PONE-D-24-28488Characterization of Indigenous Chicken Phenotypes in Liban Jawi District, Ethiopia: A Qualitative and Quantitative Analysis

PLOS ONE

Dear Dr. Desalegn Begna,

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.

==============================

Dear Dr., Desalegn Begna

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we have decided that your manuscript needs Major Revision.

Comment Editor:

1. The introduction needs to be updated with new references and rewritten to include all the research points.
2. Discussion of the results needs to be rewritten and written more clearly and in depth, with references to recent references.
3. I advise that the manuscript needs a scientific editing English language .

Kind regards,

Prof. Lamiaa Mostafa Radwan, Ph.D.

Academic Editor

PLOS ONE

Reviewer1

Introduction

The introduction is short and discusses in general the populations of native chickens in Ethiopia, there is also mention of phenotypic differences which is in line with the theme of the article. However, it should be improved. Below are my comments:

Indigenous chicken (Gallus domesticus) constitutes approximately… - please write latin species name in italics

It is not clear for me. At first there is written that “each village household typically keeping between 5 and 20 birds (Tadelle, 2003)”, and then “Under rural chicken production systems, the average flock size ranges from 7 to 10 birds per household, consisting of adult hens, a cock, and various age groups of growers (Melesse & Negesse, 2011).” Please rewrite this, for example like: according to author 1 there is… and according to author 2. The information you gave are confusing.

What means “feather contours”. Contour feathers are type of feathers? What does mean phenotypic variations of feather contours? You mean mutation that influence feather structure? Others?

I suggest to expand this thought: “Phenotypic characterization provides valuable data on the current and potential future uses of indigenous chickens in a given area.”

Aim of study was to characterize the phenotypes of local phenotypes. However, what is the purpose of this? How it can be used?

Also I have suggestion about adding some information how many breeds you have in Ethiopia and/or district where you collected data? What are the most popular and maybe how they are related to indigenous ones?

Methodologies

The methodology is far too poorly described and to be thoroughly improved. For example, the results include Pearson correlation, which is not mentioned in the methodology. Also in what programs were the analyses performed?

I'm missing information on what chicken characteristics were highlighted. How were they classified? I know how different comb types look like, but how authors classify head shape for example?

“Qualitative traits, which are observable characteristics that do not involve numerical measurement, were collected through visual observation of traits such as head shape, comb type, feather plumage, shank color, earlobe color, and skin color.” - How was the subjectivity of the evaluation eliminated? Were evaluation guidelines prepared? Was the evaluation done by one/more people?

Results and discussion

Firstly, I would suggest to separate the results and discussion. There is almost lack of real discussion at all. It is hard to evaluate in the form presented. Unfortunately this section need to be rewritten in my opinion.

The photos submitted are supposed to show the variety of characteristics of chickens, however, the photos are very (!) poor in my opinion. I have doubts whether they are suitable for publication in PLOS One . Some are blurred. From different angles, perspectives, formatted.... The photos should at least be taken against the same background, preferably with some kind of scale on photo, in the same position of the bird. These photos, and therefore the features seen in them, are incomparable to each other. Rather than these bad photos, I would suggest posting some graphs. I think readers know how different comb tyles look like, but it difficult to imagine and draw conclusions from the description of the results in form how they are presented in text.

General Socio-Economic Characteristics: I do not see the connection of this subsection with the topic/title of the work. In my opinion, this is material for a different kind of analysis.

The current study found that the indigenous chickens in the study area were predominantly normally feathered… - what does mean normally feathered? How it would be not normally? Beside, if normally feathered were 100% birds, that means that there were not predominantly normal, but all of them.

The authors write what plumage colors and other traits are the most common and results giving in percentages. However, there is no analysis of whether these differences are statistically significant or not.

It is not clear what is covered by the term “head shape”. Please explain it.

“This discrepancy may be attributed to breed differences.” – So we end up dealing with different breeds or local populations that are not breeds?

“There were highly significant differences (p < 0.03) in earlobe color among the chickens in the agroecologies for both males and females” – What statistical tests were used? Also this comment refer to other results presented like this.

“There were highly significant differences (p < 0.03) in earlobe color among the chickens in the agroecologies for both males and females (Figure 4).” – The reference to figure 4 suggests that we will see graphically the differences between agroecologies, meanwhile we end up with another poor photo.

Table 2 is not very clear. The way it is presented is not very clear where the trait category begins (Plumage color/comb type, crest…) and where the variants begin (Black, black mottled… etc.). The P-value indicates that the differences were significant, but significant between what features? Once again question what tests were used?

The found differences in the traits studied between hens and roosters are mainly due to sexual dimorphism in this species. These analyses do not contribute anything new. The authors could have analyzed whether sexual dimorphism is higher/lower between agroecologies in populations.

My impression is that the analyses were done without thinking about any what hypothesis authors have. I would suggest that a “guiding idea” need to be established and followed. Based on the data presented, I might suggest that authors may focus on the morphological differences between the agroecologies and, if they are significant, look for answers as to why this is so. Could the environmental conditions between these agroecologies have affected the morphologies of the birds? Maybe from the resulting data, can you perform cluster analyses to show how the geographic distribution of individual bird traits are represented?

Unfortunately, in its current form, in my opinion, the article is not suitable for publication. First of all, authors need to rethink what kind of analysis can be done from collected data, and how to make them meaningful. Secondly, authors need to describe the methodology in more detail, including what statistical tests were used.

Finally, there should be a separate discussion to properly discuss the results: the results against the background of other studies (which was done in the submitted manuscript), but also try to answer the reasons for the differences or lack thereof.

