PCLM-D-23-00178

A multi-criteria approach to assess the avian biodiversity and carbon benefits of climate change and forest management in Eastern North American forests

PLOS Climate

Dear Dr. Labadie,

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 Nov 24 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,

Katharina C Wollenberg Valero, Dr. rer. nat

Academic Editor

PLOS Climate

Journal Requirements:

1. Please note that PLOS CLIMATE has specific guidelines on code sharing for submissions in which author-generated code underpins the findings in the manuscript. In these cases, all author-generated code must be made available without restrictions upon publication of the work. Please review our guidelines at https://journals.plos.org/climate/s/materials-and-software-sharing#loc-sharing-code and ensure that your code is shared in a way that follows best practice and facilitates reproducibility and reuse.

Additional Editor Comments (if provided):

Dear authors,

I have now sourced two reviews for this manuscript. Both reviewers agree that the topic is timely, the analysis is well performed, and the conclusions interesting. Reviewer 2's additionally made some suggestions about how taxonomic units of birds have been treated in your analysis and write-up, and made some specific suggestions for improvement. This may involve some new analyses, so I would welcome a revised manuscript incorporating these.

One of the reviews is also provided as an annotated pdf, please make sure you see this.

With best wishes

Kat Valero

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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: I don't know

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

**********

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

In the manuscript entitled “A multi-criteria approach to assess the avian biodiversity and carbon benefits of climate change and forest management in Eastern North American forests” the authors explored bird community responses in two different regions across Eastern North American forests to study the effect of projected forest management practices and climate change. Overall, the study deals with an interesting topic and might draw the attention of many researchers giving important insights on forest bird communities and on possible future scenarios in the forest ecology, management, and conservation. The manuscript is generally well written, and the results are critically discussed in the context of recent literature.

However, I found the used bird modelling approach a bit confusing and not clear enough. In general, authors speak about species-specific modelling but at some point, they generalize the implication for entire bird community, or they divide the community into functional traits (mainly habitat association). I eventually got lost in what they have used. To my understanding, they also excluded other bird specialists from the analysis (e.g., real generalist or lowland/farmland birds), species that because of climate change could be part of future scenarios in the forests. I suggest using of an overall taxonomical index (e.g., species richness or Shannon diversity) and they may also include in the analysis a functional diversity index, since they often mention the ecosystem functions. Moreover, as the SE of the used habitat associations seems very high (see as an example what reported in S5 Table), the use of a Community Waited Mean index could help in summarising together more traits. Thus, the (bird) methods and results need some clarifications and implementations, which the authors should be able to deal with. Based on these, more robust conclusions can be drawn. Finally, I find the paragraphs of introduction not well connected, and a few clarifications are needed in the Methods regarding LANDIS-II simulations.

I hope that my comments are useful for improving this manuscript. I report here below a series of suggestions that can help to improve the manuscript. I believe the study merits publication – and “Plos Climate” would be a good outlet - after these revisions have been carried out satisfactorily.

Specific comments

Title. L.2: In my opinion, the term “biodiversity” is too broad, as it typically involves multiple taxa. I would suggest using “avian diversity” instead of “avian biodiversity”, both in the title but also along the whole manuscript (e.g., L. 39, L. 132, and L. 139, and throughout the whole manuscript).

L. 60: “21st”.

LL. 76 and 78: these two paragraphs are not very well connected, please add a sentence or two to connect them better.

L. 88: “changes”.

LL. 91-93: I think that here a reference is needed.

L. 93: “Most boreal-breeding bird species”.

LL. 117-121: very long sentence and difficult to understand. Please split.

L. 221: what do you mean with “Initial”? I suppose it refers to the initial conditions for the simulation model, but this is not clear in this context.

L. 123: never closed bracket.

L. 123: “partial harvesting [38],”.

L. 127: reference number is missing here.

L. 134: “changes”.

L. 135: reference number is missing here.

L.136: I recommend to describe a little bit more in details on ecosystem service provision also before in the first’s paragraphs of the introduction. But see comments further below (for L. 618)

L. 139-140: I would delate last sentence.

L. 146: “37,050”.

LL. 149-153: I think a reference is needed here.

L. 154: “5,669”.

L. 154: “Atlantic Maritime Ecozone” or Atlantic Maritime ecozone? Please be consistent.

L. 159: I think a reference is needed here.

L. 167: “10%”.

L. 186 why was only one General Circulation Model considered in this study? As it reads now, it sounds like it was an arbitrary decision without comparing other combinations of GCM-RCMs. Please explain.

