to the biology-BEUTI model, it may indicate the two covariate is correlated. Therefore, a correlation analysis among climate variables can help readers understand your results better.

21 Line 564. The “Suryan et al., 2021” is not found in the reference list.

22 Lines 710-731. The discussion about how we can use the results from this study to benefit management in the CCE is highly recommended.

Reviewer #2: Comments on “Tracking and forecasting community responses to climate perturbations in the California Current Ecosystem”

General comments:

The manuscript implemented a Bayesian Dynamic Factor Analysis method to track the response of California Current Ecosystem to climate perturbations and to forecast future changes in community state. Their results demonstrated strong relationships between community state and multiple climate variables, and identified that nitrate flux through the base of the mixed layer had the strongest correspondence with individual species and the community trend.

Overall, I think the paper is well written and logically presented. The analyses are conducted with solid statistical methods and supporting data. My concerns lie on the organization of the results and discussions, all of which are connected to the objectives of this study.

The study included a rich results, however, a large of texts usually make the readers difficult to follow the center idea of the paper. The author may consider to focus on the most impressive results to make it concise, by removing the less ones. This is a following result of the unclarified objectives in the introduction, where the authors attempt to include a range of goals in this study.

The discussion is tedious. I appreciate the authors’ efforts to organize the sweeping discussion, where as it should be pointed out that no all of them are necessary. I would suggest the authors to focus on the most important findings in the discussion, and if possible, try to bring new insight by summering the underlying patter and driving factors. A list of many relevant facts makes little help towards in-depth discussions.

When novel community states were considered, I wonder if it would be a issue that the very strong signals in the past may conceal any signs of changes in recent years, resulting in insignificant results, which however does not necessarily mean the lack of alternate community state. The point here is the statistical significance may influence each other if the extent of changes differ substantially among the community states, which is dependent on the variables measured in the surveys.

Specific comments:

Line 42-49: the objectives may be summarized or stated in brief in the introduction.

Line 77: The texts after “Since then” may be organized the in the following paragraph.

Line 95: it seems arbitrary to attribute all the events mentioned to the consequence of heatwaves.

Line 105: it is not quite clear how the early detection is viable here.

Line 110: No doubt there are promising progress in community modelling. Even so, I can hardly agree that “the time is ripe” for near-term forecasts, regarding the uncertainty in current modelling frameworks and the limited knowledge in community dynamics.

Line 114: “asynchrony among time series” may be explained in more details.

Line 117: PCA and MDS represent a small partition of the method used in the research field of community ecology, and a more comprehensive review is recommended on this topic.

Line 140: the goals may be revised and reorganized to be concise, distinguishing between approaches and objectives.

Line 169: In this case, it would be critical how the ROMS was calibrated and validated in the ecosystem. Some supporting information are recommended.

Line 187: how is the threshold of 15 years selected?

Line 187: It should be noted that index standardization is usually used for fishery-dependent surveys in which data are usually aggregated in resource-rich areas, but not for properly designed scientific surveys.

Line 197: it seems questionable to change all zeros to NAs, as zeros may be observations rather than missing values in surveys.

Line 199: the influences of log transformation on the DFA may be noted here.

Line 234: could nonlinear relationships be handled in the modelling framework?

Line 249: should the climate datasets and biological datasets be used in the same time span?

Line 259: more details may be needed about the LFO-CV before explaining the target of the method.

Line 270: may denote it as T-1. Also, could the prediction be considered for a scope more than one year?

Line 271: “repeated this process for a time series dataset of 10 years” or something like this may be clearer.

Line 274-277: show them in an earlier contexts. A subtitle of “model structure optimization” may be added to this section somewhere.

Line 291: How does this LOOIC relate to the LFO-CV mentioned earlier?

Line 298: could have more texts about the “community states and raw time series” here.

Line 311: the “individual species parameters and the community state” are not clear here. The last sentence of this paragraph may be revised.

Line 327: A description of trend may be placed before the correlation with climate time series.

Line 359: not quite clear how the number of states were determined here.

Line 382: may mark the occurrence of the marine heatwave in the figure.

Line 386: supplementary figures may be needed to illustrate the associations with the heatwave, as Figure 4 only showed the correlation with the single trend.

Line397-401: some of them can be moved to the discussion or SI, regarding the rich texts in the results section.

Line 424-473: consider cut short the texts in this section. Some results may be shown in the SI if they are not closely related the topic of this study.

Line 480: explanation of prediction uncertainty may be placed in the discussion.

Line 508-548: the discussion may focus on the potential insights that he study can provide, instead of listing all the relevant facts per se. otherwise, the discussion can be largely condensed.

Line 558: “Suryan et al. (2021)” was not properly included in the references.

Line 596: the discussions could be more focused on the interpretation of identified DFA trends in the biological and ecological sense.

Line 650-669: this paragraph may be removed as it is not exactly relevant to the analyses of this study.

Line 696-709: This is also not quite a proper discussion for this study, which is not designed for the purpose of methodological development.

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Reviewer #1: Yes: Shuyang Ma

Reviewer #2: Yes: Chongliang Zhang

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Tracking and forecasting community responses to climate perturbations in the California Current Ecosystem

PCLM-D-21-00040R1

Dear Dr Hunsicker,

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. The journal will begin publishing content in early 2022.

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Kind regards,

Wei Yu

Academic Editor

PLOS Climate

Additional Editor Comments (optional):

The authors have addressed all the reviewer's concerns. The manuscript is now ready to be published.

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: All comments have been addressed

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2. Does this manuscript meet PLOS Climate’s publication criteria? Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe methodologically and ethically rigorous research with conclusions that are appropriately drawn based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

**********

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 (please refer to the Data Availability Statement at the start of the manuscript PDF file)?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception. 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 Climate 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: The authors have addressed all of my concerns, so I recommend an acception of the manuscript.

Reviewer #2: (No Response)

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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.

Do you want your identity to be public for this peer review? If you choose “no”, your identity will remain anonymous but your review may still be made public.

For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: Yes: Shuyang Ma

Reviewer #2: Yes: Chongliang Zhang

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