A permutation test and spatial cross-validation approach to assess models of interspecific competition between trees

David Allen; Albert Y. Kim

doi:10.1371/journal.pone.0229930

Peer Review History

Original SubmissionSeptember 3, 2019
9 Dec 2019 Decision Letter - Jian Yang, Editor PONE-D-19-24831 A permutation test and spatial cross-validation approach to assess models of interspecies competition between trees PLOS ONE Dear Dr Allen, 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. We would appreciate receiving your revised manuscript by Jan 23 2020 11:59PM. When you are 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. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. 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Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out. We look forward to receiving your revised manuscript. Kind regards, Jian Yang 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 http://www.journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and http://www.journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2) Please upload a copy of Figure 7, to which you refer in your text on page 9. If the figure is no longer to be included as part of the submission please remove all reference to it within the text. [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 Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: 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: No Reviewer #2: 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 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: In community ecology, one of the most challenging questions in is to clarify the mechanisms of community assembly. Two theories have been widely implemented to explain species coexistence, namely niche theory and neutral theory. The most common modern metaphor of niche theory describes sub pool of species passing through environmental filters and biotic interactions (mainly competition) and then form local communities. So measuring species-specific competitive interactions is key to understanding how communities are assembled. The interspecific competitive interactions in regulating natural plant communities has been investigated in a multitude of studies that have used different methods for answering the question. Well, most studies related to species competition are manipulated experiments where density and/or the proportion of different species are varied and the biomass or fecundity of the competing species are measured. Such competition experiments are often conducted in artificial environmental conditions with a limited number of individuals in small plots. However, there has been an increasing awareness that the interspecific interactions critically depend on the abiotic and biotic setting, it is now more common to conduct ecological manipulation experiments in natural plant communities, where the density of either the neighbors (removal experiments) or the target species has been manipulated. This manuscript provides a method to measure interspecies competition between trees using repeat censured forest inventory plots’ data. Overall, I think this study is easy to read and is also timely and important within the field. However the manuscript still needs reliable English editing, especially English tense. Additionally, there are some specific suggestions as following: Comment 1: Line 26: “take” or “taken”? Comment 2: Line 38: “find” or “found”? Comment 3: The English tense problems existed in the Materials and methods section. Please confirm to keep the tenses consistent. Comment 4: Please describe the meanings or definitions of β0,j , βdbh,j and λj,k when present the Neighborhood-effect growth model. Comment 5: From the legend of Figure 3, I got that the β0,j represented the estimated baseline growth per year. Furthermore, I also got that the βdbh,j represented the estimated increase in annual growth (cm) per DBH (cm) from the legend of Figure 4. In my opinion, it would be better to change the unit in Figure 3 to be (cm/year or cm·y-1) . And what about the unit for βdbh,j ? Comment 6: Indeed, the Figure 3 and Figure 4 represented the tree growth with positive values. Whether the negative values represented negative growth due to the trees’ mortality induced by competition, disturbance (e.g. insect, wind) or senescence? Further, how to distinguish these reasons induced tree mortality? Comment 7: The Figure 5 displayed the inter-family and intra-family competitive coefficients (λ). Could the authors provide the detailed species and family information in the supporting information? Comment 8: Whether the authors could presented the phylogenetic relationships among the species occurred in the field with phylogenetic tree. If the phylogenetic tree could be provided, the authors could distinguish the families with different colors. It would be useful for authors to understand the results shown in Figure 5 from the aspect of phylogeny Comment 9: line 259-260 The result said that “There is clear spatial patterning to these residuals, with clusters of trees growing faster than the model predicts and other clusters growing slower”. I failed to understand this result shown in Figure 6. How the result shown that the clusters of trees growing faster than the model predicts and other clusters growing slower? Furthermore, what the other clusters represented for? Comment 10: The figure 7 was missed in the manuscript. Comment 11: Line 268: “found” or “find”? Comment 12: Change “illustrations” into “illustrates”. Comment 13: In the discussion section, the authors stated a limitation of neighborhood-based methods for measuring competition. So how to tackle this limitation? Reviewer #2: I enjoyed reviewing this manuscript. It is well written, concise and deals with an important topic in forest sciences. Please find attached file for especific comments, questions, and suggested edits, which I ask authors to address. ****** 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 Reviewer #2: 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 to be viewed.] 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 us at figures@plos.org. Please note that Supporting Information files do not need this step. Attachments Attachment Submitted filename: PONE-D-19-24831_reviewer.pdf https://doi.org/10.1371/journal.pone.0229930.r001
