Estimation of true dates of various flowering stages at a centennial scale by applying a Bayesian statistical state space model

Nagai Shin; Hakuryu Fujiwara; Shinjiro Sugiyama; Hiroshi Morimoto; Taku M. Saitoh

doi:10.1371/journal.pone.0317708

Peer Review History

Original SubmissionAugust 24, 2024
19 Nov 2024 Decision Letter - Bahram Heidari, Editor PONE-D-24-36692Estimation of true dates of various flowering stages at a centennial scale by applying a Bayesian statistical state space modelPLOS ONE Dear Dr. Shin, 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 Jan 03 2025 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. Please include the following items when submitting your revised manuscript: 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'. 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'. 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, Bahram Heidari Academic Editor PLOS ONE Journal Requirements: 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 2. Thank you for stating the following financial disclosure: [NS was supported by a KAKENHI grant (JSPS 21H05178) from the Japan Society for the Promotion of Science. https://www.jsps.go.jp/english/e-grants/index.html This grant supported our activities regarding data collection and preparation of the manuscript.]. Please state what role the funders took in the study. If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. 3. Thank you for stating the following in the Acknowledgments Section of your manuscript: [This study was supported by a KAKENHI grant (JSPS 21H05178) from the Japan Society for the Promotion of Science.] We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: [NS was supported by a KAKENHI grant (JSPS 21H05178) from the Japan Society for the Promotion of Science. https://www.jsps.go.jp/english/e-grants/index.html This grant supported our activities regarding data collection and preparation of the manuscript.]. Please include your amended statements within your cover letter; we will change the online submission form on your behalf. 4. In the online submission form, you indicated that [Insert text from online submission form here]. 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. 5. We note that you have referenced (unpublished) on pages 4 and 14, which has currently not yet been accepted for publication. Please remove this from your References and amend this to state in the body of your manuscript: (ie “Bewick et al. [Unpublished]”) as detailed online in our guide for authors http://journals.plos.org/plosone/s/submission-guidelines#loc-reference-style [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: This is an excellent empirical study of Bayesian state space modelling. I really enjoyed the detail and the use of novel validation data to demonstrate how this class of modelling can improve the predictive accuracy. Generally the narrative is well written and draws the reader into the problem and the approach. The statistical detail is sufficient for me as a reader with no prior experience with these specific models but who uses other forms of times series data to build predictive models. The results are quite compelling. While the embedded figures are grainy the downloaded .tiff images are excellent and helpful in showing how the validation improves the accuracy. It is an unusual in that is takes it data from phenology data from one single individual tree measure over many decades. The obvious question is why the authors kept the significance of the study merely around the modelling approach rather what the data are used for. I got the sense that the authors were trying to break up the study into one technical description of the methodology (this one) and another (not seen) about the significance of the changes in phenology and what these trends signify in and era where climate change is affection many facets of the life science... especially ecology, evolution and agricultural sciences. I think this is a mistake and missed opportunity. I would like a revision to include how this modelling approach helps us understand the temporal changes in this tree's phenology and what the significance this has for understanding more widespread changes in flower timing under climate change. This obviously has not escaped the authors attention but partitioning the methods and the significance is curious awkward. ****** 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". 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. https://doi.org/10.1371/journal.pone.0317708.r001
Revision 1
17 Dec 2024 Author Response Journal requirements: Requirement 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 Answer: We have checked it. Requirement 2: Thank you for stating the following financial disclosure: [NS was supported by a KAKENHI grant (JSPS 21H05178) from the Japan Society for the Promotion of Science. https://www.jsps.go.jp/english/e-grants/index.html This grant supported our activities regarding data collection and preparation of the manuscript.]. Please state what role the funders took in the study. If the funders had no role, please state: “The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.” If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. Answer: We have removed the “Funding statement section” in the main text. Requirement 3: Thank you for stating the following in the Acknowledgments Section of your manuscript: [This study was supported by a KAKENHI grant (JSPS 21H05178) from the Japan Society for the Promotion of Science.] We note that you have providedfunding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: [NS was supported by a KAKENHI grant (JSPS 21H05178) from the Japan Society for the Promotion of Science. https://www.jsps.go.jp/english/e-grants/index.html This grant supported our activities regarding data collection and preparation of the manuscript.]. Please include your amended statements within your cover letter; we will change the online submission form on your behalf. Answer: We have revised the Acknowledgments section as follows. In addition, please see the answer for your second query. Acknowledgement We are grateful to the editors and reviewers for their constructive comments. Requirement 4: In the online submission form, you indicated that [Insert text from online submission form here]. 