Seed Geometry in Species of the Nepetoideae (Lamiaceae)

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The manuscript submitted for review concerns the issue of analysis of seed geometry in the Nepetoideae (Lamiaceae). The authors present their analysis of seeds of selected Nepetoideae species. The manuscript is prepared correctly and meets the requirements of the journal. It also fits into the subject matter of the journal. The literature is selected correctly. The research methods used are also selected correctly. The manuscript can be a compendium of knowledge on seed morphology, with particular emphasis on seed geometry. This is a new contribution to the knowledge of seeds, and therefore has the characteristics of a novelty. However, the manuscript lacks an emphasis on the application significance of the analyses performed, and they are significant. Additionally, including photos of the analyzed plants (although the most famous representatives or the most important representatives) will significantly increase the value of the manuscript.

Author Response

The manuscript submitted for review concerns the issue of analysis of seed geometry in the Nepetoideae (Lamiaceae). The authors present their analysis of seeds of selected Nepetoideae species. The manuscript is prepared correctly and meets the requirements of the journal. It also fits into the subject matter of the journal. The literature is selected correctly. The research methods used are also selected correctly. The manuscript can be a compendium of knowledge on seed morphology, with particular emphasis on seed geometry. This is a new contribution to the knowledge of seeds, and therefore has the characteristics of a novelty.

However, the manuscript lacks an emphasis on the application significance of the analyses performed, and they are significant. Additionally, including photos of the analyzed plants (although the most famous representatives or the most important representatives) will significantly increase the value of the manuscript.

Dear Reviewer,

Thank you for your comments on the article, which have helped to improve the quality of the presentation. Following your suggestions, new images have been added, and the application and significance of the analyses for plant taxonomy and evolutionary research are now indicated in the Introduction and Discussion sections.

Best regards,

Emilio Cervantes

Corresponding author

Reviewer 2 Report

Comments and Suggestions for Authors

“Seed geometry in the Nepetoideae (Lamiaceae).” is a good topic, which focuses on the research of the geometric morphology of seeds of plants in the Nepetoideae subfamily of the Lamiaceae family. The innovative application of geometric models, the J - index, and curvature analysis to quantify the seed shapes of the Nepetoideae subfamily overcomes the constraints of traditional descriptive methods. It offers novel concepts and approaches for research in this area, which is highly crucial for gaining a more profound comprehension of the morphological disparities among seeds and for plant classification purposes.

However, there are some important points that need to be improved before further processing as follows:

Point 1, in the Introduction of the manuscript, although the research background and objectives are mentioned, the analysis of the current research status of seed morphology in the Nepetoideae subfamily is not in - depth enough. It fails to fully highlight the importance of this study in filling the knowledge gaps, nor does it elaborate on the crucial significance of seed morphology research for plant taxonomy and evolutionary research.

Point 2, in Materials and Methods of the manuscript: (1) when describing the calculation method of the J-index, it is recommended to supplement more details about model selection and adjustment, so that readers can better understand its application process. (2) Regarding the curvature analysis, it is recommended to add details about the error range and reliability assessment of the Bézier curve fitting in the methods section to enhance the credibility of the results.

Point 3, data presentation and chart making of the manuscript: It is recommended to unify the format of legends and annotations in all charts to enhance readability. For the PCA analysis chart (Figure 2), it is recommended to supplement the explanation of the contribution of the length and direction of the arrows to the principal components, so that readers can better understand the results.

Point 4, in the Discussion of the manuscript: When presenting the results of the hierarchical clustering analysis, it is advisable to offer a more in - depth interpretation of the dendrogram. This includes elaborating on the biological significance of the identified clusters, for example, discussing whether the clustering is related to plant habitats, genetic relationships, or other factors. This would help readers better understand the implications of the clustering results in the context of the Nepetoideae subfamily's characteristics.

Point 5, there is an abundance of data in the results section, and the charts are not closely correlated with the textual descriptions. This leads to a lack of emphasis on key points, making it difficult for readers to quickly extract the crucial information. It is recommended that in the textual description, important data be summarized to guide readers to focus on the core findings. For example, present the main characteristics of the seed morphological differences among different tribes and genera in a more intuitive manner.

Point 6, in the Abstract of the manuscript, it is recommended to add a sentence about the potential application prospects of the research, such as its specific uses in seed identification or plant taxonomy.

Author Response

“Seed geometry in the Nepetoideae (Lamiaceae).” is a good topic, which focuses on the research of the geometric morphology of seeds of plants in the Nepetoideae subfamily of the Lamiaceae family. The innovative application of geometric models, the J - index, and curvature analysis to quantify the seed shapes of the Nepetoideae subfamily overcomes the constraints of traditional descriptive methods. It offers novel concepts and approaches for research in this area, which is highly crucial for gaining a more profound comprehension of the morphological disparities among seeds and for plant classification purposes.