Reviewer2

Subject: Manuscript Refinement Suggestions for Submission to PLOS ONE

Dear Editor,

I have carefully reviewed the manuscript titled "Characterization of Indigenous Chicken Phenotypes in Liban Jawi District, Ethiopia: A Qualitative and Quantitative Analysis" submitted for consideration to PLOS ONE. The study offers valuable insights into the phenotypes of chickens, which could significantly contribute to the development of conservation and breeding programs. However, to enhance the quality and clarity of the manuscript, I recommend that the authors address the following points:

1. Clarification of the Problem Statement:

The authors are encouraged to provide a more detailed and clear elaboration of the statement of the problem under investigation.

2. Diversification of Citations:

It is advised that the authors include additional recent publications related to the phenotypic characterization of indigenous chickens in various regions of Ethiopia. To avoid redundancy, please refrain from citing similar references repeatedly.

3. Consistency in Referencing Style:

Ensure consistency in the referencing style throughout the manuscript.

4. Enhancements in Grammar, Spelling, and Formatting:

Please refine the grammar, spelling, and overall editing of the manuscript to align with the journal's guidelines. Additionally, ensure that tables and figures are correctly presented, with self-explanatory legends.

5. Detailed Methodology Section:

Separate the methodology section into sub-headings for data collection, sampling, and statistical analysis. Elaborate further on the statistical analysis procedures employed.

6. Comprehensive Discussion:

Clearly articulate the implications of the study in the discussion section.

7. Inclusion of Univariate and Multivariate Analyses:

It is recommended to incorporate more univariate and multivariate analyses to enrich the manuscript. Ensure that mean comparisons are conducted.

8. Consideration of Body Indices Calculation:

If feasible, include body indices calculations to provide insights into the overall conformation and functionality of the chickens studied.

9. Precision in Conclusions and Recommendations:

Ensure that the conclusions and recommendations align closely with the study results. Address the effects of agro-ecology, which should be adequately discussed throughout the manuscript, including in the abstract.

I believe that addressing these points will significantly improve the manuscript's quality and contribute to its potential acceptance for publication. Thank you for considering these suggestions.

Sincerely,

==============================

Please submit your revised manuscript by Sep 14 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,

Lamiaa Mostafa Radwan, 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. In your Methods section, please provide additional information regarding the permits you obtained for the work. Please ensure you have included the full name of the authority that approved the field site access and, if no permits were required, a brief statement explaining why.

3. We note that your Data Availability Statement is currently as follows: All relevant data are within the manuscript and its Supporting Information files.

Please confirm at this time whether or not your submission contains all raw data required to replicate the results of your study. Authors must share the “minimal data set” for their submission. PLOS defines the minimal data set to consist of the data required to replicate all study findings reported in the article, as well as related metadata and methods (https://journals.plos.org/plosone/s/data-availability#loc-minimal-data-set-definition).

For example, authors should submit the following data:

- The values behind the means, standard deviations and other measures reported;

- The values used to build graphs;

- The points extracted from images for analysis.

Authors do not need to submit their entire data set if only a portion of the data was used in the reported study.

If your submission does not contain these data, please either upload them as Supporting Information files or deposit them to a stable, public repository and provide us with the relevant URLs, DOIs, or accession numbers. For a list of recommended repositories, please see https://journals.plos.org/plosone/s/recommended-repositories.

If there are ethical or legal restrictions on sharing a de-identified data set, please explain them in detail (e.g., data contain potentially sensitive information, data are owned by a third-party organization, etc.) and who has imposed them (e.g., an ethics committee). Please also provide contact information for a data access committee, ethics committee, or other institutional body to which data requests may be sent. If data are owned by a third party, please indicate how others may request data access.

4. We note that you have referenced (Bogale, K. (2008). In Situ Characterization of Local Chicken Eco-Type for Functional Traits and Production System in Fogera Woreda, Amhara Regional State.Msc.Thesis Submitted to Haramaya University, Haramaya, Ethiopia, Halima Hassen (2007).Phenotypic and genetic characterization of indigenous chicken populations in North-West Ethiopia. Ph.D. Thesis, Submitted to the faculty of natural and Agricultural Sciences Department of animal wildlife and grassland Sciences University of the Free State, Bloemfontein, South Africa. Pp 186 and Nigussie D., (2013.)On-farm phenotypic characterization of indigenous chicken and chicken production systems in Southern Zone of Tigray, Northern Ethiopia, Thesis Submitted to the, School of Graduate Studies Haramaya University,Ethiopia,pp 106.of Poultry Sciences, 3 (1), 15-19.) 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 

5. We note that Figure 1 in your submission contain map/satellite images which may be copyrighted. All PLOS content is published under the Creative Commons Attribution License (CC BY 4.0), which means that the manuscript, images, and Supporting Information files will be freely available online, and any third party is permitted to access, download, copy, distribute, and use these materials in any way, even commercially, with proper attribution. For these reasons, we cannot publish previously copyrighted maps or satellite images created using proprietary data, such as Google software (Google Maps, Street View, and Earth). For more information, see our copyright guidelines: http://journals.plos.org/plosone/s/licenses-and-copyright.

We require you to either (1) present written permission from the copyright holder to publish these figures specifically under the CC BY 4.0 license, or (2) remove the figures from your submission:

a. You may seek permission from the original copyright holder of Figure 1 to publish the content specifically under the CC BY 4.0 license.  