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. Answer: We want to publish the part of observation records (without the copyright issue). Therefore, we have revised lines 117−120 and updated the supplementary file (csv). “Observation records, which were converted to the day of year (DOY) for analysis, in literature, photographs, and the private collection of Hakuryu Fujiwara are listed in the Supplementary file (flowering_phenology_records_Neodani_Usuzumizakura.csv).” Requirement 5: We note that you have referenced (unpublished) on pages 4 and 14, which has currently not yet been accepted for publication. Please remove this from your References and amend this to state in the body of your manuscript: (ie “Bewick et al. [Unpublished]”) as detailed online in our guide for authors http://journals.plos.org/plosone/s/submission-guidelines#loc-reference-style Answer: We have revised as follows. Lines in 108−109: “a photograph in 1930 [33], and unpublished data of Motosu City from 1981 to 1988 (Motosu City, unpublished)” Lines in 475−476: “unpublished data of Motosu City [Motosu City {Unpublished}])” Reviewers’ comments: Reviewer 1: This is an excellent empirical study of Bayesian state space modelling. I really enjoyed the detail and the use of novel validation data to demonstrate how this class of modelling can improve the predictive accuracy. Generally the narrative is well written and draws the reader into the problem and the approach. The statistical detail is sufficient for me as a reader with no prior experience with these specific models but who uses other forms of times series data to build predictive models. The results are quite compelling. While the embedded figures are grainy the downloaded .tiff images are excellent and helpful in showing how the validation improves the accuracy. It is an unusual in that is takes it data from phenology data from one single individual tree measure over many decades. The obvious question is why the authors kept the significance of the study merely around the modelling approach rather what the data are used for. I got the sense that the authors were trying to break up the study into one technical description of the methodology (this one) and another (not seen) about the significance of the changes in phenology and what these trends signify in and era where climate change is affection many facets of the life science... especially ecology, evolution and agricultural sciences. I think this is a mistake and missed opportunity. I would like a revision to include how this modelling approach helps us understand the temporal changes in this tree’s phenology and what the significance this has for understanding more widespread changes in flower timing under climate change. This obviously has not escaped the authors attention but partitioning the methods and the significance is curious awkward. Answer: Thank you for your efforts to improve our paper. In accordance with your and editors’ kind and constructive comments, we have revised the manuscript. In addition, we have re-checked all data and revised some minor points and Figs. 2 and 5 (we recalculated Fig. 5). There is no essential problem in these revisions. We will publish the part of observation records (without the copyright issue). As for your significant comment (you may have clairvoyant abilities), we have revised the third paragraph in the Discussion section as follows (lines 281−303). “The mean air temperature on the date of FFL was lower in a climatic region with a low annual mean air temperature than in one with a high annual mean air temperature [44]. This indicates a low cumulative heat requirement for the growth of flower buds in a climatic region where the chilling requirement for release from endodormancy can be met. In addition, in Hachijojima (33°06′44′′N, 139°47′01′′E), at the southern distribution limit of the full bloom of Yoshino cherry, in years when the chilling requirement for release from endodormancy was not met, the growth of flower buds had a greater heat requirement, and the FFL date tended to be delayed [45]. These facts indicate that the FFL date at a given site in a given year is determined by the balance between the chilling requirement for release from endodormancy and the heat requirement for the growth of flower buds. Therefore, in a region where cherry flowering phenology is strongly affected by global warming, the values of the coefficients β1t and γ1t (in Eq. 4) may change on decadal to centennial time scales. Unlike conventional statistical phenology models which give time-invariant constant coefficients, the proposed Bayesian statistical state space model can evaluate temporal changes in the values of coefficients β1t and γ1t (in Eq. 4). In Japan, weather stations began modern meteorological observations in the late 19th century [43], and since 1953 have recorded the dates of FFL and FFB of Yoshino cherry by standardized observations [46]. In addition, unstandardized records of the dates of FFL and FFB, which might include uncertainty due to visual inspection, can be traced back to the beginning of the 20th century at several weather stations [5−7]. By applying the proposed Bayesian statistical state space model to these data at multiple points across a wide area at a centennial scale, we can detect the spatiotemporal characteristic of the coefficients β1t and γ1t (in Eq. 4). This analysis will provide useful evidence for an understanding of the sensitivity and resilience of cherry flowering phenology to climate change. [45] Shin N, Saitoh TM, Takasu H, Morimoto H. Influence of climate change on flowering phenology of Yoshino cherry at its southern distribution limit. Int J Biometeorol 2024; https://doi.org/10.1007/s00484-024-02797-0” https://doi.org/10.1371/journal.pone.0317708.r002
3 Jan 2025 Decision Letter - Bahram Heidari, Editor Estimation of true dates of various flowering stages at a centennial scale by applying a Bayesian statistical state space model PONE-D-24-36692R1 Dear Dr. Shin, 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, Bahram Heidari Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0317708.r003
Formally Accepted
14 Jan 2025 Acceptance Letter - Bahram Heidari, Editor PONE-D-24-36692R1 PLOS ONE Dear Dr. Shin, 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. Bahram Heidari Academic Editor PLOS ONE Attachments Attachment Submitted filename: pone.0317708.docx https://doi.org/10.1371/journal.pone.0317708.r004

Open letter on the publication of peer review reports

PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.

We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.

Learn more at ASAPbio .