However, there are some important points that need to be improved before further processing as follows:

Dear Reviewer,

Thank you very much for your comments on the article, which have helped to improve the quality of the presentation. The points raised in your comments have been taken into account and a new version has been drafted which expands on these aspects. Below is a point-by-point list of comments:

Point 1, in the Introduction of the manuscript, although the research background and objectives are mentioned, the analysis of the current research status of seed morphology in the Nepetoideae subfamily is not in - depth enough. It fails to fully highlight the importance of this study in filling the knowledge gaps, nor does it elaborate on the crucial significance of seed morphology research for plant taxonomy and evolutionary research.

These aspects have been indicated in a new paragraph with added references in the Introduction. The application of seed morphological studies to the taxonomy of Nepetoideae has now been addressed with some examples and the potential of the general morphological measurements (J-index) and curvature analysis described here has been indicated.

Point 2, in Materials and Methods of the manuscript: (1) when describing the calculation method of the J-index, it is recommended to supplement more details about model selection and adjustment, so that readers can better understand its application process. (2) Regarding the curvature analysis, it is recommended to add details about the error range and reliability assessment of the Bézier curve fitting in the methods section to enhance the credibility of the results.

More details have been provided on both aspects, J index and curvature analysis, and their respective paragraphs have now been expanded in the Materials and Methods section.

Point 3, data presentation and chart making of the manuscript: It is recommended to unify the format of legends and annotations in all charts to enhance readability. For the PCA analysis chart (Figure 2), it is recommended to supplement the explanation of the contribution of the length and direction of the arrows to the principal components, so that readers can better understand the results.

The format of figure legends has been standardised. The explanation of PCA has been expanded to include the interpretation of the contribution of the length and direction of the arrows to the principal components.

Point 4, in the Discussion of the manuscript: When presenting the results of the hierarchical clustering analysis, it is advisable to offer a more in - depth interpretation of the dendrogram. This includes elaborating on the biological significance of the identified clusters, for example, discussing whether the clustering is related to plant habitats, genetic relationships, or other factors. This would help readers better understand the implications of the clustering results in the context of the Nepetoideae subfamily's characteristics.

The dendrogram has been now commented in more depth taking into account these considerations.

Point 5, there is an abundance of data in the results section, and the charts are not closely correlated with the textual descriptions. This leads to a lack of emphasis on key points, making it difficult for readers to quickly extract the crucial information. It is recommended that in the textual description, important data be summarized to guide readers to focus on the core findings. For example, present the main characteristics of the seed morphological differences among different tribes and genera in a more intuitive manner.

Subsections of Results have been rewritten to improve the clarity.

Point 6, in the Abstract of the manuscript, it is recommended to add a sentence about the potential application prospects of the research, such as its specific uses in seed identification or plant taxonomy.

The suggested sentence has been added.

Reviewer 3 Report

Comments and Suggestions for Authors

Dear Editors and Authors,

I read with interest the manuscript entitled “Seed geometry in the Nepetoideae (Lamiaceae)”. General morphological measurements and curvature analysis were carried out on a total of 21 species belonging to 9 genera, and comparisons were made between tribes as well as between genera, showing differences in both cases. Geometric models were obtained for each of the 21 species and applied by calculation of J-index to differentiate species in diverse genera. Therefore, the manuscript needs some adjustments so that it can then be forwarded to the publication process. The manuscript has the potential for publication in the journal Horticulturae and needs the following adjustments:

TITLE

- Add “in species of” Nepetoideae (Lamiaceae)

ABSTRACT

- The objectives should be described as follows: “The research objective was...”
- I suggest exploring the main results found further.

INTRODUCTION

- The excerpt mentioned in Line 82 is unnecessary: ​​“The combination of traditional morphometric measurements with J-index and curvature analysis contributes to the description of seed shape and its application in the taxonomy of the Nepetoideae.”
- Line 37. The information mentioned needs a reference. Add.
- Mention similar studies. There are many recent studies on the subject. Check.
- Insert hypotheses to support the objectives. Insert before the objectives.
- Regarding the objective, follow the suggestion in the Abstract.

MATERIAL AND METHODS

- Line 90: “The origin of the seeds and the collection date”. The collection date was not presented in the Table.
- Line 91: How was the return to nature carried out? Was it planted? Was it randomly distributed? How was it?
- Line 101: I could not find the supplementary material (Figure S1) in the submission system. Was it inserted?

