Woody species diversity, structure and community distribution along environmental gradients of Seqela Dry Afromontane forest in Northwestern Ethiopia

Liyew Birhanu; Getaneh Moges; Nigussie Amsalu; Heiko Balzter

doi:10.1371/journal.pone.0313020

Peer Review History

Original SubmissionFebruary 13, 2024
27 Feb 2024 Decision Letter - Faham Khamesipour, Editor PONE-D-24-05897Plant community distribution along environmental gradient of Seqela Dry Afromontane Forest in Northwestern EthiopiaPLOS ONE Dear Dr. Birhanu, 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: The paper needs a major revision.============================== Please submit your revised manuscript by Apr 12 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. 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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: Partly 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: 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: Manuscript Number: PONE-D-24-05897 Plant community distribution along environmental gradient of Seqela Dry Afromontane Forest in Northwestern Ethiopia PLOS ONE General comments The research work presents interesting results but the manuscript needs to improve the comments provided below. Botanical methods of plant species identification and deposition herbarium with voucher numbers are not clearly stated and need to be addressed before any further consideration. Furthermore, the title needs to be rethought. In the current state, it is not very informative. Specific comments: Title: I would suggest that your title needs to be modified in a way that it should accurately describe the contents of your manuscript. Because the phrase “Plant community distribution along environmental gradient” is not inclusive but rather a single part of your paper. Abstract Line 2: “human population growth” is an equivocal reason even if it will be an umbrella driver for the anthropogenic factors mentioned formerly. Line 7: “100 m”, is it altitudinal or geographical distance? Line 12: “A total of 68 woody plant species”, why not include herbaceous species according to your title? Line 14: Replace “Prunus Africana” with “Prunus africana” see in Table 3. Additionally, check the revised taxonomic name of “Acacia abyssinica”? Keywords/phrases: I would suggest to the authors that it is better to focus on specific and relevant words to your content rather than broad and generic long phrases like “Canonical Correspondence Analysis, Hierarchical cluster analysis”. Introduction In paragraph 1, the first two statements: The authors wrote the role of plant resources in the Ethiopian context but cited unrelated authors (Fraticelli et al., 2013)? Lack of connectivity and flow of ideas between statements such as hypotheses and objectives. Methodology Study area See the legend in your map and the caption here: “Figure 1. Sekela forest is located in the Quarit district of West Gojjam Zone, Amhara Region in Ethiopia” Which is correct “Sekela” or Seqela”? “Sekela Forest is categorised as dry evergreen Afromontane Vegetation”, this needs to be rephrased because it contradicts with demonstration of the cliamadiagram in Figure 2. Be consistent in your reference citation… See “Friis et al. (2010)” … “(Asaminew Tassew et al., 2011)”. What is your reason for your selection of the sub quadrats 5 × 5 m2 for the collection of seedling and sapling plants? Vegetation data collection I find the sampling design rather vague. Botanical methods, typically herbarium procedure are missed out. Data Analysis Plant community classification There is a mix of information herein: “agglomerative hierarchical cluster analysis”? In your result section: “Based on the hierarchical cluster analysis performed in the study area, four plant community types were identified (Figure 3).” Where is the anthropogenic factor analysis, which has been mentioned as a major threatening factor? Diversity and similarity indices Diversity is okay but where is the similarity index? Results Line 3: Replace “Cobretum molle” with “Combretum molle” Plant community types Replace “Ekebergia.capensis” with “Ekebergia capensis” “Figure 3. Dendrogram”, here is my big question why not 2 types or three community types or else? Because the author did not show the value of the cophenetic correlation coefficient where they determined the cutree. Community type I. Replace “Olea europaea subsp. Cuspidate” with “Olea europaea subsp. cuspidata” Community type II “Phytolacca dodecandra were dominant dodecandra” needs to be revised. Similarity among community types in the Sekela Forest “To find the differences in species composition between the four community types, Sorensen's similarity coefficient (Ss) was calculated.” My concern here: I did not see this part in the method section. Figures 3, 4 and 5 need to increase their resolutions. References Please correct the font type “Alelign A , Teketay D, Yemshawy, & Sue Edwards (2007)”. Reviewer #2: The following suggestions may help to improve the quality of the Ms. further. Overall, the title clearly reflects the contents. The introduction does establish the existing state of knowledge but needs minor revision as suggested. Authors should add the knowledge gap at the end of the introduction with proper citations. The set of measurements was comprehensive. Discussion part needs revision as suggested in the text. The conclusion needs concreteness. Do not repeat the results in the conclusions. Figure 5 needs proper drawing (reduce the size appropriately) The citations need up-dated. English needs improvement. I have made more corrections and suggestions directly in the manuscript. Please revise the paper accordingly. ****** 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. 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Revision 1