L. 186: “…under both scenarios [48],…”.

L. 189: I think here you need to write the reference in full.

L. 192: I would delate “(baseline, RCP 4.5, RCP 8.5)”.

L. 192 what do you mean by “parameterize forest landscape simulations”. Models are typically parameterized and validated against long term observational data. Or did you mean that the climate series were used as inputs?

L. 195: very long subchapter here, maybe you can consider moving something in the supplementary material?

L. 196 I browsed in the LANDIS-II website and noticed that now LANDIS is available in v.7. Actually, LANDIS-II is available since five years already (2018). LANDIS-II v.6 has been retired by the developers and it is not available anymore. Why did you now use the most recent version of the model? Also, if the model version is not available to download meaning the study is not fully reproducible. Do you intend to provide the model executables, as well as the extensions used, in an online repository?

L.209 what is an “initial community” Is this a LANDIS-specific term?

L. 217 what is a “succession extension”? Only by going through the LANDIS-II website I realized that the model is built with a modular structure, with multiple extensions being used as a user choice. This is not clear in the manuscript. Please explain it better.

L. 252-253 “Wildfire are not a major disturbance” Even if I am not from Canada, all I heard from the news last summer were about the dramatic impacts of wildfire on boreal forests in Canada, following massive wildfires occurring in the past months. Or perhaps you refer specifically to your two study areas? But on L. 670 you clearly stated that wildfire is a major disturbance in boreal forest… Please clarify.

L. 254: reference number is missing here.

L. 268: “of the two areas”; you mainly talk about areas, be consistent with the terms to define them.

L. 287: reference number is missing here.

L. 302 “replicated five times” Why? This might not be clear for non-modellers.

L. 303: reference number is missing here. And also “…2021). For…”.

L. 304 “LANDIS-II models” So are they multiple models? Or do you consider extensions being standing alone models?

L. 317: “…atlas-oiseaux.qc.ca) with various…”.

L. 318: “each area based” see comment at line 268.

LL. 317-318: you say here that you “retained only 318 forest landbird species…”. Did I get right that you excluded other species like generalists or grassland birds? Why? Maybe some future scenarios may favourite them…why did you not account for them as part of the modelled communities? I would suggest modelling some taxonomical index as species richness or Shannon diversity, to have an overall overview of the changes for future bird communities. Otherwise please include an explanation for selecting these bird species.

L. 320: I suggest including a paragraph in which you explain the bird indices used. To me it is not clear enough how you calculated the bird indices that were eventually used for your models. The text refers to individual species but at some point, you describe the bird communities divided per habitat specialisations. Can you please include a brief section in the method where you clarify all these passages about the used indices? See also comment before (LL. 317-318).

L. 322: reference number is missing here.

LL. 339-340: reference number is missing here.

LL. 354-355: I would short the title here.

L. 357: you first speak about “bird community dissimilarity” here, but how do you calculate it? Please see comment at L 320.

L. 375: and also here you speak about the “bird communities” but is not clear how you define a bird community or which index or indices you used.

L. 417: how many bird individuals did you have in the starting situation?

L. 436: “(Acer rubrum; S3 Fig).”.

L471: the last bracket was never open.

L. 476: I think that in your case are more “Forest generalist species…”.

L. 493: “study area”.

L. 504: I think “= -24 ±15),”.

L. 526: in general, I find weird to have sometime only English common names (because second time it appears in the text), sometime also the Latin name (because first time it appears). In my opinion I would always add Latin name in brackets but maybe in the second time that it appears you could abbreviate the genus: first time Spinus spinus second S. spinus. It would be more harmonic.

L. 549: “(i.e., Percent change < -25%; S6 Table).”.

L. 563: “(i.e., Percent change < 25%; S6 Table).”.

L. 564-565: here another example for the comment at line 526. Please revise all the manuscript.

L. 618 “multi-criteria approach” and L. 632 “both ecosystem services” As mentioned above, I think this study is not comprehensive enough to talk about ecosystem services, as you only focus on carbon storage and bird diversity. Are these the only two good and services provide by forest in these study regions? How about other cultural services, or provisional and regulating services? How about other taxa for biodiversity? I don’t think that by analyzing only carbon storage and bird diversity you can talk about multi-criteria approach in forest management, but more of a two-criteria approach? I suggest smoothing down the tone when talking about multiple provision of ecosystem services, or add a section in the limitations acknowledging the omission of other important goods and services these forests might provide but not considered in the study. Same comment for the title in L. 786 “multi-objective forest management”.

L. 629: “regional bird diversity”.

LL. 642-644: in general, I think that always there will be winners and losers, maybe explain that anyway there will be some species that would benefit others not reporting some real results out of your species models.

