Same streams in a different forest? Investigations of forest harvest legacies and future trajectories across 30 years of stream habitat monitoring on the Tongass National Forest, Alaska

Michael J. Moore J.; Rebecca L. Flitcroft; Emil Tucker; Katherine M. Prussian; Shannon M. Claeson

doi:10.1371/journal.pone.0301723

Peer Review History

Original SubmissionNovember 30, 2023
27 Dec 2023 Decision Letter - Alejandro Huertas Herrera, Editor PONE-D-23-40089Same streams in a different forest? Investigations of forest harvest legacies and future trajectories across 30 years of stream habitat monitoring on the Tongass National Forest, AlaskaPLOS ONE Dear Dr. Moore, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by Feb 10 2024 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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The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. Please note that PLOS ONE 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/plosone/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. 3. Thank you for stating the following financial disclosure: "No external funding was used in the analysis represented by this manuscript, rather the United States Forest Service providing salary to support the involvement of all authors." 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The following resources for replacing copyrighted map figures may be helpful: USGS National Map Viewer (public domain): http://viewer.nationalmap.gov/viewer/ The Gateway to Astronaut Photography of Earth (public domain): http://eol.jsc.nasa.gov/sseop/clickmap/ Maps at the CIA (public domain): https://www.cia.gov/library/publications/the-world-factbook/index.html and https://www.cia.gov/library/publications/cia-maps-publications/index.html NASA Earth Observatory (public domain): http://earthobservatory.nasa.gov/ Landsat: http://landsat.visibleearth.nasa.gov/ USGS EROS (Earth Resources Observatory and Science (EROS) Center) (public domain): http://eros.usgs.gov/# Natural Earth (public domain): http://www.naturalearthdata.com/ 6. Please upload a copy of Supporting Information Figure/Table/etc. S1 Table and S2 Table which you refer to in your text on page 54. 7. Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. Additional Editor Comments: Dear Authors, After reviewing the manuscript, I believe it merits publication in PLOS ONE following revisions based on the reviewer`s comments. Title: • Better the short title: “Impacts of Forest Harvest Legacies on Stream Habitat in the Tongass National Forest, Alaska” Materials and Methods: • Include information about the restored and reference sites and provide details about the forests. Enhance the paper with relevant photos or illustrations that immerse the reader in the context of the forests. Additionally, incorporate more visual material related to the harvesting treatments, such as photos and illustrations. • Provide additional information about the stream`s characteristics and consider including a map displaying the streams or an illustrative example. • Expand on details about the floodplain. • Enhance the information on the climate dataset, for example, specifying details like pixel size and the GIS geoprocessing involved. • Relocate tables 1 and 3 to the appendixes. Statistical Analyses: • Eliminate subtitles. • Clearly explain or provide more precise indications of the statistical analyses underlying Figures 4, 5, and 6. Consider moving relevant information from table and figure captions to the statistical analysis section. Results: • Move Table 4 to the appendixes. Discussion: • Condense the “Management Acting Upon the Template” section to a concise summary (no more than four paragraphs) that succinctly conveys the key points and transitions smoothly to the main ideas. • Include a section discussing the weaknesses of the study. • Consider adding a conclusion section for a more comprehensive overview. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes ****** 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 ****** 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 ****** 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: Dear author, The manuscript entitled "Same streams in a different forest? Investigations of forest harvest legacies and future trajectories across 30 years of stream habitat monitoring on the Tongass National Forest, Alaska" is a very interesting paper that captures the reader's attention. The paper is well written, and I think it is pleasant to read. This research emphasizes the imperative for sustainable practices to preserve fish habitats and maintain the overall health of southeast Alaska´s forest ecosystems. In my opinion, understanding these dynamics is crucial for anticipating and addressing future management challenges in this ecologically sensitive region. I enclose my specific comments in the PDF. Bests ****** 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. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: 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". 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Revision 1