1 Apr 2024 Author Response Manuscript number: PONE-D-24-05897 Title: Plant community distribution along environmental gradient of Seqela Dry Afromontane Forest in Northwestern Ethiopia Journal Name: PLOS ONE Article type: Research Paper We would like to thank the reviewers for their efforts in reviewing the manuscript and providing valuable suggestions for improving the article. All comments and suggestions were addressed. The changes are marked in yellow color as shown in the revised manuscript. We detailed response for each comment is provided below. Editor Dear Dr. Birhanu, 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: The paper needs a major revision. Author’s Response: Thanks a lot for letting us revise our paper. Below are the responses to all reviewer comments. Reviewer #1: General comments 1. The research work presents interesting results but the manuscript needs to improve the comments provided below. Botanical methods of plant species identification and deposition herbarium with voucher numbers are not clearly stated and need to be addressed before any further consideration. Furthermore, the title needs to be rethought. In the current state, it is not very informative. Author’s Response: Thanks a lot for this positive feedback. We are sorry that some of the information about Botanical methods of plant species identification and deposition herbarium was not included, and we have improved this in the revised manuscript. Specific comments: 2. Title: I would suggest that your title needs to be modified in a way that it should accurately describe the contents of your manuscript. Because the phrase “Plant community distribution along environmental gradient” is not inclusive but rather a single part of your paper. 3. Author’s Response: We appreciate the reviewer observation. The title was corrected as Woody species diversity, Vegetation structure and Plant community distribution along environmental gradients of Seqela Dry Afromontane Forest in Northwestern Ethiopia Abstract 4. Line 2: “human population growth” is an equivocal reason even if it will be an umbrella driver for the anthropogenic factors mentioned formerly. Author’s Response: Thank you for this suggestion. 5. Line 7: “100 m”, is it altitudinal or geographical distance? 6. Line 14: Replace “Prunus Africana” with “Prunus africana” see in Table 3. Additionally, check the revised taxonomic name of “Acacia abyssinica”? Author’s Response: Again, we appreciate the reviewer observation reviewer. We have corrected the genus Acacia to Vachellia in the revised version of the manuscript.We have corrected as Vachellia abyssinica 7. /phrases: I would suggest to the authors that it is better to focus on specific and relevant words to your content rather than broad and generic long phrases like “Canonical Correspondence Analysis, Hierarchical cluster analysis”. Author’s Response: Thanks for this suggestion and improved clarity of the paper in the revised document. Introduction 8. In paragraph 1, the first two statements: The authors wrote the role of plant resources in the Ethiopian context but cited unrelated authors (Fraticelli et al., 2013) Author’s Response: Thank you for this suggestion. Methodology Study area 9. See the legend in your map and the caption here: “Figure 1. Sekela forest is located in the Quarit district of West Gojjam Zone, Amhara Region in Ethiopia” Which is correct “Sekela” or Seqela”? Author’s Response: Seqela is the correct one.The correction has been made in the revised manuscript 10. Seqela Forest is categorised as dry evergreen Afromontane Vegetation”, this needs to be rephrased because it contradicts with demonstration of the cliamadiagram in Figure 2. Author’s Response:Olea europaea subsp. cuspidata, Juniperus procera, and Podocarpus falcatus are indicator species to the dry Afromontane forest. Therefore, Olea europaea subsp. Cuspidate species is found in the Seqela forest. Actually the vegetation type classification based on elevation, climate and indicator species…. Thus it is categorised as dry evergreen Afromontane forest and grassland complex (DAF). 11. Be consistent in your reference citation… See “Friis et al. (2010)” … “(Asaminew Tassew et al., 2011)”. Author’s Response: Thank you very much for your excellent observation. We have corrected any inconsistency written of reference citation Vegetation data collection 12. I find the sampling design rather vague. Botanical methods, typically herbarium procedure are missed out. Author’s Response: Thanks for this suggestion and improved clarity of the paper in the revised manuscript. Data Analysis Plant community classification 13. There is a mix of information herein: “agglomerative hierarchical cluster analysis”? In your result section: “Based on the hierarchical cluster analysis performed in the study area, four plant community types were identified (Figure 3).” Author’s Response: Agglomerative hierarchical cluster analysis. We have corrected the inconsistency writing of this word. 14. Where is the anthropogenic factor analysis, which has been mentioned as a major threatening factor? Author’s Response: No anthropogenic data collection and analysis in our study. Diversity and similarity indices 18. Diversity is okay but where is the similarity index? Author’s Response: We have added the information in the method section of revised manuscript. Results 19. Line 3: Replace “Cobretum molle” with “Combretum molle” Author’s Response: Corrected in the revised manuscript. Plant community types 20. Replace “Ekebergia.capensis” with “Ekebergia capensis” Author’s Response: Corrected in the revised manuscript. 