We recommend that you contact the original copyright holder with the Content Permission Form (http://journals.plos.org/plosone/s/file?id=7c09/content-permission-form.pdf) and the following text:

“I request permission for the open-access journal PLOS ONE to publish XXX under the Creative Commons Attribution License (CCAL) CC BY 4.0 (http://creativecommons.org/licenses/by/4.0/). Please be aware that this license allows unrestricted use and distribution, even commercially, by third parties. Please reply and provide explicit written permission to publish XXX under a CC BY license and complete the attached form.”

Please upload the completed Content Permission Form or other proof of granted permissions as an ""Other"" file with your submission.

In the figure caption of the copyrighted figure, please include the following text: “Reprinted from [ref] under a CC BY license, with permission from [name of publisher], original copyright [original copyright year].”

b. If you are unable to obtain permission from the original copyright holder to publish these figures under the CC BY 4.0 license or if the copyright holder’s requirements are incompatible with the CC BY 4.0 license, please either i) remove the figure or ii) supply a replacement figure that complies with the CC BY 4.0 license. Please check copyright information on all replacement figures and update the figure caption with source information. If applicable, please specify in the figure caption text when a figure is similar but not identical to the original image and is therefore for illustrative purposes only.

The following resources for replacing copyrighted map figures may be helpful:

USGS National Map Viewer (public domain): http://viewer.nationalmap.gov/viewer/

The Gateway to Astronaut Photography of Earth (public domain): http://eol.jsc.nasa.gov/sseop/clickmap/

Maps at the CIA (public domain): https://www.cia.gov/library/publications/the-world-factbook/index.html and https://www.cia.gov/library/publications/cia-maps-publications/index.html

NASA Earth Observatory (public domain): http://earthobservatory.nasa.gov/

Landsat: http://landsat.visibleearth.nasa.gov/

USGS EROS (Earth Resources Observatory and Science (EROS) Center) (public domain): http://eros.usgs.gov/#

Natural Earth (public domain): http://www.naturalearthdata.com/

6. We note that Figures 2, 3 and 4 in your submission contain copyrighted images. All PLOS content is published under the Creative Commons Attribution License (CC BY 4.0), which means that the manuscript, images, and Supporting Information files will be freely available online, and any third party is permitted to access, download, copy, distribute, and use these materials in any way, even commercially, with proper attribution. For more information, see our copyright guidelines: http://journals.plos.org/plosone/s/licenses-and-copyright.

We require you to either (1) present written permission from the copyright holder to publish these figures specifically under the CC BY 4.0 license, or (2) remove the figures from your submission:

a. You may seek permission from the original copyright holder of Figures 2, 3 and 4 to publish the content specifically under the CC BY 4.0 license. 

We recommend that you contact the original copyright holder with the Content Permission Form (http://journals.plos.org/plosone/s/file?id=7c09/content-permission-form.pdf) and the following text:

“I request permission for the open-access journal PLOS ONE to publish XXX under the Creative Commons Attribution License (CCAL) CC BY 4.0 (http://creativecommons.org/licenses/by/4.0/). Please be aware that this license allows unrestricted use and distribution, even commercially, by third parties. Please reply and provide explicit written permission to publish XXX under a CC BY license and complete the attached form.”

Please upload the completed Content Permission Form or other proof of granted permissions as an ""Other"" file with your submission. 

In the figure caption of the copyrighted figure, please include the following text: “Reprinted from [ref] under a CC BY license, with permission from [name of publisher], original copyright [original copyright year].”

b. If you are unable to obtain permission from the original copyright holder to publish these figures under the CC BY 4.0 license or if the copyright holder’s requirements are incompatible with the CC BY 4.0 license, please either i) remove the figure or ii) supply a replacement figure that complies with the CC BY 4.0 license. Please check copyright information on all replacement figures and update the figure caption with source information. If applicable, please specify in the figure caption text when a figure is similar but not identical to the original image and is therefore for illustrative purposes only.

Additional Editor Comments:

Dear Dr., Desalegn Begna

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we have decided that your manuscript needs Major Revision.

Comment Editor:

1- The introduction needs to be updated with new references and rewritten to include all the research points.

2- Discussion of the results needs to be rewritten and written more clearly and in depth, with references to recent references.

3- I advise that the manuscript needs a scientific editing English language .

Kind regards,

Prof. Lamiaa Mostafa Radwan, Ph.D.

Academic Editor

PLOS ONE

Reviewer1

Introduction

The introduction is short and discusses in general the populations of native chickens in Ethiopia, there is also mention of phenotypic differences which is in line with the theme of the article. However, it should be improved. Below are my comments:

Indigenous chicken (Gallus domesticus) constitutes approximately… - please write latin species name in italics

It is not clear for me. At first there is written that “each village household typically keeping between 5 and 20 birds (Tadelle, 2003)”, and then “Under rural chicken production systems, the average flock size ranges from 7 to 10 birds per household, consisting of adult hens, a cock, and various age groups of growers (Melesse & Negesse, 2011).” Please rewrite this, for example like: according to author 1 there is… and according to author 2. The information you gave are confusing.

What means “feather contours”. Contour feathers are type of feathers? What does mean phenotypic variations of feather contours? You mean mutation that influence feather structure? Others?

I suggest to expand this thought: “Phenotypic characterization provides valuable data on the current and potential future uses of indigenous chickens in a given area.”

Aim of study was to characterize the phenotypes of local phenotypes. However, what is the purpose of this? How it can be used?

Also I have suggestion about adding some information how many breeds you have in Ethiopia and/or district where you collected data? What are the most popular and maybe how they are related to indigenous ones?

Methodologies

The methodology is far too poorly described and to be thoroughly improved. For example, the results include Pearson correlation, which is not mentioned in the methodology. Also in what programs were the analyses performed?

