This paper was transferred from another journal. As a result, its full editorial history (including decision letters, peer reviews and author responses) may not be present.

PONE-D-22-05031Depth and temperature preferences of meagre, Argyrosomus regius, as revealed by satellite telemetryPLOS ONE

Dear Dr. Winkler,

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.

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Johann Mourier, Ph.D.

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PLOS ONE

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2. Thank you for stating the following financial disclosure: 

Abecasis D (PI Project applicant):This study was funded by national funds by the Portuguese Foundation for Science and Technology (FCT), through the transitional norm DL57/2016/CP1361/CT0036, and projects UID/Multi/04326/2020 and BECORV (PTDC/BIA-BMA/30278/2017). BECORV was also financed by CRESC Algarve 2020 through Portugal 2020 and the European Regional Development Fund (FEDER). 

Winkler AC(full time researcher on project: national funds by the Portuguese Foundation for Science and Technology (FCT), through the transitional norm DL57/2016/CP1361/CT0036, and projects UID/Multi/04326/2020 and BECORV (PTDC/BIA-BMA/30278/2017). BECORV was also financed by CRESC Algarve 2020 through Portugal 2020 and the European Regional Development Fund (FEDER)

Bovim L (MsC student): Part of this work was the result of a IMBRSea MSc thesis

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Additional Editor Comments:

Dear Dr. Claus Winkler,

I would like to apologies for the long delay. One reviewer told me that he could send a report but I have not received any news for a few days. As such, in order to avoid any further delay, I decided to serve as a reviewer and take a decision using my opinion and the report of the reviewer who sent a report.

I think the dataset is interesting and provides a real addition to the literature as the behaviour of this species is poorly known. However, I tend to agree with the reviewer that some analyses need some considerations (i.e. GAMM) and that some additional analyses could be also conducted or other details provided (e.g. depth and temperature histograms). Another approach could be the use of Continuous wavelet transformations (CWTs) or FFTs to investigate for cyclical patterns in depth use.

Like the reviewer, I do not understand why depth is found as the response variable (i.e. in depth bin) and in the explanatory variable... this need to be addressed or explained.

Here are additional comments:

Line 56: present only in the Eastern Mediterranean?

Line 208-209: I do not understand the difference between ‘programmed period’ and ‘entire time planned’...

Line 213: check the spaces between the numbers ‘261 121 81’

Figure 1: It could have been nice, if available, to add a picture of these traps and a picture of a tagged meagre (from Figure S1 for example)

As such, I invite you to submit a revised version of your manuscript addressing the reviewer’ comments and additional ones I provided above.

Kind regards

Johann

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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: Partly

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

Reviewer #1: No

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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

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

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

Reviewer #1: Yes

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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: General comments

This study used satellite telemetry to investigate the seasonal and diel depth and temperature preferences of meagre off the south coast of Portugal. While the data collected is important to understanding the movements and habitat use of this fish and informing its management, I have a number of concerns with the analyses that need to be addressed before I could recommend this manuscript for publication.

Firstly, the statistical analysis exploring the effect of season and water temperature on depth usage is very confusing, and in its current state, seems to be confounded. Having depth as both the response and an explanatory variable is confounded (i.e. not independent). I’m not sure why depth needs to be included as a smoother? Also, given the response is a specific depth bin, shouldn’t there be different smoothers for each specific depth bin?

Secondly, there is more than enough data to take a statistical approach to exploring diel differences in vertical habitat use. Why was this only visually done? Either GAMMs could be used on hourly metrics for recovered tags, or simple t-tests (or non-parametric equivalents) could be conducted.

Thirdly, the way the data is currently visualized is confusing and hard to define the general distribution. Given this is the first report of satellite tag results from this fish species, I think it would be worth having depth and temperature histograms to simply show the mean distributions of the species (and if possible, split into diel sections).