21. “Figure 3. Dendrogram”, here is my big question why not 2 types or three community types or else? Because the author did not show the value of the cophenetic correlation coefficient where they determined the cutree. Author’s Response: We appreciate the reviewer observation. We agree that before doing cluster analysis, we need to determine the optimum cluster number (K). Among the methods we use to decide the optimum cluster are Elbow, silhouette, gap statistics and K-means partitioning using cascadeKM (calinski) and Similarity Ratio. We have access to scripts for each method. We tried to check the matrified vegetation data with elbow method and simple visual observation during the field work. Accordingly, we have done full analysis and found 4 plant community types. BTW, methods use to decide the optimum cluster alone may not show a clear classification. So visual observation during the field work also helps. Community type I. Replace “Olea europaea subsp. Cuspidate” with “Olea europaea subsp. cuspidata” Author’s Response: corrected in the revised manuscript. Community type II “Phytolacca dodecandra were dominant dodecandra” needs to be revised. Author’s Response: corrected Similarity among community types in the Seqela Forest “To find the differences in species composition between the four community types, Sorensen's similarity coefficient (Ss) was calculated.” My concern here: I did not see this part in the method section. Author’s Response: We have added the information in the method section of revised manuscript Figures 3, 4 and 5 need to increase their resolutions. Author’s Response: We have tried to clearly drown and describe the caption of the figure under the diagram and check the revised manuscript. References Please correct the font type “Alelign A , Teketay D, Yemshawy, & Sue Edwards (2007)”. Author’s Response: The correction has been made in the revised manuscript Reviewer #2: The following suggestions may help to improve the quality of the Ms. further. Overall, the title clearly reflects the contents. The introduction does establish the existing state of knowledge but needs minor revision as suggested. Authors should add the knowledge gap at the end of the introduction with proper citations. The set of measurements was comprehensive. Discussion part needs revision as suggested in the text. The conclusion needs concreteness. Do not repeat the results in the conclusions. Figure 5 needs proper drawing (reduce the size appropriately).The citations need up-dated. English needs improvement. I have made more corrections and suggestions directly in the manuscript. Please revise the paper accordingly. Please note that Introduction should be started with the general statement not by specific first. As it is an International paper and will be viewed by international audience not only by Ethiopian’s. Author’s Response: Thank you for your efforts in reviewing the manuscript and providing valuable suggestions for improving the article. You have corrected many things of our manuscript. We have tried to clearly correct the manuscript and check the revised manuscript. Attachments Attachment Submitted filename: Point by point response to the Reviewer Comments_PLOS ONE.docx https://doi.org/10.1371/journal.pone.0313020.r002
4 Apr 2024 Decision Letter - Faham Khamesipour, Editor PONE-D-24-05897R1Woody species diversity, Vegetation structure and Plant community distribution along environmental gradients of Seqela Dry Afromontane Forest in Northwestern EthiopiaPLOS ONE Dear Dr. Birhanu, 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. The authors have appropriately revised the manuscript and answered all the questions of the reviewers satisfactorily. I recommend the revised version of the manuscript be accepted for publication in PLOS One after minor revision. Please submit your revised manuscript by May 19 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. 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'. 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Kind regards, Faham Khamesipour, Ph.D. Academic Editor PLOS ONE Journal Requirements: 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: The authors have appropriately revised the manuscript and answered all the questions of the reviewers satisfactorily. I recommend the revised version of the manuscript be accepted for publication in PLOS One after minor revision. [Note: HTML markup is below. Please do not edit.] 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 ******** 2. 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 ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes ****** 4. 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 ****** 5. 