I'm missing information on what chicken characteristics were highlighted. How were they classified? I know how different comb types look like, but how authors classify head shape for example?

“Qualitative traits, which are observable characteristics that do not involve numerical measurement, were collected through visual observation of traits such as head shape, comb type, feather plumage, shank color, earlobe color, and skin color.” - How was the subjectivity of the evaluation eliminated? Were evaluation guidelines prepared? Was the evaluation done by one/more people?

Results and discussion

Firstly, I would suggest to separate the results and discussion. There is almost lack of real discussion at all. It is hard to evaluate in the form presented. Unfortunately this section need to be rewritten in my opinion.

The photos submitted are supposed to show the variety of characteristics of chickens, however, the photos are very (!) poor in my opinion. I have doubts whether they are suitable for publication in PLOS One . Some are blurred. From different angles, perspectives, formatted.... The photos should at least be taken against the same background, preferably with some kind of scale on photo, in the same position of the bird. These photos, and therefore the features seen in them, are incomparable to each other. Rather than these bad photos, I would suggest posting some graphs. I think readers know how different comb tyles look like, but it difficult to imagine and draw conclusions from the description of the results in form how they are presented in text.

General Socio-Economic Characteristics: I do not see the connection of this subsection with the topic/title of the work. In my opinion, this is material for a different kind of analysis.

The current study found that the indigenous chickens in the study area were predominantly normally feathered… - what does mean normally feathered? How it would be not normally? Beside, if normally feathered were 100% birds, that means that there were not predominantly normal, but all of them.

The authors write what plumage colors and other traits are the most common and results giving in percentages. However, there is no analysis of whether these differences are statistically significant or not.

It is not clear what is covered by the term “head shape”. Please explain it.

“This discrepancy may be attributed to breed differences.” – So we end up dealing with different breeds or local populations that are not breeds?

“There were highly significant differences (p < 0.03) in earlobe color among the chickens in the agroecologies for both males and females” – What statistical tests were used? Also this comment refer to other results presented like this.

“There were highly significant differences (p < 0.03) in earlobe color among the chickens in the agroecologies for both males and females (Figure 4).” – The reference to figure 4 suggests that we will see graphically the differences between agroecologies, meanwhile we end up with another poor photo.

Table 2 is not very clear. The way it is presented is not very clear where the trait category begins (Plumage color/comb type, crest…) and where the variants begin (Black, black mottled… etc.). The P-value indicates that the differences were significant, but significant between what features? Once again question what tests were used?

The found differences in the traits studied between hens and roosters are mainly due to sexual dimorphism in this species. These analyses do not contribute anything new. The authors could have analyzed whether sexual dimorphism is higher/lower between agroecologies in populations.

My impression is that the analyses were done without thinking about any what hypothesis authors have. I would suggest that a “guiding idea” need to be established and followed. Based on the data presented, I might suggest that authors may focus on the morphological differences between the agroecologies and, if they are significant, look for answers as to why this is so. Could the environmental conditions between these agroecologies have affected the morphologies of the birds? Maybe from the resulting data, can you perform cluster analyses to show how the geographic distribution of individual bird traits are represented?

Unfortunately, in its current form, in my opinion, the article is not suitable for publication. First of all, authors need to rethink what kind of analysis can be done from collected data, and how to make them meaningful. Secondly, authors need to describe the methodology in more detail, including what statistical tests were used.

Finally, there should be a separate discussion to properly discuss the results: the results against the background of other studies (which was done in the submitted manuscript), but also try to answer the reasons for the differences or lack thereof.

Reviewer2

Subject: Manuscript Refinement Suggestions for Submission to PLOS ONE

Dear Editor,

I have carefully reviewed the manuscript titled "Characterization of Indigenous Chicken Phenotypes in Liban Jawi District, Ethiopia: A Qualitative and Quantitative Analysis" submitted for consideration to PLOS ONE. The study offers valuable insights into the phenotypes of chickens, which could significantly contribute to the development of conservation and breeding programs. However, to enhance the quality and clarity of the manuscript, I recommend that the authors address the following points:

1. Clarification of the Problem Statement:

The authors are encouraged to provide a more detailed and clear elaboration of the statement of the problem under investigation.

2. Diversification of Citations:

It is advised that the authors include additional recent publications related to the phenotypic characterization of indigenous chickens in various regions of Ethiopia. To avoid redundancy, please refrain from citing similar references repeatedly.

3. Consistency in Referencing Style:

Ensure consistency in the referencing style throughout the manuscript.

4. Enhancements in Grammar, Spelling, and Formatting:

Please refine the grammar, spelling, and overall editing of the manuscript to align with the journal's guidelines. Additionally, ensure that tables and figures are correctly presented, with self-explanatory legends.

5. Detailed Methodology Section:

Separate the methodology section into sub-headings for data collection, sampling, and statistical analysis. Elaborate further on the statistical analysis procedures employed.

6. Comprehensive Discussion:

Clearly articulate the implications of the study in the discussion section.

7. Inclusion of Univariate and Multivariate Analyses:

It is recommended to incorporate more univariate and multivariate analyses to enrich the manuscript. Ensure that mean comparisons are conducted.

8. Consideration of Body Indices Calculation:

If feasible, include body indices calculations to provide insights into the overall conformation and functionality of the chickens studied.

9. Precision in Conclusions and Recommendations:

Ensure that the conclusions and recommendations align closely with the study results. Address the effects of agro-ecology, which should be adequately discussed throughout the manuscript, including in the abstract.

I believe that addressing these points will significantly improve the manuscript's quality and contribute to its potential acceptance for publication. Thank you for considering these suggestions.