19 Mar 2024 Author Response Response to Comments on Journal Requirements: Note that all of this information is in an easier to read formatted word document version that was uploaded with the resubmission. When submitting your revision, we need you to address these additional requirements. 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf We changed figure and supplemental figure format to match in-text names as described in the link above. 2. Please note that PLOS ONE 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/plosone/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. Code has been cleaned and prepared for release. It will be released through GitHub upon publication of the work. 3. Thank you for stating the following financial disclosure: "No external funding was used in the analysis represented by this manuscript, rather the United States Forest Service providing salary to support the involvement of all authors." At this time, please address the following queries: We were a bit confused by the requests for additional details on the topic of funding. See our best attempts to address them below. a) Please clarify the sources of funding (financial or material support) for your study. List the grants or organizations that supported your study, including funding received from your institution. The source of funding was the United States Forest Service. No external funding was used in this study. b) State what role the funders took in the study. If the funders had no role in your study, please state: “The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.” No external funders had any role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. c) If any authors received a salary from any of your funders, please state which authors and which funders. All authors received salary through the US Forest Service. d) If you did not receive any funding for this study, please state: “The authors received no specific funding for this work.” NA Please include your amended statements within your cover letter; we will change the online submission form on your behalf. Included in cover letter. 4. In the online submission form, you indicated that "The data underlying the results presented in the study are available from Michael Moore mooremj@iastate.edu." All PLOS journals now require all data underlying the findings described in their manuscript to be freely available to other researchers, either 1. In a public repository, 2. Within the manuscript itself, or 3. Uploaded as supplementary information. This policy applies to all data except where public deposition would breach compliance with the protocol approved by your research ethics board. If your data cannot be made publicly available for ethical or legal reasons (e.g., public availability would compromise patient privacy), please explain your reasons on resubmission and your exemption request will be escalated for approval. Michael Moore is now a USGS employee. To avoid conflicting data sharing rules in the USFS and USGS, we would like to establish Rebecca Flitcroft rebecca.flitcroft@usda.gov as the primary contact for data and code for this research. The master dataset for this project is currently being reviewed for release through the US Forest Service’s repository, which will provide public access. Data will be available in repository upon publication. 5. We note that Figure 1 in your submission contain [map/satellite] images which may be copyrighted. All PLOS content is published under the Creative Commons Attribution License (CC BY 4.0), which means that the manuscript, images, and Supporting Information files will be freely available online, and any third party is permitted to access, download, copy, distribute, and use these materials in any way, even commercially, with proper attribution. For these reasons, we cannot publish previously copyrighted maps or satellite images created using proprietary data, such as Google software (Google Maps, Street View, and Earth). For more information, see our copyright guidelines: http://journals.plos.org/plosone/s/licenses-and-copyright. We require you to either (1) present written permission from the copyright holder to publish these figures specifically under the CC BY 4.0 license, or (2) remove the figures from your submission: 1. You may seek permission from the original copyright holder of Figure 1 to publish the content specifically under the CC BY 4.0 license. We recommend that you contact the original copyright holder with the Content Permission Form (http://journals.plos.org/plosone/s/file?id=7c09/content-permission-form.pdf) and the following text: “I request permission for the open-access journal PLOS ONE to publish XXX under the Creative Commons Attribution License (CCAL) CC BY 4.0 (http://creativecommons.org/licenses/by/4.0/). Please be aware that this license allows unrestricted use and distribution, even commercially, by third parties. Please reply and provide explicit written permission to publish XXX under a CC BY license and complete the attached form.” Please upload the completed Content Permission Form or other proof of granted permissions as an ""Other"" file with your submission. In the figure caption of the copyrighted figure, please include the following text: “Reprinted from [ref] under a CC BY license, with permission from [name of publisher], original copyright [original copyright year].” 