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 ****** 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: Manuscript Number: PONE-D-24-05897R1 Woody species diversity, Vegetation structure and Plant community distribution along environmental gradients of Seqela Dry Afromontane Forest in Northwestern Ethiopia PLOS ONE General comments The authors have satisfactorily addressed the majority of my concerns and comments, although some minor ones still need to be addressed. Title: It needs minor revision “Woody species diversity, structure, and community distribution along environmental gradients of Seqela Dry Afromontane Forest in Northwestern Ethiopia” Introduction In paragraph 2, replace “[25; 26]” with “[25, 26]. “… environmental factors [e.g. 27- 31]” please restate this statement. Additionally, use proper punctuation and writing techniques throughout your paper such as, replace “27- 31” with “27–31”. Methodology Study area Paragraph 2 replace “Eragrostis teff” with “Eragrostis tef”. Data Analysis Plant community classification ##There is a mix of information herein: “agglomerative hierarchical cluster analysis”? Select either “agglomerative cluster analysis” or “hierarchical cluster analysis” with acceptable reason. ##The author did not give sufficient response for this question raised in the first draft. Results Plant community types ## “Figure 3. Dendrogram”, here is my big question why not 2 types or 3 community types or else? Because the author did not show the value of the cophenetic correlation coefficient where they determined the cutree. ##The author did not give sufficient response for this question raised in the first round of review rather they replied very subjective suggestions. Reviewer #2: Dear Author(s) Thank you for submitting the revised manuscript. You have appropriately revised the manuscript and answered all the questions of the reviewers satisfactorily. I recommend the revised version be accepted for publication in PLOS One. ****** 7. 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.] 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. Attachments Attachment Submitted filename: PONE-D-24-05897R1.docx https://doi.org/10.1371/journal.pone.0313020.r003
Revision 2
6 Apr 2024 Author Response Manuscript Number: PONE-D-24-05897R2 Woody species diversity, Vegetation structure and Plant community distribution along environmental gradients of Seqela Dry Afromontane Forest in Northwestern Ethiopia PLOS ONE Article type: Research Paper We would like to thank the reviewers for their efforts in reviewing the manuscript and providing valuable suggestions for improving the article. All comments and suggestions were addressed. The changes are marked in yellow color as shown in the revised manuscript. We detailed response for each comment is provided below. Editor The authors have appropriately revised the manuscript and answered all the questions of the reviewers satisfactorily. I recommend the revised version of the manuscript be accepted for publication in PLOS ONE after minor revision. Author’s Response: Thanks a lot for letting us revise our paper. Below are the responses to a reviewer one comments. Reviewer #1: 1. General comments The authors have satisfactorily addressed the majority of my concerns and comments, although some minor ones still need to be addressed. Author’s Response: Thanks a lot for this very positive feedback. 2. Title: It needs minor revision “Woody species diversity, structure, and community distribution along environmental gradients of Seqela Dry Afromontane Forest in Northwestern Ethiopia” Author’s Response: Thank you for this. 3. In paragraph 2, replace “[25; 26]” with “[25, 26]. “… environmental factors [e.g. 27- 31]” please restate this statement. Additionally, use proper punctuation and writing techniques throughout your paper such as, replace “27- 31” with “27–31”. Author’s Response: The correction has been made in the revised manuscript. 4. Study area Paragraph 2 replaces “Eragrostis teff” with “Eragrostis tef”. Author’s Response: Thank you very much for your excellent observation. We have corrected in the revised version of the manuscript. Data Analysis Plant community classification ##There is a mix of information herein: “agglomerative hierarchical cluster analysis”? Select either “agglomerative cluster analysis” or “hierarchical cluster analysis” with acceptable reason. ##The author did not give sufficient response for this question raised in the first draft. Author’s Response: Based on your previous comment, we have corrected it as “agglomerative hierarchical cluster analysis”. Let's clarify this comment. Cluster analysis in ecology is a statistical method used to classify objects (such as species, communities, or individuals) into groups or clusters based on similarity. There are several types of cluster analysis techniques commonly used in ecology. Basically the methods of cluster analysis fall into hierarchical and non-hierarchical (partitioning) techniques. 1. Hierarchical clustering � Hierarchical clustering is an assembling technique of vegetation stands that could be classified into groups, the processes being repeated at different levels to form a tree. � There are two types of hierarchical clustering methods, namely agglomerative and divisive. A. Agglomerative hierarchical clustering: It starts with each object as a separate cluster and then iteratively merges the closest clusters until only one cluster remains. called “bottom up method”, construct a tree-like hierarchy, B. Divisive Hierarchical Clustering : Divisive hierarchical clustering method is the opposite of agglomerative classification in that the clustering start at the top and work downwards, beginning with the whole collection of plots, and dividing them to form successive subclasses and ultimately form a more or less similar groups. This method is not too common method for plant classification. • Agglomerative Hierarchical Clustering is often preferred for plant community classification because it starts with individual data points and progressively groups them together based on similarity, mirroring the natural progression of plant community formation where individual plants come together to form larger groupings. This approach aligns well with the hierarchical structure often observed in plant communities, making it a suitable method for classification. 