Sincerely,

[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: No

Reviewer #2: Partly

**********

2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: No

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: No

Reviewer #2: No

**********

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: Introduction

The introduction is short and discusses in general the populations of native chickens in Ethiopia, there is also mention of phenotypic differences which is in line with the theme of the article. However, it should be improved. Below are my comments:

Indigenous chicken (Gallus domesticus) constitutes approximately… - please write latin species name in italics

It is not clear for me. At first there is written that “each village household typically keeping between 5 and 20 birds (Tadelle, 2003)”, and then “Under rural chicken production systems, the average flock size ranges from 7 to 10 birds per household, consisting of adult hens, a cock, and various age groups of growers (Melesse & Negesse, 2011).” Please rewrite this, for example like: according to author 1 there is… and according to author 2. The information you gave are confusing.

What means “feather contours”. Contour feathers are type of feathers? What does mean phenotypic variations of feather contours? You mean mutation that influence feather structure? Others?

I suggest to expand this thought: “Phenotypic characterization provides valuable data on the current and potential future uses of indigenous chickens in a given area.”

Aim of study was to characterize the phenotypes of local phenotypes. However, what is the purpose of this? How it can be used?

Also I have suggestion about adding some information how many breeds you have in Ethiopia and/or district where you collected data? What are the most popular and maybe how they are related to indigenous ones?

Methodologies

The methodology is far too poorly described and to be thoroughly improved. For example, the results include Pearson correlation, which is not mentioned in the methodology. Also in what programs were the analyses performed?

I'm missing information on what chicken characteristics were highlighted. How were they classified? I know how different comb types look like, but how authors classify head shape for example?

“Qualitative traits, which are observable characteristics that do not involve numerical measurement, were collected through visual observation of traits such as head shape, comb type, feather plumage, shank color, earlobe color, and skin color.” - How was the subjectivity of the evaluation eliminated? Were evaluation guidelines prepared? Was the evaluation done by one/more people?

Results and discussion

Firstly, I would suggest to separate the results and discussion. There is almost lack of real discussion at all. It is hard to evaluate in the form presented. Unfortunately this section need to be rewritten in my opinion.

The photos submitted are supposed to show the variety of characteristics of chickens, however, the photos are very (!) poor in my opinion. I have doubts whether they are suitable for publication in PLOS One . Some are blurred. From different angles, perspectives, formatted.... The photos should at least be taken against the same background, preferably with some kind of scale on photo, in the same position of the bird. These photos, and therefore the features seen in them, are incomparable to each other. Rather than these bad photos, I would suggest posting some graphs. I think readers know how different comb tyles look like, but it difficult to imagine and draw conclusions from the description of the results in form how they are presented in text.

General Socio-Economic Characteristics: I do not see the connection of this subsection with the topic/title of the work. In my opinion, this is material for a different kind of analysis.

The current study found that the indigenous chickens in the study area were predominantly normally feathered… - what does mean normally feathered? How it would be not normally? Beside, if normally feathered were 100% birds, that means that there were not predominantly normal, but all of them.

The authors write what plumage colors and other traits are the most common and results giving in percentages. However, there is no analysis of whether these differences are statistically significant or not.

It is not clear what is covered by the term “head shape”. Please explain it.

“This discrepancy may be attributed to breed differences.” – So we end up dealing with different breeds or local populations that are not breeds?

“There were highly significant differences (p < 0.03) in earlobe color among the chickens in the agroecologies for both males and females” – What statistical tests were used? Also this comment refer to other results presented like this.

“There were highly significant differences (p < 0.03) in earlobe color among the chickens in the agroecologies for both males and females (Figure 4).” – The reference to figure 4 suggests that we will see graphically the differences between agroecologies, meanwhile we end up with another poor photo.

Table 2 is not very clear. The way it is presented is not very clear where the trait category begins (Plumage color/comb type, crest…) and where the variants begin (Black, black mottled… etc.). The P-value indicates that the differences were significant, but significant between what features? Once again question what tests were used?

The found differences in the traits studied between hens and roosters are mainly due to sexual dimorphism in this species. These analyses do not contribute anything new. The authors could have analyzed whether sexual dimorphism is higher/lower between agroecologies in populations.

My impression is that the analyses were done without thinking about any what hypothesis authors have. I would suggest that a “guiding idea” need to be established and followed. Based on the data presented, I might suggest that authors may focus on the morphological differences between the agroecologies and, if they are significant, look for answers as to why this is so. Could the environmental conditions between these agroecologies have affected the morphologies of the birds? Maybe from the resulting data, can you perform cluster analyses to show how the geographic distribution of individual bird traits are represented?

Unfortunately, in its current form, in my opinion, the article is not suitable for publication. First of all, authors need to rethink what kind of analysis can be done from collected data, and how to make them meaningful. Secondly, authors need to describe the methodology in more detail, including what statistical tests were used.

Finally, there should be a separate discussion to properly discuss the results: the results against the background of other studies (which was done in the submitted manuscript), but also try to answer the reasons for the differences or lack thereof.

Reviewer #2: Subject: Manuscript Refinement Suggestions for Submission to PLOS ONE

Dear Editor,

I have carefully reviewed the manuscript titled "Characterization of Indigenous Chicken Phenotypes in Liban Jawi District, Ethiopia: A Qualitative and Quantitative Analysis" submitted for consideration to PLOS ONE. The study offers valuable insights into the phenotypes of chickens, which could significantly contribute to the development of conservation and breeding programs. However, to enhance the quality and clarity of the manuscript, I recommend that the authors address the following points:

1. Clarification of the Problem Statement:

The authors are encouraged to provide a more detailed and clear elaboration of the statement of the problem under investigation.