- What program was used to analyze the images?
- It is interesting to detail how the image processing was done.
- I suggest adding a step-by-step guide as supplementary material. This will help other researchers who want to repeat the analyses in studies on this topic.
- I did not see the supplementary materials in the submission system. After the corrections, I would like to see them.
- Line 142: What would be the factor analysis? Does this analysis exist?
- Line 146: It is unnecessary to mention that p-values ​​below 0.05 were considered significant. This is an ANOVA rule.
- Mention that grouping was performed. This was shown in Figure 3 (Results).

RESULTS

- The legend of Table 2 needs to be completed.
- In Figure 2, correct the axes “Dim1” and “Dim2” for PC1 and PC2.

DISCUSSION

It is necessary to include other studies as a topic and try to relate them to the main results obtained with this research.

CONCLUSION

- It was mentioned several times that there were differences in the seeds evaluated. Review and avoid citing repeated information.

Author Response

Dear Editors and Authors,

I read with interest the manuscript entitled “Seed geometry in the Nepetoideae (Lamiaceae)”. General morphological measurements and curvature analysis were carried out on a total of 21 species belonging to 9 genera, and comparisons were made between tribes as well as between genera, showing differences in both cases. Geometric models were obtained for each of the 21 species and applied by calculation of J-index to differentiate species in diverse genera. Therefore, the manuscript needs some adjustments so that it can then be forwarded to the publication process. The manuscript has the potential for publication in the journal Horticulturae and needs the following adjustments:

TITLE

Add “in species of” Nepetoideae (Lamiaceae)

Done

ABSTRACT

- The objectives should be described as follows: “The research objective was...”
- I suggest exploring the main results found further.

Done

INTRODUCTION

- The excerpt mentioned in Line 82 is unnecessary: ​​“The combination of traditional morphometric measurements with J-index and curvature analysis contributes to the description of seed shape and its application in the taxonomy of the Nepetoideae.”

This sentence has been deleted

- Line 37. The information mentioned needs a reference. Add.

The sentence has been modified.

- Mention similar studies. There are many recent studies on the subject. Check.

Additional studies have been mentioned in the introduction.

- Insert hypotheses to support the objectives. Insert before the objectives.
- Regarding the objective, follow the suggestion in the Abstract.

Done

MATERIAL AND METHODS

- Line 90: “The origin of the seeds and the collection date”. The collection date was not presented in the Table.

The date of collection is presented for all those seeds that are not commercial.

- Line 91: How was the return to nature carried out? Was it planted? Was it randomly distributed? How was it?

This aspect has been expanded in the new version.

- Line 101: I could not find the supplementary material (Figure S1) in the submission system. Was it inserted?

As indicated in the Supplementary materials section, the supplementary materials are available in the following address:

https://zenodo.org/records/14654418

- What program was used to analyze the images?

The program used is Corel Photo-Paint 2020, and this has been now indicated in the section 2.4 of the Materials and Methods

- It is interesting to detail how the image processing was done.
- I suggest adding a step-by-step guide as supplementary material. This will help other researchers who want to repeat the analyses in studies on this topic.

A detailed explanation of the protocol has been given now  in section 2.4.

- I did not see the supplementary materials in the submission system. After the corrections, I would like to see them.

Please see:

https://zenodo.org/records/14654418

(It was indicated in the Supplementary materials section)

 
- Line 142: What would be the factor analysis? Does this analysis exist?

Factorial analysis is described in Sect. 3.1.

- Line 146: It is unnecessary to mention that p-values ​​below 0.05 were considered significant. This is an ANOVA rule.

The sentence has been deleted.

- Mention that grouping was performed. This was shown in Figure 3 (Results).

This is indicated in Sect. 3.1.

RESULTS

- The legend of Table 2 needs to be completed.

Done
- In Figure 2, correct the axes “Dim1” and “Dim2” for PC1 and PC2.

Done

DISCUSSION

It is necessary to include other studies as a topic and try to relate them to the main results obtained with this research.

Done

CONCLUSION

- It was mentioned several times that there were differences in the seeds evaluated. Review and avoid citing repeated information.