2. Partitioning (non-hierarchical clustering): Partitioning is a method of classifying vegetation stands in the same level, not in hierarchy ( eg. K- means clustering, Fuzzy clustering). Results Plant community types ## “Figure 3. Dendrogram”, here is my big question why not 2 types or 3 community types or else? Because the author did not show the value of the cophenetic correlation coefficient where they determined the cutree. The author did not give sufficient response for this question raised in the first round of review rather they replied very subjective suggestions. Author’s Response: Again, Let's clarify this comment. The cophenetic correlation coefficient can be used as some kind of measure of the goodness of fit of a particular dendrogram. Based on the agglomerative hierarchical cluster analysis performed in the study area, four plant community types were identified. The cophenetic correlation coefficient reached a value of 0.774, indicating a considerable degree of similarity in the classification. This information included in the revised manuscript. Figure 3. Dendrogram”, here is my big question why not 2 types or 3 community types or else? Author’s Response: we appreciate you raising this question. I (corresponding author) frequently inquire about this question when examining the students or reviewing manuscripts. Determining the number of groups in a cluster analysis is often the primary goal. Among the methods we used to decide the optimum cluster is Elbo method, finally we have got 4 plant community types. Attachments Attachment Submitted filename: Point by point response to the Reviewer Comments__R2.docx https://doi.org/10.1371/journal.pone.0313020.r004
19 Jun 2024 Decision Letter - Faham Khamesipour, Editor PONE-D-24-05897R2Woody species diversity,structure and community distribution along environmental gradientsof Seqela Dry Afromontane Forest in Northwestern EthiopiaPLOS ONE Dear Dr. Birhanu, 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 recommend the revised version of the manuscript be accepted for publication in PLOS One after minor revision. ============================== Please submit your revised manuscript by Aug 03 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. 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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, Faham Khamesipour, Ph.D. Academic Editor PLOS ONE Journal Requirements: 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. [Note: HTML markup is below. Please do not edit.] 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: All comments have been addressed Reviewer #3: (No Response) ******** 2. 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 #3: Partly ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #3: No ****** 4. 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 #3: No ****** 5. 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 #3: No ****** 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: I found that the authors have addressed the comments I made in the second round revised manuscript. I appreciate the great efforts that the authors have made in response to my questions and concerns. Thus, I recommend the manuscript for publication after a correction of some minor technical writing problems such as, Introduction-line 7: replace "10-12" with "10–12"; line 10: replace "15, 16" with "15,16" and the like. Reviewer #3: The study focuses on an interesting and timely area of research. However, the write up, organization, grammar and especially the methodology are not to the standard. The methodology missed how the environmental factors such as altitude, aspect and slope were considered during plot establishment, while most of the data and the conclusion relied on. There are some data such as Shannon diversity index and evenness already collected, but not presented. ****** 7. 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 #3: 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. Attachments Attachment Submitted filename: PONE-D-24-05897_R2.docx https://doi.org/10.1371/journal.pone.0313020.r005
Revision 3
5 Aug 2024 Author Response We have corrected the 3rd revised version of the manuscript. Attachments Attachment Submitted filename: Point by point.docx https://doi.org/10.1371/journal.pone.0313020.r006