2. Diversification of Citations:

It is advised that the authors include additional recent publications related to the phenotypic characterization of indigenous chickens in various regions of Ethiopia. To avoid redundancy, please refrain from citing similar references repeatedly.

3. Consistency in Referencing Style:

Ensure consistency in the referencing style throughout the manuscript.

4. Enhancements in Grammar, Spelling, and Formatting:

Please refine the grammar, spelling, and overall editing of the manuscript to align with the journal's guidelines. Additionally, ensure that tables and figures are correctly presented, with self-explanatory legends.

5. Detailed Methodology Section:

Separate the methodology section into sub-headings for data collection, sampling, and statistical analysis. Elaborate further on the statistical analysis procedures employed.

6. Comprehensive Discussion:

Clearly articulate the implications of the study in the discussion section.

7. Inclusion of Univariate and Multivariate Analyses:

It is recommended to incorporate more univariate and multivariate analyses to enrich the manuscript. Ensure that mean comparisons are conducted.

8. Consideration of Body Indices Calculation:

If feasible, include body indices calculations to provide insights into the overall conformation and functionality of the chickens studied.

9. Precision in Conclusions and Recommendations:

Ensure that the conclusions and recommendations align closely with the study results. Address the effects of agro-ecology, which should be adequately discussed throughout the manuscript, including in the abstract.

I believe that addressing these points will significantly improve the manuscript's quality and contribute to its potential acceptance for publication. Thank you for considering these suggestions.

Sincerely,

**********

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.]

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: Comments in highlight PONE-D-24-28488.pdf

Attachment

Submitted filename: General comments in Ms-word.docx

PONE-D-24-28488R1Characterization of Indigenous Chicken Phenotypes in Liban Jawi District, Ethiopia: A Qualitative and Quantitative AnalysisPLOS ONE

Dear Dr.  Begna,

<o:p></o:p>

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.

==============================

Dear Dr., Desalegn Begna,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we have decided that your manuscript needs Major Revision.

Kind regards,

Prof. Lamiaa Mostafa Radwan, Ph.D.

Academic Editor

PLOS ONE

Reviewer 2

Dear Authors,

I have carefully reviewed the manuscript titled "Characterization of Indigenous Chicken Phenotypes in Liban Jawi District, Ethiopia: A Qualitative and Quantitative Analysis" (PONE-D-24-28488R1). Below are my comments and feedback on the content presented in the manuscript.

Abstract

1. What type of sampling analysis method you used. It should be mentioned.

2. The length of the shank has been identified as the most reliable indicator of body weight for both female (r=0.45) and male (r=0.44) chickens. Considering the relatively modest correlation coefficients, how do you interpret the efficacy of using shank length to predict body weight? Is this level of correlation practically useful in predicting body weight accurately?

3. The study revealed significant variations in both qualitative and quantitative traits among the indigenous chicken population, suggesting the potential for improvement through selective breeding at the community level.

- ICs found in d/t agro-ecologies or what?

4. The statistical significance levels for the factors included in the model, namely AE, Sex, and their interaction, have not been explicitly stated. It is crucial to ascertain the significance levels of these factors to accurately interpret their impact on the outcome variable . STATISTICAL TEST?

Introduction

1. Please correct the citation style throughout the manuscript. What referencing tool you utilized. For example. According to (9)), each village household typically keeps between 5 and 20 indigenous… AND Understanding the unique traits, adaptation to the environment, and socio-cultural importance of indigenous chickens is essential for their conservation and utilization (8,(7,15) (.

Statement of problem

1. Do you think this statement is important here. ‘’However, these native chickens generally exhibit poor egg production performance, delayed maturity, and extended broodiness, as they have primarily been selected for their adaptive traits(18)’’.

2. Please re-write statement of the problem. Please write in the following order: Importance of characterization then previous studies and limitation then your objective in a precise way.

3. Ethiopia hosts over 30 distinct indigenous chicken ecotypes and breeds found across different regional districts, including the well-known Horro, Koekoek, Fayoumi, and Tilili populations… What mean indigenous and local chicken ecotypes? Are Fayoumi and Koekoek indigenous to Ethiopia?

Data collection and sample size

1. Thus, a total of 2166 households and 2452 chickens were surveyed in the our kebeles

2. Please keep the coherence and avoid redundancy. The formula then the samples taken.

Results and Discussion

1. Where are the results of PCA, cluster analysis and body index values in tables/figures

General

Still there are problems in editing, coherence, and spelling. Please check throughout the manuscript.

Reviewer 3

The authors of this manuscript "Characterization of Indigenous Chicken Phenotypes in Liban Jawi District, Ethiopia: A Qualitative and Quantitative Analysis". perform a great efforts to try to address both the qualitative and quantitative phenotypes of Liban Jawi district indigenous chicken. This study offers valuable insights into these chicken phenotypes, which will significantly contribute to set an accurate breeding program to improve and enhance these genetic resources in Ethiopia.

However, authors should revise the manuscript one more time to ensure that the grammar, spelling, and overall editing of the manuscript follow the journal's guidelines.

==============================

Please submit your revised manuscript by Nov 16 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,

Lamiaa Mostafa Radwan, Ph.D.

Academic Editor

PLOS ONE

Journal Requirements:

Additional Editor Comments (if provided):

Dear Dr., Desalegn Begna,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we have decided that your manuscript needs Major Revision.

Kind regards,

Prof. Lamiaa Mostafa Radwan, Ph.D.