Lastly, given that a relatively high number of tags were recovered, I think it would be worth going into a little more detail about what the fine-scale vertical behaviour of these fish look like. For example, are they oscillating through the water column through the day, or following the contour of the seabed?

More detail is included in the specific comments below.

Specific comments

Abstract

Line 16: This is the only mention of the swim bladders being in demand from this species.. It would be worth disclosing this in the introduction alongside a reason for this demand.

Line 21-23: Add the mean and range deployment duration of the tags here.

Line 23: I do not think you can claim that you found these fish to be ‘strictly coastal’ from the available data as horizontal spatial positions were not investigated. Fish may remain shallow despite being in offshore locations. I understand that this fish is primarily demersal so it is likely it was in shallower coastal locations, but as it cannot be proved from the dataset, so soften these statements.

Introduction

Line 72: Replacing ‘tagging’ with ‘tracking’

Line 88: Replace ‘Redlisted’ with ‘listed’

Materials and Methods:

Line 112: Check consistency of how common names and scientific names are reported throughout. Also check which is used on second mention.

Line 136: Replace ‘deployment period’ with ‘programmed deployment period’

Line 137: as above, replace ‘deployment periods’ with ‘programmed deployment periods’

Line 152: Replace ‘retrieval’ with ‘physical retrieval’

Line 158-159: Specify how data were examined to confirm tag detachment i.e. was this done through investigating the depth record?

Line 166: Delete ‘against time’. Not required as it is already mentioned that these are time series data.

Line 173: How was this cutoff decided on?

Line 175: Was this conducted for all depth bins? And what was the temporal unit of measurement? Daily proportions?

Line 187: Given fish ID has been added as a random effect, this model should technically be referred to as a Generalised Additive Mixed Model (GAMM) at line 175

Line 189: Why is depth being added as an explanatory variable? The response and explanatory variable are therefore not independent… This also goes against the aims of the model stated at line 174 (to evaluate the effect of season and water temperature).

Line 194: What was the cutoff used for this? It’s surprising that temperature and depth were not correlated..

Line 202: Why were these visually assessed? There is more than enough data to evaluate this statistically. For instance, GAMMs could be modelled using hourly vertical metrics, or simple t-tests could be used to explore day versus night distributions for each individual and/or all the data as per Braun et al (2014) and Curnick et al (2020).

Results:

Line 209: Do you have any ideas why early detachment may have occurred? This would be useful for informing future tagging efforts.

Line 230: This is misleading as positions were not estimated (and only deployment and pop-up locations were recorded). It would also be worth noting the class/accuracy of the reported pop-up positions. Also, given that three pop-up positions were recorded offshore (beyond the 200 m depth contour), I think it would be worth softening this statement (I know these three were drifting for a few days, but there is still a possibility that these animals moved offshore).

Lines 243-249: Diel depth histograms would be a great way to visualize and interpret this data.

Lines 243-249: Given access to the archived depth record, it would be great to add some additional detail on the behaviours observed. For instance, are these animals oscillating through the water column at finer temporal scales? Or generally remaining at a level depth while following the seabed?

Discussion:

Line 298: Replace ‘archival’ with ‘satellite’ or ‘electronic’. Some data was transmitted, not archival.

Line 301-302: Soften this slightly. Sample sizes were relatively limited in summer months.

Line 309: delete ‘eventually’. Perhaps replace with ‘occasionally’

Line 310-312: This could be explored and visualized using the archival depth time-series data.

Line 327: As above, need to choose to use scientific or common name on second mention.

Line 369: Delete ‘coastal’ here.

Line 388: watch consistency of capitalization of seasons

Figures and Tables:

Table 3: What is the specific depth bin? And shouldn’t there be unique smoothers for each depth bin modelled?

Histograms of the depth/temperature usage of the tagged individuals would be very useful! This could even perhaps be broken up by season to aid in the interpretation of seasonal differences.

Figure 1: Make the symbol denoting the location of the tuna trap more obvious.

