An Angiosperm Species Dataset Reveals Relationships between Seed Size and Two-Dimensional Shape

Round 1

Reviewer 1 Report

The objectives for this desk-based research on applying geometric models to seed shape are well argued and logical. Such an approach clearly has the potential to significantly improve precision and consistency when describing seed shape (supported by the J index for similarity to geometric shape). This will be of value in seed morphology and species taxonomic studies. As the authors note, they have created a preliminary version. But is does feel like a step in the right direction.
I have a few minor comments for the authors to address:
1. There are some typos in the manuscript and some inconsistencies (e.g., not underlining all orders) that need ironing out;
2) I was not sure about the argument concerning Arecaceae on Line273. Certainly many palm seeds are ellipsoid in shape. But Phoenix dactylifera is mentioned and its seed is elongated.
3) Figure 2 addressing the intra-generic variation in shape. But what attempt was made to explore any heterogeneity in shape within a seed lot? Is this seen to be a problem?
4) It would be good to know what plans the authors have to take the database forward. What needs to be done next?

Author Response

Dear Reviewer,

Thank you for your comments on our article that have contributed to improve the clarity of the presentation and the quality of the final version.

Concerning Phoenix dactylifera, seeds have an elongated shape that can be well adjusted to an elongated ellipse.

The question raised about attempts made to explore any heterogeneity in shape within a seed lot is very interesting. This is highly dependent on the seed species and variable also with seed lots, changing with the conditions of plant growth. Stable and favourable conditions result in a more homogeneous seed shape. This is one of the questions that may be the subject of further studies in particular concerning intraspecific variability.

We have added a Conclusions section with a paragraph mentioning our future plans concerning new versions of the database and the future of this line of research.

Reviewer 2 Report

Point 1: First of all, it is not clear to what type the manuscript belongs? Research article, review article or data descriptor?

Point 2: The title does not reflect the content. The database is given on a limited set of seeds, and the name says about all possible seeds.

Point 3 (about Excel file): On what device it was possible to ensure the accuracy of weighing the mass of 1000 seeds to four significant digits after the decimal point. In this case, the maximum and minimum values are even more accurate (up to 12 significant digits after the decimal point)?

How are the minimum and maximum seed weights the same, the average is missing, and the weight of 1000 seeds is greater (see line 12 in Excel)?

Why is there a bibliography at the end of the sheet (lines 346-354)? These strings make it difficult to retrieve data when creating, for example, SQL queries.

etc.

Point 4: In what units are the data presented in table 1? Why does the mean and standard deviation have a different number of digits after the decimal point?

Cited (line 240), "ANOVA revealed differences between samples and the 240 result of Scheffé test is shown in Table 1". However, the results are not shown in table 1, but in table 2.

Reference does not correspond to the template
https://www.mdpi.com/files/word-templates/horticulturae-template.dot

See Line 121 in template
"References must be numbered in order of appearance in the text (including citations in tables and legends) and listed individually at the end of the manuscript. We recommend preparing the references with a bibliography software package, such as EndNote, ReferenceManager or Zotero to avoid typing mistakes and duplicated references. Include the digital object identifier (DOI) for all references where available". 

See Line 148 in template

Title of Site. Available online: URL (accessed on Day Month Year).

Resume: I think that the manuscript confuses the reader and should be carefully revised in terms of its type, dimension of physical quantities, and carelessness in design.

Author Response

Dear Reviewer

Thank you for your comments on our article that have contributed to improve the clarity of the presentation and the quality of the final version.

Point 1: First of all, it is not clear to what type the manuscript belongs? Research article, review article or data descriptor?

Reply: The article was presented as a Research Article. Apart from the description of the data, it contains an introduction were the bibliography is reviewed and emphasis is made on the importance of shape quantification when possible. The results explore the relationship between seed shape and size by an original approach and the discussion reviews the distribution of the main seed types (based on similarity with geometric figures) in the families of Angiosperms. 

Point 2: The title does not reflect the content. The database is given on a limited set of seeds, and the name says about all possible seeds.

 Reply: Our intention is to increase the database with data of more species in the course of future research. Nevertheless the title is a Database of Seed Shape, and it does not promise to include shapes for all seeds, containing instead a representative number of species fitting geometric figures.

Point 3 (about Excel file): On what device it was possible to ensure the accuracy of weighing the mass of 1000 seeds to four significant digits after the decimal point. In this case, the maximum and minimum values are even more accurate (up to 12 significant digits after the decimal point)?

How are the minimum and maximum seed weights the same, the average is missing, and the weight of 1000 seeds is greater (see line 12 in Excel)?

Why is there a bibliography at the end of the sheet (lines 346-354)? These strings make it difficult to retrieve data when creating, for example, SQL queries.

etc.