Academic Editor

PLOS ONE

Reviewer 2

Dear Authors,

I have carefully reviewed the manuscript titled "Characterization of Indigenous Chicken Phenotypes in Liban Jawi District, Ethiopia: A Qualitative and Quantitative Analysis" (PONE-D-24-28488R1). Below are my comments and feedback on the content presented in the manuscript.

Abstract

1. What type of sampling analysis method you used. It should be mentioned.

2. The length of the shank has been identified as the most reliable indicator of body weight for both female (r=0.45) and male (r=0.44) chickens. Considering the relatively modest correlation coefficients, how do you interpret the efficacy of using shank length to predict body weight? Is this level of correlation practically useful in predicting body weight accurately?

3. The study revealed significant variations in both qualitative and quantitative traits among the indigenous chicken population, suggesting the potential for improvement through selective breeding at the community level.

- ICs found in d/t agro-ecologies or what?

4. The statistical significance levels for the factors included in the model, namely AE, Sex, and their interaction, have not been explicitly stated. It is crucial to ascertain the significance levels of these factors to accurately interpret their impact on the outcome variable . STATISTICAL TEST?

Introduction

1. Please correct the citation style throughout the manuscript. What referencing tool you utilized. For example. According to (9)), each village household typically keeps between 5 and 20 indigenous… AND Understanding the unique traits, adaptation to the environment, and socio-cultural importance of indigenous chickens is essential for their conservation and utilization (8,(7,15) (.

Statement of problem

1. Do you think this statement is important here. ‘’However, these native chickens generally exhibit poor egg production performance, delayed maturity, and extended broodiness, as they have primarily been selected for their adaptive traits(18)’’.

2. Please re-write statement of the problem. Please write in the following order: Importance of characterization then previous studies and limitation then your objective in a precise way.

3. Ethiopia hosts over 30 distinct indigenous chicken ecotypes and breeds found across different regional districts, including the well-known Horro, Koekoek, Fayoumi, and Tilili populations… What mean indigenous and local chicken ecotypes? Are Fayoumi and Koekoek indigenous to Ethiopia?

Data collection and sample size

1. Thus, a total of 2166 households and 2452 chickens were surveyed in the our kebeles

2. Please keep the coherence and avoid redundancy. The formula then the samples taken.

Results and Discussion

1. Where are the results of PCA, cluster analysis and body index values in tables/figures

General

Still there are problems in editing, coherence, and spelling. Please check throughout the manuscript.

Reviewer 3

The authors of this manuscript "Characterization of Indigenous Chicken Phenotypes in Liban Jawi District, Ethiopia: A Qualitative and Quantitative Analysis". perform a great efforts to try to address both the qualitative and quantitative phenotypes of Liban Jawi district indigenous chicken. This study offers valuable insights into these chicken phenotypes, which will significantly contribute to set an accurate breeding program to improve and enhance these genetic resources in Ethiopia.

However, authors should revise the manuscript one more time to ensure that the grammar, spelling, and overall editing of the manuscript follow the journal's guidelines.

[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 #2: (No Response)

Reviewer #3: 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 #2: Partly

Reviewer #3: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #2: No

Reviewer #3: 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 #2: Yes

Reviewer #3: 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 #2: No

Reviewer #3: 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 #2: Dear Authors,

I have carefully reviewed the manuscript titled "Characterization of Indigenous Chicken Phenotypes in Liban Jawi District, Ethiopia: A Qualitative and Quantitative Analysis" (PONE-D-24-28488R1). Below are my comments and feedback on the content presented in the manuscript.

Abstract

1. What type of sampling analysis method you used. It should be mentioned.

2. The length of the shank has been identified as the most reliable indicator of body weight for both female (r=0.45) and male (r=0.44) chickens. Considering the relatively modest correlation coefficients, how do you interpret the efficacy of using shank length to predict body weight? Is this level of correlation practically useful in predicting body weight accurately?

3. The study revealed significant variations in both qualitative and quantitative traits among the indigenous chicken population, suggesting the potential for improvement through selective breeding at the community level.

- ICs found in d/t agro-ecologies or what?

4. The statistical significance levels for the factors included in the model, namely AE, Sex, and their interaction, have not been explicitly stated. It is crucial to ascertain the significance levels of these factors to accurately interpret their impact on the outcome variable . STATISTICAL TEST?

Introduction

1. Please correct the citation style throughout the manuscript. What referencing tool you utilized. For example. According to (9)), each village household typically keeps between 5 and 20 indigenous… AND Understanding the unique traits, adaptation to the environment, and socio-cultural importance of indigenous chickens is essential for their conservation and utilization (8,(7,15) (.

Statement of problem

1. Do you think this statement is important here. ‘’However, these native chickens generally exhibit poor egg production performance, delayed maturity, and extended broodiness, as they have primarily been selected for their adaptive traits(18)’’.

2. Please re-write statement of the problem. Please write in the following order: Importance of characterization then previous studies and limitation then your objective in a precise way.

3. Ethiopia hosts over 30 distinct indigenous chicken ecotypes and breeds found across different regional districts, including the well-known Horro, Koekoek, Fayoumi, and Tilili populations… What mean indigenous and local chicken ecotypes? Are Fayoumi and Koekoek indigenous to Ethiopia?

Data collection and sample size

1. Thus, a total of 2166 households and 2452 chickens were surveyed in the our kebeles

2. Please keep the coherence and avoid redundancy. The formula then the samples taken.

Results and Discussion

1. Where are the results of PCA, cluster analysis and body index values in tables/figures

General

Still there are problems in editing, coherence, and spelling. Please check throughout the manuscript.