Reference list:

Braun, C.D., Skomal, G.B., Thorrold, S.R., and Berumen, M.L. (2014). Diving behavior of the reef manta ray links coral reefs with adjacent deep pelagic habitats. PLoS ONE 9(2), e88170. doi: 10.1371/journal.pone.0088170.

Curnick, D.J., Andrzejaczek, S., Jacoby, D.M.P., Coffey, D.M., Carlisle, A.B., Chapple , T.K., et al. (2020). Behaviour and ecology of silky sharks around the Chagos Archipelago and evidence of Indian Ocean wide movement. Frontiers in Marine Science. doi: 10.3389/fmars.2020.596619.

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Reviewer #1: No

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PONE-D-22-05031R1Depth and temperature preferences of meagre, Argyrosomus regius, as revealed by satellite telemetryPLOS ONE

Dear Dr. Winkler,

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.

==============================

Dear Dr. Winkler,

Thank you for submitting your revised version of “Depth and temperature preferences of meagre, Argyrosomus regius, as revealed by satellite telemetry” to Plos One.

The reviewer found that your manuscript considerably improved from the original version, however, the reviewer remained unconvinced about the inclusion of depth as a smoother in your model.

Could you please address this comment by doing the corrections of the statistical model or clearly explain why the model is correct and why the reviewer may have missed something or misunderstood the model implementation.

Kind regards

Johann

==============================

Please submit your revised manuscript by Sep 29 2022 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,

Johann Mourier, Ph.D.

Academic Editor

PLOS ONE

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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.

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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: (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

**********

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

Reviewer #1: I Don't Know

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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

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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

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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: Thank you for addressing my comments - I can see that the manuscript has substantially improved as a result.

I do, however, remain unconvinced about the inclusion of depth as a smoother in the model. What purpose was this serving? It still seems to me that the response variable is not independant from this explanatory variable (high time in a certain depth bin will inherently be highly correlated with the depth smoother).

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Reviewer #1: No

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PONE-D-22-05031R2

Depth and temperature preferences of meagre, Argyrosomus regius, as revealed by satellite telemetry

PLOS ONE

Dear Dr. Winkler,

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.

Both reviewers feel that this manuscript is a valuable contribution that would deserve publication. One of them, however, has made suggestions that may help improve the final quality of your work, and I would like you to address before final acceptance.

Please submit your revised manuscript by May 29 2023 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

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• 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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• 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,

Antonio Medina Guerrero, 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.

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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: (No Response)

Reviewer #2: Yes

********** 

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

Reviewer #1: (No Response)

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: (No Response)

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: (No Response)

Reviewer #2: Yes

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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: General comments

This study presents a valuable contribution to the knowledge of meagre ecology using satellite tags (though largely based on archived records from physically recovered devices).

This is already a second revision to the original manuscript and it seems the authors have made significant efforts to respond and accommodate the reviewer of the original and R1 submissions. This has been taken into account when carrying out the current review.

Overall, I find the manuscript scientifically sound, once the original reviewer statistical caveats have been addressed. Therefore, I recommend it for publication.

I have some minor comments/suggestions which are indicated below which might help improve some elements of the MS, but most of which are up to the authors to consider (i.e., recommendation for publication is not conditional on those).

Possibly, the major point is that some statements regarding diel patterns could be softened, due to the low sample size or reduced variation in vertical behaviour, notably in summer months.

Additionally, it is a bit strange the authors do not make reference to the horizontal habitat of the fish tracked, noting this information is likely available after the processing through Wildlife Computers data portal. The complex oceanography around the Gulf of Cadiz/Strait of Gibraltar and the different oceanographic regimes in this region, might also help explain some of the vertical patterns observed.

Specific comments

L16 The combination of “demand for this species, and their swim bladders” sounds a bit strange in the abstract without further explanation. Consider removing or rephrasing (e.g., demand for this species, particularly their swim bladders; demand for this species flesh and, in most recent times, swim bladders for the Asian market…).