L. 649: “understanding of how bird”.

LL. 666 and 669: “area” not “site”.

L. 673: trembling aspen, Latin name?

LL. 675-676 “by its higher elevation” first time elevation is mentioned. How high is Montmorecy forest? From a quick search in Google, it doesn’t look very high to be considered a mountainous area at “higher altitude” (600-800 m a.s.l.). Please clarify.

LL. 677-678: I disagree here, since high elevational habitats and landscapes in general will be the most threatened by climate change in future years (e.g., https://doi.org/10.1111/ibi.12585).

L. 687: missing reference number here.

LL. 693-697: these sentences are not so clear. Please, rephrase them.

L. 703: a reference is needed here.

LL. 707-779: I would recommend use of a functional index to have an idea also on the functions the bird communities may change in a changing landscape. See for example: https://doi.org/10.1016/j.baae.2023.04.006 and https://doi.org/10.1007/s00442-022-05134-7 . I know that you acknowledged as a limitation of your manuscript, but I think that an estimation of the overall functional diversity in your scenarios will strongly improve your manuscript. If not, please explain better why you have not done those analysis and include a part in the discussion.

L. 781: “bird diversity” not “biodiversity”.

L. 817: “such as mammals (e.g., boreal caribou Rangifer tarandus caribou)…”.

L. 838: “bird diversity” not “biodiversity” that in general is more bird richness.

Fig. 1: Besides the poor quality of the figure, which I hope they will be improved in the revised submission, the two study area can be hardly seen. I would suggest having a smaller panel showing the entire Quebec, and a separate zoomed view of the two distinct areas. Maybe in the two zoomed areas you could integrate a land cover map showing the forest composition, which would help readers who are not familiar with these forest ecosystems.

Table 1: “natural succession”; no space between number and %.

S1 Table: why some species have different habitat association within areas?

Fig. 5: I would put full species name already in the figure, maybe only the Latin names.

Table 2: “Yes”, “No” and “Bird diversity”. You could also centre text in the cells.

S5 Table: SEs seem very high. Maybe too few species per each class. I would suggest the use of cumulative weighted mean indices. See as an example: https://doi.org/10.1016/j.baae.2023.04.006. This is may be an easier and clearer way to represent the bird communities in a certain landscape.

S6 Tables a and b. I would enter already full species names in the Table, I find to difficult to change table every row to recognize the species.

Reviewer #2: Overall, this is a well-written and meritorious manuscript. It tackles a very serious global challenge--can we take actions to mitigate catastrophic climate change without directly impacting biodiversity?--using a thoughtful local example from Québec, Canada. The authors combine innovative methods from forestry and statistical ecology to produce a paper that could (and should!) be a model for other such analyses elsewhere.The figures are excellent and clearly visualize important results. It was an easy read, which is not what I can usually say about methods-heavy modelling papers like these!

I do my best thinking 'on paper', and have included a PDF with editorial and line-level comments. I hope the authors will endeavour to implement these (they are quite minor), but I do not need to see a point by point response to comments on the PDF. Please check all the pages for those (including figures). I did not comment on the supplementary material.

There are a few small areas where I think the manuscript could be strengthened prior to publication:

1. A rethink on the title, which I don't think adequately captures your objectives here. An idea I came up with: "Can forest management practices to optimize carbon sequestration and emissions mitigation be compatible with maintaining avian biodiversity? A case study on forest birds in Eastern North America." Maybe that's not quite right, but the 'carbon benefits of climate change' doesn't sound right, I think you need to get either 'climate change mitigation' or 'carbon sequestration and and emissions mitigation' right into the title.

2. Just be mindful in your next edit of language specificity. Sometimes the authors say 'climate change' when they actually mean carbon sequestration. Clarify in the methods being applied to 'climate change mitigation' would be more helpful in the introduction in particular.

3. I'd like to see the introduction be more explicitly about the proposed management techniques early on and how they might sequester carbon or avert fossil fuel emissions (e.g. bioenergy). I'd like to see these be tied more directly to current policy objectives and programs happening in North America that are encouraging these approaches, to make this exercise more applied and less purely theoretical. For example, bioenergy is a very controversial topic right now and one might question why even include it as a pathway, so I think you need to add some explanation and justification.

4. Somewhere in the introduction I'd like to see you situate your paper within the domain of 'ecological forecasting', which is what you are doing, but it will help to connect to broader literature and efforts around this as we try to build towards better, more integrated tools that can consider more variables simultaneously.