2. If you are unable to obtain permission from the original copyright holder to publish these figures under the CC BY 4.0 license or if the copyright holder’s requirements are incompatible with the CC BY 4.0 license, please either i) remove the figure or ii) supply a replacement figure that complies with the CC BY 4.0 license. Please check copyright information on all replacement figures and update the figure caption with source information. If applicable, please specify in the figure caption text when a figure is similar but not identical to the original image and is therefore for illustrative purposes only. The following resources for replacing copyrighted map figures may be helpful: USGS National Map Viewer (public domain): http://viewer.nationalmap.gov/viewer/ The Gateway to Astronaut Photography of Earth (public domain): http://eol.jsc.nasa.gov/sseop/clickmap/ Maps at the CIA (public domain): https://www.cia.gov/library/publications/the-world-factbook/index.html and https://www.cia.gov/library/publications/cia-maps-publications/index.html NASA Earth Observatory (public domain): http://earthobservatory.nasa.gov/ Landsat: http://landsat.visibleearth.nasa.gov/ USGS EROS (Earth Resources Observatory and Science (EROS) Center) (public domain): http://eros.usgs.gov/# Natural Earth (public domain): http://www.naturalearthdata.com/ 6. Please upload a copy of Supporting Information Figure/Table/etc. S1 Table and S2 Table which you refer to in your text on page 54. GIS Data used in figure 1 comes primarily from shapefiles we built from our own data from our analysis dataset that was collected by the USFS (now provided as supplementary info). The Alaska State Boundary Shapefile is owned by the United States Census and available for free use. The only other externally accessed GIS data would be the ArcGIS Pro World Ocean basemap. Basemaps can be used freely in academic publications as explained in ESRI online terms of use resources such as:https://doc.arcgis.com/en/arcgis-online/reference/static-maps.htm. and https://support.esri.com/en-us/knowledge-base/what-is-the-correct-way-to-cite-an-arcgis-online-basema-000012040, and through consultation with our USFS GIS specialist. In accordance with online guidelines for attribution and examples in other PlosOne publications, we added the following to the caption of Figure 1: “Alaska state boundaries shapefile produced by the United States Census Bureau was accessed from: https://www.census.gov/geographies/mapping-files/time-series/geo/carto-boundary-file.html. ESRI World Oceans Basemap accessed from: https://www.arcgis.com/home/item.html?id=67ab7f7c535c4687b6518e6d2343e8a2; Sources: Esri, GEBCO, NOAA, National Geographic, DeLorme, HERE, Geonames.org, and other contributors,” on lines 63-87 of the revised. 7. 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. We reviewed references and made a few minor changes to citation styles. Editor Specific Comments Title: • Better the short title: “Impacts of Forest Harvest Legacies on Stream Habitat in the Tongass National Forest, Alaska” Change made on lines 5-6 of the revised. Materials and Methods: • Include information about the restored and reference sites and provide details about the forests. Enhance the paper with relevant photos or illustrations that immerse the reader in the context of the forests. Additionally, incorporate more visual material related to the harvesting treatments, such as photos and illustrations. We agree that a visual illustration of stream sites in different management categories would be beneficial. Therefore, we created a three paneled map with a representative example of each treatment. We included this as the new S1 fig for now and adjusted other SFig numbers, but are open to its inclusion in the main text if the editors think it would be better placed there. We cite it in text on line 289 of the revised and add a caption as well that reads: “S1 Fig. Examples of stream sites in the “reference”, “harvested”, and “restored” management categories. Panel A shows a stream in reference condition with no riparian buffer and limited subwatershed harvest. Panel B shows a site with substantial buffer and subwatershed harvest. Panel C shows a restored site that had buffer harvest and wood was installed to help improve stream habitat conditions. Collectively, these panels illustrate the multi-storied forest condition of reference stands, the conversion to Alder dominated riparian forest post-harvest that is discussed in the paper, and it shows some installed wood pieces at restoration sites.” • Provide additional information about the stream`s characteristics and consider including a map displaying the streams or an illustrative example. We left stream lines off of the figure 1 map because the stream density in the stream network is too dense to show any meaningful information. See comment and figure example in response to comment on line 175 below. We add additional information describing the characteristics of the primary process groups and provide citations of Paustian’s classification framework and the Tongass Management plan where these are described in greater detail on lines 241-253 of the revised. The added text is: “Floodplain systems are low-gradient alluvial depositional channels, situated in valley bottoms and lowlands with high stream flows not commonly contained within the active channel banks and some degree of flood plain development is evident. The channels are predominantly composed of series of pools and riffles, with large wood the predominant pool forming mechanism. They often have more multi-threaded channels, greater sinuosity, and greater amounts of off channel habitats such as beaver ponds and sloughs [33]. The moderate gradient channels usually have channel gradients of 2-6 percent and occur near the transition between headwater streams and floodplain and alluvial fan channels. These streams usually have more confined valleys and coarser alluvial substrates ranging from gravel to boulder size comprising the channel beds and banks. Large woody debris can form log-step pools and lateral scour pools in these channels [33]. Across process groups a variety of stream channel sizes are represented ranging from channel bed widths of 1.9 to 