Populations of arable weed species show intra-specific variability in germination base temperature but not in early growth rate

Jana Bürger; Andrey V. Malyshev; Nathalie Colbach

doi:10.1371/journal.pone.0240538

Peer Review History

Original SubmissionMay 30, 2020
14 Jul 2020 Decision Letter - Shahid Farooq, Editor PONE-D-20-16133 Arable weed species show local adaptation in germination base temperature but not in seedling growth rate PLOS ONE Dear Dr. Bürger, 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. ============================== ACADEMIC EDITOR: I have now had time to evaluate the reports submitted by 2 referees on your submitted manuscript. Both the referees think that your work is worth publishing; however, suggested MAJOR revisions. For example, both referees think that the data of France can be excluded from the manuscript for easier readability of the manuscript. Nonetheless, the current version contradicts with the hypothesis. I suggest to use same populations (at least include in the manuscript) for both traits studied in the manuscript. Revise your manuscript carefully in the light of the comments. I look forward to receive your revised manuscript. ============================== Please submit your revised manuscript by Aug 28 2020 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. 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Kind regards, Shahid Farooq, Ph.D. 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. Please ensure that you refer to Figure 4 in your text as, if accepted, production will need this reference to link the reader to the figure. 3. Please include a copy of Table 5 which you refer to in your text on line 288. [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: No ****** 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 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: Generally, a good research has been done to provide useful information on the germination of some important weeds, especially in Germany. There were some problems with the material and the method, which I wrote in the main file of manuscript. My most important suggestion is to exclude the experiment in France from manuscript and only present the results of the experiment in Germany, which is due to the following two cases. First of all, the complexity of the article is lessened and it is easier for the reader to understand it. Secondly, the repetition has not been done properly. Therefore, after deleting the results of the French experiments and re-analyzing the data, manuscript should be resubmitted That's why I didn't check the results section because it really causes headaches. Reviewer #2: I have evaluated the manuscript PONE-D-20-16133 submitted by Bürger et al. Overall it is an interesting study which would contribute towards the development of Weed Ecology. There are several major flaws which need to be addressed before the manuscript can be published. I am interested to review the revised version of the manuscript. 1. I suggest to exclude the results for French side due to 2 reasons. First, it seems that you are doing inter-specific variaiton studies and secondly it makes the manuscript complex. Keep it simple and include only results from Germany. 2. There are different number of species in both studied traits. Is it possible to balance and further possible to include same species for both traits? 3. There is no info in MM which constant temperatures were used. 4. Results and discussion are too long. Please reduce them by 50% 5. Restate conclusion based on the revised statistical analysis. Please see attached file for other comments. ****** 6. 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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.0240538.r001
Revision 1
24 Sep 2020 Author Response Dear Shahid Farooq, we have now had time to revise our manuscript according to your recommendations as well as the reviewers’ comments. We have changed the title, taken strong efforts to increase the readability, and edited minor errors. We would like to answer to the main comments within this letter. Other comments are answered in the annotated versions of the reviewer’s pdfs. 1.) Editor’s Recommendations: For example, both referees think that the data of France can be excluded from the manuscript for easier readability of the manuscript. -> Omitting the data from France would mean to omit the intra-specific trait variability between seed populations. As the aim of the analysis is explicitly to look at this kind of variability it does not seem practical to just use German data. The question of readability arose due to the length of the manuscript, particularly results section. Could you please condense the results keeping the results of both regions, i.e., Germany and France for improving the readability for a layman? I guess this will solve the issue and comment of both reviewers regarding exclusion of France from the analysis. -> The results section was shortened, for example by moving Table 5 to the Supporting Material. Nonetheless, the current version contradicts with the hypothesis. Regarding the hypothesis issue, the possible solution could be to change the title a bit, which can be reflective of both intra and inter-population variation. -> Our results indeed contradicted the hypothesis, which should happen fairly regularly in research. We chose a new title to the manuscript and included “intra-specific variability”. I suggest to use same populations (at least include in the manuscript) for both traits studied in the manuscript. -> Do you suggest to use the same sets of species for analysis of the two experiments? Unfortunately, this would diminish the data base for the analyses a lot. Both experiments were quite different in their resource requirements (room, time, timing, seed numbers). The base temperature experiment is also more prone to errors and failures than the growth rate experiment. Therefore, we could handle a much lower number of species in the base temperature experiment than in the growth rate experiment. -> Although the larger set of species in the growth rate analysis may be irritating at first, it increases the power of the analysis: even though we have 21 contrasting species in the analysis, we find no general evidence for local adaptation in this trait. On the other hand, local adaptation in base temperature is evident even when we only look at 6 species. Please ensure that you refer to Figure 4 in your text as, if accepted, production will need this reference to link the reader to the figure. -> Reference was included. Please include a copy of Table 5 which you refer to in your text on line 288. -> Table 5 was moved to supporting Material, and reference changed accordingly. 