Done

 

 

Reviewer 4 Report

Comments and Suggestions for Authors

This is one of the relatively rare papers devoted to seed morphology and dealing with 21 species belonging to 9 genera (out of total 124 genera) in the subfamily Nepetoideae. Most of the representatives of this taxonomic group are medicinal plants and culinary herbs. Seed morphology is analysed in terms of geometry by using a modern open source software ImageJ developed for scientific image analysis. Basically, the manuscript is well-written, but there are some points to be considered and improved. From the botanical point of view it is a bit doubtful if the analyzed numbers of taxa may adequately represent their higher taxonomic ranks, e. g., the question is if one species (Perilla frutescens) may serve as a proxy for the whole tribe Elsholtzieae (Table 3). In any case, it would be useful to try and justify the number of species taken for the analysis and drawing inferences about higher taxa.
From the technical point of view it would be useful to define the major terms or keywords used with ImageJ software, such as area (bearing in mind that seed is a three-dimensional object), circularity, roundness, and solidity (2.3. Morphological measurements). Also, consider if a more technical term such as ‘contour‘ could replace the artistic one, ‘silhouette‘.
Other comments and suggestions (also indicated in the manuscript pdf):
Table 1: Consider correcting the header of the first column.
Lines 96 and 97: Replace ‘Tokio‘ with ‘Tokyo‘.
Line 100 and elsewhere: Replace ‘ppp‘ with ‘ppi‘.
Line 104: Replace “Image J“ with “ImageJ“.
Line 113: Teplace “J – index“ with “J-index“.
Table 2: Replace headers 1, 2, and 3 with PC1, PC2, and PC3, correspondingly.
Table 3: Add information to the table caption, like this: Different superscript letters denote significant differences within columns at p≤0.05, N – number of ...
Correct the header title in column one. Also, indicating genera in parentheses in the first column would be useful for readers.
Table 4: See above comment. Indicating species in parentheses in the first column would be useful for readers.
Figure 3: Indicating species (or their numbers) in parentheses for each genus would be useful for readers.
Table 5: Improve caption as suggested in the pdf.
Table 6: Correct header title of the column one.
Table 7: Improve caption as suggested in Table 5.
Table 8: Improve caption as suggested in Table 5.
Table 9: Correct header title of the column one.
Table 10: Improve caption as suggested in Table 5.
Table 11: Improve caption as suggested in Table 5.
Lines 387-388: Replace ‘subfamilie.‘ with ‘subfamily‘.
Line 426: Consider citation of a newer edition of Judd et al.: 4th edition, 2015.

See attached manuscript pdf for details.

Comments for author File: Comments.pdf

Author Response

This is one of the relatively rare papers devoted to seed morphology and dealing with 21 species belonging to 9 genera (out of total 124 genera) in the subfamily Nepetoideae. Most of the representatives of this taxonomic group are medicinal plants and culinary herbs. Seed morphology is analysed in terms of geometry by using a modern open source software ImageJ developed for scientific image analysis. Basically, the manuscript is well-written, but there are some points to be considered and improved. From the botanical point of view it is a bit doubtful if the analyzed numbers of taxa may adequately represent their higher taxonomic ranks, e. g., the question is if one species (Perilla frutescens) may serve as a proxy for the whole tribe Elsholtzieae (Table 3). In any case, it would be useful to try and justify the number of species taken for the analysis and drawing inferences about higher taxa.
From the technical point of view it would be useful to define the major terms or keywords used with ImageJ software, such as area (bearing in mind that seed is a three-dimensional object), circularity, roundness, and solidity (2.3. Morphological measurements). Also, consider if a more technical term such as ‘contour‘ could replace the artistic one, ‘silhouette‘.

Dear Reviewer,

Thank you very much for your commentaries to the article that have contributed to improve the quality of the presentation. The aspects raised in your commentary have been taken into consideration and a new version has been elaborated expanding on these aspects. Below follow commentaries point by point:

From the botanical point of view it is a bit doubtful if the analyzed numbers of taxa may adequately represent their higher taxonomic ranks, e. g., the question is if one species (Perilla frutescens) may serve as a proxy for the whole tribe Elsholtzieae (Table 3). In any case, it would be useful to try and justify the number of species taken for the analysis and drawing inferences about higher taxa.

The discussion on this aspect has been expanded in the explanations to the dendrogram in the discussion section.

From the technical point of view it would be useful to define the major terms or keywords used with ImageJ software, such as area (bearing in mind that seed is a three-dimensional object), circularity, roundness, and solidity (2.3. Morphological measurements). Also, consider if a more technical term such as ‘contour‘ could replace the artistic one, ‘silhouette‘.

Technical aspects are explained in section 2.3.

The term silhouette has been replaced by contour through the article.

Other comments and suggestions (also indicated in the manuscript pdf):

All the corrections indicated in the PDF have been done.

With best regards,

Emilio Cervantes

Corresponding author

 

 

Round 2

Reviewer 2 Report

Comments and Suggestions for Authors

Accept  in present form 

Reviewer 3 Report

Comments and Suggestions for Authors

The article has been corrected.