50.1 meters.” We also provide representative photos in Figure S1. • Expand on details about the floodplain. See previous comment where floodplain and stream channels characteristics were described in greater detail. • Enhance the information on the climate dataset, for example, specifying details like pixel size and the GIS geoprocessing involved. The hydrologic classifications were developed by Sergeant et al. 2020. They classified stream flows from a complex runoff model for the Gulf of Alaska watershed that is based on a digital elevation model, landcover dataset, glacier inventory, and soil characteristics. We believe it is appropriate to add this short descriptor of the model and refer the reader to the source paper for a comprehensive presentation of the methodological details. The paper does not present the resolution of a raster model and summarizes the results to watersheds. The revised sentence reads: “To capture differences in stream habitat that could be related to hydrologic regimes, we used published hydrologic classifications of rain-dominated and snow-dominated developed for watersheds in the Gulf of Alaska based on a classification of stream flows from a complex runoff model that incorporates a digital elevation model, landcover dataset, glacier inventory, and soil characteristics” On lines 278-285 of the revised. • Relocate tables 1 and 3 to the appendixes Made change as suggested and renumbered main-text and supplemental figures and tables Statistical Analyses: • Eliminate subtitles. Deleted subtitles for statistical analyses. • Clearly explain or provide more precise indications of the statistical analyses underlying Figures 4, 5, and 6. Consider moving relevant information from table and figure captions to the statistical analysis section. We added text explaining analyses from the figure captions to statistical analysis sections as explained below. We do not believe that this information should be removed from these figure captions because figure captions should be able to stand alone with the reader being able to interpret them without consulting the methods section of the paper. Our USGS Bureau approving official requires this level of detail in figure captions. Additional explanation of marginal effects calculations that are shown in figure 4: “We calculated marginal effect sizes with our top models in order to illustrate the magnitude of expected changes in habitat metrics in response to predictor variable changes. To do this we predicted the percent change in the habitat metric response variable to a 25% change of the observed range of a given continuous management or intrinsic predictor variable while holding all other continuous predictor variables constant at their mean. For binomial predictors such as restoration status or hydroclass, we predicted a percent change in response variables from one level to the other.” on lines 364-370 of the revised. Note that Figure 4 illustrates the model results for a single response variable. We feel that it is more appropriate to explain the results and methods in the figure caption that directly corresponds to that particular variable than to explain a single model in the methods section. For explanation of the plots in figure 5 representing Attachments Attachment Submitted filename: ADPResponsetoReviewPlosOne031624.docx https://doi.org/10.1371/journal.pone.0301723.r002
22 Mar 2024 Decision Letter - Alejandro Huertas Herrera, Editor Same streams in a different forest? Investigations of forest harvest legacies and future trajectories across 30 years of stream habitat monitoring on the Tongass National Forest, Alaska PONE-D-23-40089R1 Dear Dr. Moore, 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. An invoice will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Alejandro Huertas Herrera Academic Editor PLOS ONE Additional Editor Comments (optional): Dear Michael, Thank you for addressing the revision suggestions for your manuscript and for your efforts in clarifying the issue regarding the data and code. Having thoroughly reviewed the new version of the manuscript, cover letter, response to the review file, and even the Author Query to Editor PONE-D-23-40089R1, I am confident that the paper merits publication in PLOS ONE. Please consider the following minor details: In both the manuscript and supporting information files, please add an asterisk next to Rebecca Flitcroft's name (Corresponding author): Flitcroft, R. L. 2*. In Fig 2. (line 320), please include the abbreviation "AIC" (Akaike Information Criterion). In the supporting information captions section, please ensure the following corrections: Line 1105: Add "CBW - Channel Bed Width" to the main text. Line 1110: Include "See table S1 and Table 1 for variable abbreviation explanations." Line 1112: Add "Multi Response Permutation Procedure (MRPP)." Please ensure consistency in caption information across both files. Best regards, Alejandro Reviewers' comments: https://doi.org/10.1371/journal.pone.0301723.r003
Formally Accepted
30 May 2024 Acceptance Letter - Alejandro Huertas Herrera, Editor PONE-D-23-40089R1 PLOS ONE Dear Dr. Moore, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks to review your paper and let you know the next and final steps. Lastly, if your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. If we can help with anything else, please email us at customercare@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Alejandro Huertas Herrera Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0301723.r004

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