Reviewer #3: The authors of this manuscript "Characterization of Indigenous Chicken Phenotypes in Liban Jawi District, Ethiopia: A Qualitative and Quantitative Analysis". perform a great efforts to try to address both the qualitative and quantitative phenotypes of Liban Jawi district indigenous chicken. This study offers valuable insights into these chicken phenotypes, which will significantly contribute to set an accurate breeding program to improve and enhance these genetic resources in Ethiopia.

However, authors should revise the manuscript one more time to ensure that the grammar, spelling, and overall editing of the manuscript follow the journal's guidelines.

**********

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 #2: 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.

PONE-D-24-28488R2Characterization of Indigenous Chicken Phenotypes in Liban Jawi District, Ethiopia: A Qualitative and Quantitative AnalysisPLOS ONE

Dear Dr. Desalegn Begna

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.

==============================

Dear Dr., Desalegn Begna,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we have decided that your manuscript needs Major Revision.

Kind regards,

Prof. Lamiaa Mostafa Radwan, Ph.D.

Academic Editor

PLOS ONE

Reviewer 1

There is a lot of progress compared to the first version, however, much still needs to be improved, especially with discussion

Reviewer 2

Comments and Suggestions

Dear authors, I appreciate your efforts to improve the manuscript; however, some issues remain that require attention.

Esteemed authors, I would be pleased if your manuscript were deemed suitable for publication following the rectification of the following remarks and other reviewer’s comments (If any).

1. It would be advantageous for the problem statement, lines 94-96, to precede the objectives section.

2. Please incorporate references pertaining to the description of the study area.

3. Kindly re-evaluate the spelling, grammar, table formatting, and referencing style once more.

4. I remain dissatisfied with Table 2, the PCA, the cluster analysis, and the indices along with the discussion spanning lines 336-342. I would appreciate the inclusion of figures in these multivariate analyses, with morphological indices clearly delineated and analyzed by proposing their functional significance.

5. Please refine the conclusions and recommendations section, as the conclusion appears to function merely as a summary.

Reviewer 3

Accept

==============================

Please submit your revised manuscript by Dec 06 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,

Lamiaa Mostafa Radwan, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments:

Dear Dr., Desalegn Begna,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we have decided that your manuscript needs Major Revision.

Kind regards,

Prof. Lamiaa Mostafa Radwan, Ph.D.

Academic Editor

PLOS ONE

Reviewer 1

There is a lot of progress compared to the first version, however, much still needs to be improved, especially with discussion

Reviewer 2

Comments and Suggestions

Dear authors, I appreciate your efforts to improve the manuscript; however, some issues remain that require attention.

Esteemed authors, I would be pleased if your manuscript were deemed suitable for publication following the rectification of the following remarks and other reviewer’s comments (If any).

1. It would be advantageous for the problem statement, lines 94-96, to precede the objectives section.

2. Please incorporate references pertaining to the description of the study area.

3. Kindly re-evaluate the spelling, grammar, table formatting, and referencing style once more.

4. I remain dissatisfied with Table 2, the PCA, the cluster analysis, and the indices along with the discussion spanning lines 336-342. I would appreciate the inclusion of figures in these multivariate analyses, with morphological indices clearly delineated and analyzed by proposing their functional significance.

5. Please refine the conclusions and recommendations section, as the conclusion appears to function merely as a summary.

Reviewer 3

Accept

[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

Reviewer #3: 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: No

Reviewer #2: Yes

Reviewer #3: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: 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

Reviewer #3: 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

Reviewer #3: 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: There is a lot of progress compared to the first version, however, much still needs to be improved, especially with discussion

Reviewer #2: Comments and Suggestions

Dear authors, I appreciate your efforts to improve the manuscript; however, some issues remain that require attention.

Esteemed authors, I would be pleased if your manuscript were deemed suitable for publication following the rectification of the following remarks and other reviewer’s comments (If any).

1. It would be advantageous for the problem statement, lines 94-96, to precede the objectives section.

2. Please incorporate references pertaining to the description of the study area.

3. Kindly re-evaluate the spelling, grammar, table formatting, and referencing style once more.

4. I remain dissatisfied with Table 2, the PCA, the cluster analysis, and the indices along with the discussion spanning lines 336-342. I would appreciate the inclusion of figures in these multivariate analyses, with morphological indices clearly delineated and analyzed by proposing their functional significance.

5. Please refine the conclusions and recommendations section, as the conclusion appears to function merely as a summary.

Reviewer #3: (No Response)

**********

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

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: review, chicken plos one.docx

Characterization of Indigenous Chicken Phenotypes in Liban Jawi District, Ethiopia: A Qualitative and Quantitative Analysis

PONE-D-24-28488R3

Dear Dr. Begna,

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,

Lamiaa Mostafa Radwan, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Accept

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 #2: All comments have been addressed

Reviewer #3: 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 #2: Yes

Reviewer #3: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #2: Yes

Reviewer #3: 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 #2: Yes

Reviewer #3: 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 #2: Yes

Reviewer #3: 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 #2: Dear Authors, Thank you for the improvement of your manuscript. Please delete the statement ''Therefore, this study aims to phenotypically characterize

83 indigenous chickens in the Liben Jawi district, focusing on both qualitative and

84 quantitative traits, to document their unique physical characteristics and identify

85 desirable traits for genetic improvement, thus laying the groundwork for effective

86 conservation and sustainable utilization of these valuable local poultry genetic

87 resources''. Which is redundant.

Reviewer #3: I think the authors carefully addressed all reviewer comments.

The manuscript significantly improved.

**********

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 #2: No

Reviewer #3: No

**********