2.) Reviewer # 1 There were some problems with the material and the method, which I wrote in the main file of manuscript. -> see comments there. My most important suggestion is to exclude the experiment in France from manuscript and only present the results of the experiment in Germany, which is due to the following two cases. First of all, the complexity of the article is lessened and it is easier for the reader to understand it. -> please see comment to Editor regarding exclusion of French data. -> We thoroughly revised the manuscript, mainly in the Materials and Methods section, subsection on statistical analysis to clarify and make reading easier. Secondly, the repetition has not been done properly. -> A paragraph was included explaining that our study is not based on a repeated experimental design, but rather uses advanced statistical methods to account for any problems of combining data from different sources. Therefore, after deleting the results of the French experiments and re-analyzing the data, manuscript should be resubmitted That's why I didn't check the results section because it really causes headaches. 3.) Reviewer #2 I have evaluated the manuscript PONE-D-20-16133 submitted by Bürger et al. Overall it is an interesting study which would contribute towards the development of Weed Ecology. There are several major flaws which need to be addressed before the manuscript can be published. I am interested to review the revised version of the manuscript. 1. I suggest to exclude the results for French side due to 2 reasons. First, it seems that you are doing inter-specific variaiton studies -> Our analysis contains both inter-specific and intra-specific variability. Especially for the growth rate experiment, this gives more power to our analysis: on one hand we can show that there is little intra-specific difference between French and German populations of the same species; on the other hand, we can show that we used a wide set of contrasting species. Finally, we could show that the inter-specific variation even within each region is three times higher than the intra-specific variation for any of the single species. and secondly it makes the manuscript complex. Keep it simple and include only results from Germany. -> please see comment to Editor regarding exclusion of French data. 2. There are different number of species in both studied traits. Is it possible to balance and further possible to include same species for both traits? -> please see comment to editor for the same suggestion 3. There is no info in MM which constant temperatures were used. -> This information was included in the Supporting Material because it is a lot of detail. We added a reference to the appropriate table within the M&M text. 4. Results and discussion are too long. -> We revised the whole manuscript, aiming at a concise language and discussion, but with necessary detail regarding that experiments and analysis are complex. The discussion was shortened by 15%, some tables transferred to the supporting information. Overall, the manuscript now has less than 8000 words (including all references). 5. Restate conclusion based on the revised statistical analysis. -> The intended analysis is not possible without the data from France. We therefore would like to keep the French data as well as the conclusion. Lastly, we were asked by the editorial office to explain the abbreviation INRAE, the institution of our co-Author Nathalie Colbach. INRAE is short for Institut national de recherche pour l’agriculture, l’alimentation et l’environnement. We hope we could answer to all problems and hope to receive a positive vote to publish our article in its revised form. Thank you very much. On behalf of all authors, Jana Bürger Attachments Attachment Submitted filename: PONE-D-20-16133_reviewer2_Response.pdf https://doi.org/10.1371/journal.pone.0240538.r002
29 Sep 2020 Decision Letter - Shahid Farooq, Editor Populations of arable weed species show intra-specific variability in germination base temperature but not in early growth rate PONE-D-20-16133R1 Dear Dr. Bürger, 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 for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. 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 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, Shahid Farooq, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): I have now gone through the revised manuscript. I commend authors for thoroughly revising their manuscript and addressing all comments. The current version can be accepted for publication in Plos One. Reviewers' comments: https://doi.org/10.1371/journal.pone.0240538.r003
Formally Accepted
1 Oct 2020 Acceptance Letter - Shahid Farooq, Editor PONE-D-20-16133R1 Populations of arable weed species show intra-specific variability in germination base temperature but not in early growth rate Dear Dr. Bürger: I'm 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 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 plosone@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. Shahid Farooq Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0240538.r004

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