PCLM-D-23-00183

Climate impacts to inland fishes: Shifting research topics over time

PLOS Climate

Dear Dr. Lynch,

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.

Please submit your revised manuscript by Oct 27 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 climate@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pclm/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

• A rebuttal letter that responds to each point raised by the 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'.

Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

We look forward to receiving your revised manuscript.

Kind regards,

Jennifer Lee Wilkening, Ph.D

Academic Editor

PLOS Climate

Journal Requirements:

1. 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 If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references.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 If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

2. Please ensure that Funding Information and Financial Disclosure Statement are matched.

3. In the Funding Information you indicated that no funding was received. Please revise the Funding Information field to reflect funding received.

4. Please provide separate figure files in .tif or .eps format.

For more information about figure files please see our guidelines:

https://journals.plos.org/climate/s/figures 

https://journals.plos.org/climate/s/figures#loc-file-requirements

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

Reviewer #3: Partly

**********

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

**********

3. Have the authors made all data underlying the findings in their manuscript fully available (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

Reviewer #3: Yes

**********

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

Reviewer #3: Yes

**********

5. Review Comments to the Author

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

Reviewer #1: General comments:

1) This is a very interesting review paper using recent topic modelling methodology to identify potential gaps and overlaps in the quest to appreciate how inland fishes may have been affected by climate change and perhaps much more in the future.

2) I wonder if the ChatGPT sections of the paper are really necessary and overall do not appear to affect the final conclusions. Perhaps this material might be put in an on-line supplementary materials unit or deleted completely.

3) The geography of the papers in the database is not mentioned though apart from a couple of mentions of European species North American species are the main focus. Given this database only uses papers written in English, is it worth some speculation about the role that papers in say French or German or Spanish might have impacted the analyses?

4) In the discussion section of the paper there is no consideration of potential shortcomings of the approach taken.

5) Overall the figures do a nice job providing an overview of the results of these analyses. Figures 1-4 in the review copy of the MS were fuzzy – need to pay attention viz appearance in final version.

Specific comments:

L68 – double rather than doubling?

L90 – Further rather than Additionally?

L94 – Shouldn’t the first reference for topic modelling occur here?

L100 – a corpus rather than the corpus?

L118 – Could be useful to put here to the exact R app used to perform the LDA, presumably within topicmodels

L119 – Why only 323 papers from a database of more than 1200 papers?

L240 – “papers most like the”?

Reviewer #2: This manuscript uses topic modeling to examine trends and relationships in the nearly 400 papers examining impacts of climate on freshwater fishes in the FiCli database. The authors also compare the topics identified through modeling methods with a list of topics/themes generated by ChatGPT. This is to my knowledge a novel, objective, approach which has generated some interesting insight. The paper is well written, aside from minor comments I include below. I also have some more general thoughts and suggestions.

First, I know that this follows previous work, but I find the definition of a topic gap as dissimilarity between two topics as somewhat limiting. It seems to be expected that some of these topics will have more overlap than others (and likely with a lower k-parameter similar topics collapse). If I were to try an identify a gap in knowledge I would start with understudied topics generally, then consider interactions between multiple topics. Are there potential topics that are not in the top 10 identified here which are understudied? Are the four topics identified by ChatGPT and not in some of these? What about for example genetic impacts? Or mortality?

Second, looking at Table 1, many of the topic words stand out to me as somewhat surprising. Particularly for invasive species and for populations. I wonder if some discussion of this is warranted.

Third, I think the paper may benefit from organizing topics an alternative way, rather than alphabetical. Some topics are quite different in nature and classification/re-organization may provide additional insights. For example, moving up levels of biological organization physiology, growth, reproduction, populations, assemblages, etc…or non-organismal topics: drivers, invasive species, conservation and management. If topics are re-organized, the authors might consider a figure linking across topics with arrows of different weights instead of or in addition to the gap distance matrix.

Fourth, I know that ‘habitat types’ are in the too common words which were excluded, but I would be interested to know whether climate impacts are more frequently studied in lakes or streams and whether there are interactions between habitat type and topics or gaps within topics by habitat type.

Finally, I also know this is likely beyond the scope of this paper, but it would be interesting to know whether these topics have followed similar trends in general fisheries research (e.g. not just related to climate). Is there a way to capture this?

Minor comments-

L 63-67 Is there peer-reviewed literature that should be cited on the number of fishes and the proportion that are threatened with extinction in addition to the WWF report?

L 152 It is unclear to me what it means to “average the topic with the highest weight for each paper”

L158 So topic gaps are topics that are rarely investigated together? Could this be weighted by overall how common a topic is? Some of the explanation in 330-331 could be moved up.