Revision 1
6 Jan 2020 Author Response Dear PLOS One Editor: Thank you for the opportunity to revise and resubmit our manuscript (PONE- D-19-24831). We also thank the reviewers for their thoughtful comments. We have addressed these comments and think that the manuscript is much stronger as a result. • The data used in this manuscript are now available on the University of Michigan data repository Deep Blue Data. They have a DOI which is linked in the article. https://doi.org/10.7302/wx55-kt18 • We have addressed the grammar and wording suggests of the reviewers. This includes making sure that the manuscript is written in the past tense. • There was no Figure 7, this was a mistake in the latex code which re- ferred to a figure that didn’t exist. We have removed this reference to the nonexistent figure. • As suggested by reviewer 1, we have added a species list (Appendix 2) and phylogenetic tree of the families in the plot (Figure S2). • We have explicitly defined the parameters — β0,j , βDBH,j , λj,k — when we introduce them in the methods section. We made interpretation of them clearer by explaining the fit values in figure legends and the results section. We clearly stated the unit of each parameter (e.g, β0,j is in cm y-1). For λj,k we discussed what it means for this parameter to be positive versus negative. • As suggested by both reviewers, we make more clear what we mean by the spatial pattern of residuals in Figure 6. • As suggested by reviewer 1, we have added some discussion on how to overcome the limitation of neighborhood-based approaches for measuring competition. • Reviewer 2 suggested that we remove the last two paragraphs from the introduction. The second to last paragraph summarized our methods and the last paragraph summarized our results. We feel that this summary of methods and results in the introduction helps the reader understand the manuscript as a whole. By giving a summary of the methods and results the reader is better able to understand as they go through the manuscript. We prefer including this end-of-introduction summary, but if the reviewers and editor feels strongly that it should be removed we will. • Reviewer 2 wanted a link to Allen et al. (2019) (line 80 of the revised manuscript). That article is currently in revisions. We think that it will December 26, 2019 be published by the time this current manuscript is published, so can be updated with final citation. If not we will provide some other access to the manuscript draft. We are happy to share a copy with the reviewer before that if requested. • We have provided justification for our use of 7.5 m as the distance for the competitive neighborhood. See lines 115–116 of the revised manuscript. • We have included the sample sizes in Figures 3 and 4. Furthermore, we have included an additional figure of the sample sizes of the focal and competitor families pairs (Figure S3); this will facilitate the interpretation of Figure 5. Thanks again for the opportunity to resubmit this manuscript. If you have any questions, do not hesitate to ask me. Attachments Attachment Submitted filename: Response to Reviewers.pdf https://doi.org/10.1371/journal.pone.0229930.r002
19 Feb 2020 Decision Letter - Jian Yang, Editor A permutation test and spatial cross-validation approach to assess models of interspecific competition between trees PONE-D-19-24831R1 Dear Dr. Allen, We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements. Within one week, you will receive an e-mail containing information on the amendments required prior to publication. When all required modifications have been addressed, you will receive a formal acceptance letter and your manuscript will proceed to our production department and be scheduled for publication. Shortly after the formal acceptance letter is sent, an invoice for payment will follow. To ensure an efficient production and billing process, please log into Editorial Manager at https://www.editorialmanager.com/pone/, click the "Update My Information" link at the top of the page, and update your user information. If you have any billing related questions, 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 enable them to help maximize its impact. If they will be preparing press materials for this manuscript, you must inform our press team as soon as possible and 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. With kind regards, Jian Yang Academic Editor PLOS ONE Additional Editor Comments: L114: Missing "of" between the word "amount" and "the". https://doi.org/10.1371/journal.pone.0229930.r003
Formally Accepted
24 Feb 2020 Acceptance Letter - Jian Yang, Editor PONE-D-19-24831R1 A permutation test and spatial cross-validation approach to assess models of interspecific competition between trees Dear Dr. Allen: I am pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please notify them about your upcoming paper at this point, to enable them to help maximize its impact. If they will be preparing press materials for this manuscript, 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. For any other questions or concerns, please email plosone@plos.org. Thank you for submitting your work to PLOS ONE. With kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Jian Yang Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0229930.r004

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