Reply (about Excel file): Data on seed mass are not original for this publication. They were taken from other, previous databases for seed size and seed weight, as quoted in the text. Data of the line 12 in the old Excel document refers to Sesuvium portulacastrum seeds. Average value has now been included. Please note that maximum, minimum and average values refer to volume, not weight. The database has been corrected and all data adjusted to two digits after the decimal point. A new version of the database has been elaborated and uploaded taking in consideration all these aspects.

Bibliography that was at the end of the sheet has been moved to a new sheet.

Point 4: In what units are the data presented in table 1? Why does the mean and standard deviation have a different number of digits after the decimal point?

Cited (line 240), "ANOVA revealed differences between samples and the 240 result of Scheffé test is shown in Table 1". However, the results are not shown in table 1, but in table 2.

Reply: Units in table 1 are mm³ and this is now indicated in the corresponding legend to this table. All data have been adjusted to one digit after the decimal point in this table.

The sentence: "ANOVA revealed differences between samples and the result of Scheffé test is shown in Table 1" has been changed to:

"ANOVA revealed differences between samples and the result of Scheffé test is shown in Table 2". 

All references with a DOI have been corrected according to the instructions to authors. The manuscript has been revised according to your indications.

 

Reviewer 3 Report

The subject is interesting; however, I would suggest to modify the current manuscript as follow:

1. In the introduction: the Authors described the difficulties of seed shape description in different sections, but they did not discuss this problem based on the obtained result later on (in discussion).

2. In material methods: supplementary information of seed shape were provided, which contain different samples without any data (only name). I would suggest to remove them.

Line 154 was mentioned "... or new measurements...", It was not clear for me, which one the authors mean. May I also ask why the author did not do new measurement for the missing data.

3. the complete name of all abbreviation should be added.

4. The discussion should be modified based on different sections in the introduction and abstract.

 

Author Response

Dear Reviewer

Thank you for your comments on our article that have contributed to improve the clarity of the presentation and the quality of the final version.

1. In the introduction: the Authors described the difficulties of seed shape description in different sections, but they did not discuss this problem based on the obtained result later on (in discussion).

Reply： While the introduction presents a summary of the publications in the field, the discussion is written considering both the information presented in the introduction as well as the data from the results. The discussion has been now enlarged with the aspects indicated and a Conclusions section has been added indicating future avenues for research. All the entries in the seed shape database containing no data on J index (magnitude used for seed shape measurement) have been deleted. A new table has been elaborated and uploaded.

2. In material methods: supplementary information of seed shape were provided, which contain different samples without any data (only name). I would suggest to remove them.

Line 154 was mentioned "... or new measurements...", It was not clear for me, which one the authors mean. May I also ask why the author did not do new measurement for the missing data.

Reply: This sentence: "... or new measurements..." refeers to the origin of data in the database. Information related to it has been now indicated in the corresponding section of Materials and Methods, when related to the database it is mentioned:"...the database is provided in supplementary information; it contains a list of references for the entries."

3. the complete name of all abbreviation should be added.

Reply: The complete name of Cleome has been added when it was abbreviated.

4. The discussion should be modified based on different sections in the introduction and abstract.

Reply: The discussion has been modified according to the other sections and a Conclusions section has been added indicating future avenues for research.

Reviewer 4 Report

Comments to the manuscript entitled ‘A Database of Seed Shape’ (Manuscript Number: 545775) written by Emilio Cervantes, José Javier Martín Gómez, Diego Gutiérrez del Pozo and Luís Silva Dias.

 

In the manuscript, authors try to create a database of seed shape. Although there are already existing some seed shape databases (authors write about them in well written Introduction), the concept of the idea of linking the shape of the seeds with the geometric figure is new and interesting.

Despite this, reviewed manuscript cannot be published in the present form because:

It does not contain clearly define hypothesis and aim. The discussion is  poor and requires a complete rewriting. There is no conclusion. Conclusion(s) should answer the hypothesis and aim. In Material and methods authors should explain why they use diaspores other than seeds and how they can be compared with “naked” seeds. How many seeds (photos) of one species were used to choose fitting geometric figure?

 

There are also some smaller errors i.e. Figure 2 caption - ..(cardioid, oval and ellipse)… according to photo it should be …(cardioids, ellipse and oval).

 

Thus, I recommend the manuscript for publication but after the thorough major improvement.

Author Response

Dear Reviewer

Thank you for your comments on our article that have contributed to improve the clarity of the presentation and the quality of the final version.

The hypothesis of depart is that quantification of seed shape by comparison with geometric figures may help to clarify the relationships between seed shape and size, as well as in the long term with plant life style and contribute to open new ways for taxonomy and phylogeny. This is now indicated at the end of the introduction. The aims are indicated in the Abstract and they are: the classification of plant species according to their geometric type of seed, and seed shape quantification. As indicated in the abstract, there are no other databases of seed shape in the literature, the other seed databases concern volume and weight as described in the introduction.