L 240 I think the word “those” is misplaced and should be removed.

L316 revise “population reproduction” to something more clear like population reproductive rates? Or reproduction within a population or across populations?

L352 I suggest adding “we identified” after ”topics”

L371 This sentence is unclear—the physiological changes are simply warmer or colder?

Reviewer #3: 1) I enjoyed seeing how topic modeling and ChatGPT could be used to explore changes in climate change research foci over time. It would be interesting to see how those approaches compare with a more traditional approach of searching journal databases using the same key words (e.g. GoogleScholar). The authors indicate that the papers included in FiCli were explicitly related to organismal responses to climate change, so relatively few papers in the database focused on the human-impacts angle. Thus, a major topic was not represented in their analysis: management and conservation strategies. I suspect that a major trend in topics has involved an early focus on projections about how fish will be affected by climate change to a more recent focus on what managers can and are doing to manage fish populations in a changing climate. This trend was not apparent in the current analysis. Conservation and management strategies was a topic noted by the ChatGPT search and a quick GoogleScholar search using the terms ‘climate change’, ‘fisheries management’ and ‘freshwater’ for 1985-2021 returned thousands of articles. Adding a more traditional literature search approach for comparison to topic modeling and ChatGPT would strengthen the ms.

Specific comments:

I offer the following more specific comments on the ms.

1) L 30. The superscript “6” for Daria Gundermann in the authors list appears as “2” instead of “6”

2) L 47. “almost 40 years”, why not just state the actual number of years (1985-2021 = 36 years)?

3) L 53 “and” does not appear necessary.

4) L 95-96. “which topics are being researched, the prevalence of those themes in the literature, the trajectories of those themes over time, and the relationships among those themes.” The terms “topics” and “themes” appear to be used synonymously throughout this paragraph so to avoid confusion, I suggest sticking with one. “Topic” would appear to be the best choice since it directly corresponds to “topic modeling”

5) Table 1. What does € refer to regarding invasive species?

6) Line 216. Fig. 2. “Mean annual change in topic popularity expressed as a percentage” Is the change being measured from the previous year? For example, a topic that represented 10% of the articles published in 1985 but 9% of the articles published in 1986 would have annual change of -1% for 1985-1986. A similar value would be calculated for all subsequent annul periods and the mean of these values is presented in Fig. 2. If this interpretation is correct, it would help to provide more explanation for how mean annual change was calculated.

7) Fig 2. Based on the y-axis, the change in popularity values appear to be quite small (around 0.1%). In Fig. 1, the total number of papers published is 30 or fewer most years. Thus the smallest change that could be detected year to year is an increase or decrease of one paper on a given topic (1/33 = 3.3%). How did you end up with values on the order of 0.1%?

8) Fig. 3. It is common in ordinations to interpret the axes as gradients. In Fig. 3, NMDS2 (y-axis) appears to represent a gradient of documented studies (high scores) versus projection studies (low scores). What is the interpretation of the NMDS1 (x-axis). The ends of that axis are populations versus distributions. Could this represent a gradient from studies that use abundance data (e.g. population trends, vital rates, growth, reproductive output) versus studies that use presence/absence data (distributions, invasive species, projections of species occurrence under future climate scenarios). Can the authors provide their interpretation of NMDS1?

**********

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

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: Charles K. Minns

Reviewer #2: No

Reviewer #3: No

**********

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

Climate impacts to inland fishes: Shifting research topics over time

PCLM-D-23-00183R1

Dear Dr. Lynch,

We are pleased to inform you that your manuscript 'Climate impacts to inland fishes: Shifting research topics over time' has been provisionally accepted for publication in PLOS Climate.

Before your manuscript can be formally accepted you will need to complete some formatting changes, which you will receive in a follow-up email from a member of our team. 

Please note that your manuscript will not be scheduled for publication until you have made the required changes, so a swift response is appreciated.

I recommend using the two vertical panels for Figure 2. I believe these are slightly easier to read.

IMPORTANT: The editorial review process is now complete. PLOS will only permit corrections to spelling, formatting or significant scientific errors from this point onwards. Requests for major changes, or any which affect the scientific understanding of your work, will cause delays to the publication date of your manuscript.

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 climate@plos.org.

Thank you again for supporting Open Access publishing; we are looking forward to publishing your work in PLOS Climate.

Best regards,

Jennifer Lee Wilkening, Ph.D

Academic Editor

PLOS Climate

***********************************************************

Reviewer Comments (if any, and for reference):