5. I struggled with Table 1. The conservation scenario shows an INCREASED annual harvest rate, which didn't seem correct. Maybe this is offset because there is a larger 'conservation zone' but this wasn't specified in the table. Overall I had a hard time following the table and it could benefit from a clearer redesign.

6. The limitations section could benefit from some expansion. I note in the PDF a few places in the Discussion that I felt slightly redundant, where I think sentences could be trimmed to expand the limitations section. Ecological limitations of the models are discussed, but not technical ones. Some limitations I see that were not discussed include:

- whether a 250m cell size can actually be accurate for modelling future conditions, especially in places like the hemiboreal with small, heterogenous stands and using partial or uneven cutting systems. I think this is likely to introduce quite a bit of uncertainty that isn't fully characterized

- whether the scenarios at hand actually have enough empirical basis to

- the relative proportionality of the costs and benefits. I'm making up numbers here, but what if using the industrialized scenario in the boreal forest results mitigates global climate change by 0.001% but reduces the global population of the Rusty Blackbird by 0.1%? To me, there needs to be some discussion of the difference in scales here (or how one could go forward to calculate that) so managers can assess risk and make informed decisions.

7. Right at the very end of the paper, you discuss something that looks an awful lot like the triad model of forestry. Given the increasing adoption and popularity of this approach, I suggest you explicitly discuss it in a dedicated paragraph (or two) and pitch your approach as a tool that governments and industry can use for decision-making about make decisions about zoning the landbase into intensive management, extensive management, and conservation lands. 7. The authors don't come right out and make recommendations about if or how their approach could be adopted elsewhere or guide decision-making. I understand this might be out of your comfort zone, but, I dare you to give it a go.

Great paper overall and I look forward to the final version!

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Reviewer #1: No

Reviewer #2: Yes: Alana R. Westwood

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PCLM-D-23-00178R1

Are forest management practices to improve carbon balance compatible with maintaining avian diversity under climate change? A case study in Eastern North America

PLOS Climate

Dear Authors,

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 as soon as possible. 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,

Munesh Kumar

Academic Editor

PLOS Climate

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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)

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

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

Reviewer #1: Yes

Reviewer #2: Yes

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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: No

Reviewer #2: Yes

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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: Dear Editor,

I sincerely appreciated the remarkable efforts by the authors who significantly enhanced the clarity and comprehensiveness of the manuscript. Pending some additional minor revisions and one main comment (here after), I believe the article will be suitable for publication.

Thank you for involving me, I hope my comments are of help.

Specific comments:

Title: I would prefer “bird diversity” then “avian diversity”.

Keywords line 55: here and after I would prefer to call them “threatened species”.

Line 81: I would suggest adding this reference: https://doi.org/10.1016/j.foreco.2023.121673 .

Line 86: also, this work could be important here: http://dx.doi.org/10.1007/s00442-022-05134-7 .

Line 154: a space is missing here after 39.

Line 214: Thank you for your previous explanation to my old comment on the use of Landis-2 v6. Still, this is not very clear to me why a deprecated model version would be necessary to give meaningful results compared to the current one, as they are in fact the same model. I suppose you are using the old model version because the current one is not compatible with some extensions. If so, could you please be more specific? Your availability of providing executables on request is welcomed, but this does not improve the transparency and reproducibility of your study. If I am not incorrect, a requirement by PLOS Climate is to "adheres to appropriate reporting guidelines and community standards for data availability" and "Authors must follow standards and practice for data deposition in publicly available resources". Therefore, I strongly suggest archiving the data supporting the study in a long-term repository linked with a DOI (Dryad, Zenodo; not in a personal github repository), including the model installer/executable, since they refer to a version that is not available anymore.

Line 375: again, I would prefer “threatened species”.

Line 650: this citation is needed here http://dx.doi.org/10.1007/s10342-022-01485-1 .

Line 726: this is the first time you mention Lincoln’s Sparrow, please also add the Latin name, and please check if you put the Latin names every first mention of a bird species.

Line 784 and line 854: “threatened”.

Line 889: a space before “Indeed”.

Reviewer #2: Thank you for your revisions, which have addressed my prior comments.

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Reviewer #1: No

Reviewer #2: Yes: Alana R. Westwood

**********

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Are forest management practices to improve carbon balance compatible with maintaining bird diversity under climate change? A case study in Eastern North America

PCLM-D-23-00178R2

Dear Dr Labadie,

We are pleased to inform you that your manuscript 'Are forest management practices to improve carbon balance compatible with maintaining bird diversity under climate change? A case study in Eastern North America' 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.

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,

Munesh Kumar

Academic Editor

PLOS Climate

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