In some instances diaspores have been used because it is very complicated or sometimes impossible to leave the seed naked without breaking it, and also these accompanying structures do allow us to clearly observe the shape of the seeds and compare or assign a defined shape.

The discussion has been rewritten and a conclusion has now been added indicating future avenues for research and smaller errors have been corrected.

Round 2

Reviewer 2 Report

To the comments submitted by me, the authors give rather vague vague answers.

 

Despite the point changes made by the authors in the manuscript, in my opinion, it still does not contain a clear reference to the type of article.

 

If this is a research paper, there is not enough data for statistical processing by the coefficient J.

If the authors took some of the data from other sources (they are given in the Excel file), it is a simple rewriting of the data.

 

To review article the manuscript is also not well suited, as it contains little specific and generic data.

There is no description of forms, tables, and interactions between them in the database for the data descriptor to which the manuscript is best named.

 

And, most importantly, the title of the article does not correspond to its content. First, it should contain a specific name indicating the types of seeds and the purpose of the database. Secondly, there is no classical database model in the article, without which neither the reader nor the researcher can judge its efficiency as a tool for the study of the form. Third, there is a clear conclusion, why and why do we need this database? Fourth, the file in the application is not a database, as the authors claim, but only a set of data in the form of a single table, which still lacks the designation of physical quantities of volume.

 

The relevance and significance of the shape of the seed no doubt, but with the same name it casts somenenie classical relational theory of databases.

 

I consider it expedient to recommend the authors to determine as specifically as possible the goals and objectives, the type of article, perhaps to carry out the necessary statistical calculations of the coefficient J and submit the article again with a clearer and more precise title.

Author Response

 

Thank you very much for your commentaries.

Following your advice we have classified and re-submit the work as “data descriptor”.

The title of the article has been changed to a more specific name and it is entitled now: “Seed shape quantification with geometric models reveals new relations between seed size and shape”.

The database has been corrected to include the designation of physical quantities of volume. The new version has a new DOI that has been indicated in the text.

The main hypotheses are presented in the abstract and in the introduction and results are presented in agreement with these and discussed. The main conclusion is now in relation to the title: Cardioid shape is more frequent in smaller seeds while, in the other two figures, the ellipse corresponds to larger seeds.

Concerning statistical analysis we agree that our data are not enough for a comparison of seed shape between species. What we have done, nevertheless, is not a comparison of seed shape between species but a comparison of seed size distribution between groups of species having the same shape (cardioid, ellipse, oval). We have done it by means of the Weibull equation which in this study allowed the identification of differences, as well as their limits, between the groups used. The following sentence has been added to the abstract: The application of Weibull equations to the interaction between size and shape shows smaller size in cardioid-type when compared to ellipse or ovoid-type seeds.

Reviewer 3 Report

Unfortunately, I could not see clear correlation between the described sources of confusion in Introduction (contain 3 points) and discussed results.

In line 145-147, A hypothesis is added, but I could not see any conclusion if the quantification of seed shape by comparison with geometric figures  help to clarify the relationships between seed shape and size, as well as in the long term with plant life style and contribute to open new ways for taxonomy and phylogeny.

 

Author Response

Thank you very much for your commentaries.

The correlation between the described sources of confusion in Introduction and discussed results is now highlighted in a new sentence in the discussion: “The similarity of seeds with geometric figures allows quantification of seed shape based on high values of J index. This allows unequivocal classification in seed types that is required for the study of the interaction between seed shape and other factors such as for example seed size, plant size, life cycle and others.”

The main hypotheses are presented in the abstract and in the introduction and the results are in agreement with these and discussed. The main conclusion is now in relation to the title: Cardioid shape is more frequent in smaller seeds while, in the other two figures, the ellipse corresponds to larger seeds.

The application of the Weibull equation allows to establish a difference that is statistically significant between the between groups of species having the same shape (cardioid, ellipse, oval). The following sentence has been added to the abstract: The application of Weibull equations to the interaction between size and shape shows smaller size in cardioid-type when compared to ellipse or ovoid-type seeds.

Reviewer 4 Report

The authors corrected manuscript as indicated. I recommend manuscript for publication.

Author Response

Thank you very much for your commentaries. They have contributed to improve the presentation of this article.

 

Round 3

Reviewer 2 Report

I believe that the article after even more specific clarification of the title and replacement throughout the text of the concept of " database "on the concept of" dataset", will be more interesting to the reader than in its original form.

See the attached file for some notes.

Comments for author File: Comments.pdf

Author Response

Thank you very much for this new review.

 

The word "database" has been changed to "dataset" across all the manuscript.

 

The manuscript title has been changed.

 

The "Author Contributions" section has been modified changing full authors names by initials.

Reviewer 3 Report

-

Author Response

Dear Reviewer,

We have changed the manuscript according to the latest comments and suggestions for authors from reviewer 2. We could not find any comment on the report of reviewer 3 corresponding to the 2nd review.