L25 do not venture

L46 consider: “thermal preferences may be used as one of the main factors to explain” (i.e., it is true temperature explains a lot but there are other factors that condition species distribution- prey abundance, dissolved oxygen..).

L52 Consider the following change: The depth and thermal envelopes occupied by a given species also define their environmental niche… (it is somehow obvious the depth envelope defines the vertical niche, as it is now).

L96 Additionally, in the case of A. regius (the previous sentences seem to be related to sciaenids in general)

L118 The figure caption is embedded in the main text. Figure captions are generally placed elsewhere separately.

L150 Premature releases are generally detected as the tag staying at a constant depth (+- x meters during y days). This can be due to the factors explained, but also to fish death after tagging and it remaining at the seabed. This does not seem to be the case in the current study, but evaluation of fish mortality based on this (or on the breakage of the pin when depth exceeds a maximum depth to prevent implosion) is frequent in large pelagics satellite tagging studies.

L160 It is a very remarkable rate, and most times difficult to achieve in the field. How were tags physically recovered, just verifying they had beached and using Argos transmission location or by means of a radiogoniometer?. Consider specifying a bit the procedure.

L163 Consider changing “quality and quantity” by “resolution and coverage”

L173 Transmitted data

L184 PDT has not been defined before. I imagine it refers to specific files by WC providing depth-temperature profiles, it should be described.

On the other hand, I am not fully aware on how the depths in the PDT file are generated from the archived records (I guess equally spaced from minimum and maximum depths) but if the hours per histogram is not set at 24 h (i.e., if tags are programmed to summarise data in less than 24 h intervals), depths can be biased low for those days when not all histograms are received. Therefore, some further clarification might be beneficial (e.g., if tags were programmed to summarized TAD, TAT and PDT on a daily basis and the way PDT profiles are generated).

L221 (table 1) Fish 8 is not noted as having been recaptured.

L13 The estimated positions refer to the tracks?. If so, some indication on the post-processing (GPE3, WC…) would be desirable. If it refers to tagging and pop-off positions, noting the former is recorded by the taggers and the later is obtained in the argos transmission ,with a relatively high accuracy (e.g., less than 350 in class 2 transmissions), I would remove the word “estimated”.

L229 Consider changing July and August by early and mid-summer, respectively

L245-246 Construction of this sentence seems a bit strange. Consider beginning with: Fish spent on average 23.2% of their time at temperatures above…

L270 The practical totality of what is described in summer months is based on one fish (#20) with just few days from fish #8 in May and July. It is acknowledged in the discussion section, but it should better be also indicated elsewhere, because as it is now it seems to be a conclusion supported by at least several animals.

L272 Shallowest water during the middle of the day… it does not seem very clear from figure 4. I can only observe a slight deeper behaviour around dusk, but it seems mostly constant throughout the day… maybe it is due to the colour palette, but might be worth considering it further (again noting they are data from just one fish).

Moreover, from figure S2, it seems data were averaged by hour and month, not hour and julian day (every tag data begin or end with the month, not in the middle of it, please double-check). Also, sometimes smoothing masks results, hence, in supplementary information, some raw data can be of help also (ie average depth by hour and julian day).

L291 Note data from most May and June originate from one fish, and in July from two.

L299-300 I would just mention demersal or pelagic behaviour would need to be determined using other methodology (I do see other available methods- e.g acoustic tracking) as more suitable for this objective.

L312 Not sure what standar-tagged refers to. Conventional tags?.

L341-343 Does it mean “In winter, in waters with low stratification, forages to the surface were rare”?

L343-344 There are several studies on large pelagic fish (e.g. bluefin tuna) indicating preference to stay over the thermocline particularly at nighttime or when waters are highly stratified.

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Depth and temperature preferences of meagre, Argyrosomus regius, as revealed by satellite telemetry

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