25 Sep 2024 Decision Letter - Faham Khamesipour, Editor PONE-D-24-05897R3Woody species diversity,structure and community distribution along environmental gradientsof Seqela Dry Afromontane Forest in Northwestern EthiopiaPLOS ONE Dear Dr. Birhanu, 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: The manuscript is ready for publication after minor revision. It requires some minor improvements for enhanced clarity. ============================== Please submit your revised manuscript by Nov 09 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. 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, Faham Khamesipour, Ph.D. Academic Editor PLOS ONE Journal Requirements: 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. [Note: HTML markup is below. Please do not edit.] 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 #3: All comments have been addressed Reviewer #4: All comments have been addressed ******** 2. 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 #3: Yes Reviewer #4: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #3: Yes Reviewer #4: Yes ****** 4. 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 #3: Yes Reviewer #4: Yes ****** 5. 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 #3: No Reviewer #4: 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 #3: - The authors have addressed the comments given in the first round revision and the manuscript is very much improved. The comments for further improvement include 1. The size of the study forest is not mentioned. However, in the discussion under woody species composition, a sentence saying the variation in Shannon diversity index might be due to the size of the forest is included. Therefore, including the size the forest in the paper helps to see such comparisons 2. I couldn't see disturbance data in this manuscript. However, a significant portion of the conclusion is about the effect of disturbances. Thus, the conclusion should focus on the findings of the manuscript. 3. The width of the bars in Figure 3 is not to the standard Reviewer #4: Please correct the species names in the abstract. The objectives can be fine tuned to align with the results. ****** 7. 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 #3: No Reviewer #4: Yes: Emiru Birhane ******** [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.0313020.r007
Revision 4
2 Oct 2024 Author Response We would like to thank the reviewers for their efforts in reviewing the manuscript and providing valuable suggestions for improving the article. All comments and suggestions were addressed. The changes are marked in yellow color as shown in the revised manuscript. We detailed response for each comment is provided below. Reviewer #3: - The authors have addressed the comments given in the first round revision and the manuscript is very much improved. The comments for further improvement include 1. The size of the study forest is not mentioned. However, in the discussion under woody species composition, a sentence saying the variation in Shannon diversity index might be due to the size of the forest is included. Therefore, including the size the forest in the paper helps to see such comparisons 2. I couldn't see disturbance data in this manuscript. However, a significant portion of the conclusion is about the effect of disturbances. Thus, the conclusion should focus on the findings of the manuscript. 3. The width of the bars in Figure 3 is not to the standard Author’s Response: Thank you for your valuable feedback; we have included the size of the Seqela Forest (197.6 ha) in the manuscript, revised the conclusion to focus on the findings, and corrected the width of the bars in Figure 3 to meet standard requirements. Reviewer #4: Please correct the species names in the abstract. The objectives can be fine tuned to align with the results. Author’s Response: Thank you for your valuable feedback. We have corrected the objectives in the revised manuscript to align more closely with the results. However, we would like to clarify that the species names in the abstract are correct as originally presented, except for Acacia abyssinica, which has been updated to Vachellia abyssinica as per the recent taxonomic classification. Attachments Attachment Submitted filename: Point by point_R4.docx https://doi.org/10.1371/journal.pone.0313020.r008
17 Oct 2024 Decision Letter - Faham Khamesipour, Editor Woody Species Diversity, Structure and Community Distribution Along Environmental Gradients of Seqela Dry Afromontane Forest in Northwestern Ethiopia PONE-D-24-05897R4 Dear Dr. Birhanu, 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. 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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 #3: All comments have been addressed Reviewer #4: All comments have been addressed ******** 2. 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 #3: Yes Reviewer #4: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #3: Yes Reviewer #4: Yes ****** 4. 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 #3: Yes Reviewer #4: Yes ****** 5. 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 #3: Yes Reviewer #4: 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 #3: The comments given are well entertained and the manuscript can be published in the present condition Reviewer #4: The comments are addressed. No further comment. The authors critically addressed the comments given to improve the paper. ****** 7. 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 #3: No Reviewer #4: Yes: Emiru Birhane ******** https://doi.org/10.1371/journal.pone.0313020.r009
Formally Accepted
19 Nov 2024 Acceptance Letter - Faham Khamesipour, Editor PONE-D-24-05897R4 PLOS ONE Dear Dr. Birhanu, 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. Faham Khamesipour Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0313020.r010

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