Can the Morphological Variation of Amazonian Bufonidae (Amphibia, Anura) Be Predicted by Their Habits and Habitats?

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

 

The manuscript titled “Can the morphological variation of Amazonian Bufonidae (Amphibia, Anura) be predicted by their habits and habitats?” is in a good presentation and contains a very relevant study. All the finds were minuncialy detailed and provides important data for the understanding of herpetofauna patterns of morphology, habits and habitats, specifically, to the Bufonidae family. So, I accept the manuscript with minor reviews described below.

 

Line 21:

We aimed to identify in this work the existence of morphological patterns in habitat use and diurnal or nocturnal habits of Bufonidae in the Brazilian Amazon.

 

Better use:

We aimed to identify in this work the existence of morphological patterns related to habitat use and diurnal or nocturnal habits of Bufonidae in the Brazilian Amazon.

 

Line 179

Which is the limit in each size, “large, medium, and small” ?

 

In results you could represent on the figures, the Three group you ant to represent. It turns better to understand.

Author Response

Altamira, Brazil, November 22, 2024

Ms. Bojana Radonjic

Section Managing Editor

Dear Bojana Radonjic,

We are pleased to resubmit our revised manuscript entitled “Can the morphological variation of Amazonian Bufonidae (Amphibia, Anura) be predicted by their habits and habitats?” (Previous submission ID: jzbg-3318899).

We sincerely appreciate the time and effort that you and the reviewers have dedicated to evaluating our manuscript. The insightful comments provided have significantly enhanced the quality of our work, and we have carefully addressed each of them in this revised version. At the conclusion of this letter, we outline the specific points raised by the reviewers (in bold) and detail the corresponding changes and justifications.

We remain open to further suggestions for improvement, should the reviewers require additional revisions, and we would be happy to continue refining the manuscript as necessary. We look forward to your feedback and hope the revised manuscript is now suitable for publication in Journal of Zoological and Botanical Gardens.

Sincerely,

The Authors

 

Comments and Suggestions for Authors

The manuscript titled “Can the morphological variation of Amazonian Bufonidae (Amphibia, Anura) be predicted by their habits and habitats?” is in a good presentation and contains a very relevant study. All the finds were minuncialy detailed and provides important data for the understanding of herpetofauna patterns of morphology, habits and habitats, specifically, to the Bufonidae family. So, I accept the manuscript with minor reviews described below.

Line 21: We aimed to identify in this work the existence of morphological patterns in habitat use and diurnal or nocturnal habits of Bufonidae in the Brazilian Amazon.

Better use: We aimed to identify in this work the existence of morphological patterns related to habitat use and diurnal or nocturnal habits of Bufonidae in the Brazilian Amazon.

Thank you for your suggestion. We have made the changes, and we believe the manuscript is now improved.

Line 179: Which is the limit in each size, “large, medium, and small” ?

We have added the information regarding the values for large, medium, and small sizes.

In results you could represent on the figures, the Three group you ant to represent. It turns better to understand.

We have added the information regarding the values for large, medium, and small sizes in the figure.

Comments and Suggestions for Authors

Dear authors,

This work is interesting because it aims to analyze a community of Amazonian toads, trying to connect morphological and ecological variation. Yet, I found some major issues with analyses that must be addressed by the authors to make the work more robust. Below are my specific comments.

Introduction

I think the hypothesis stated at the end of the introduction is interesting, but then it is good to have a paragraph on water balance in frogs, maybe touching on the water conservation hypothesis, to make the predictions more connected with theory and previous work.

Thank you for your valuable comment. We have added a paragraph on the proposed topic, incorporating relevant studies.

Material and Methods

General comment: If the hypothesis is about risk of desiccation, why not use climatic variables, such as precipitation, as relevant ecological variables to relate with morphology?

We thank the reviewer for the suggestion. However, in our case, the use of this metric would not be feasible, as the climatic variables would be the same for all points, and the study area would be too small for this test. Nonetheless, we appreciate the idea and plan to implement it in a new manuscript aimed at testing the precipitation gradient and body size.

Section 2.1 How many species were analyzed and what was the average sample size per species? This is written in the Results but should be moved up to this section.

We have added the requested information.

Section 2.2 I did not have access to the supplementary tables, but there should be a supplementary table that shows the classification for each ecological variable for every species. It would be important to know if a single species lives in more than one forest type for example.

Depending on the variable studied, a species can indeed be included in more than one category, such as species that can occupy upland, wetland, and riparian areas. This information is quite complex to assess by simply looking at the table; therefore, we conducted a Multiple Correspondence Analysis (MCA), which is like PCA but designed for categorical data. The relationship between species and habitat types was summarized through the MCA and is presented in Supplementary Table 03. Additionally, we can provide the original data upon request and subject to usage conditions.  

Section 2.3 I’m not familiar with MCA, however, the authors should better explain what this analysis does in general terms. From Table 2, I understood that it combines variables in single dimensions. Yet, why are there dimensions with several levels of the categorical variable grouped (e.g., PPxSFxAA) but also dimensions with just one single level of the categorical variable (e.g., just PP) for vegetation type, environment and spawning environment?

The combinations were necessary due to the presence of species that occupy more than one category. For example, species that occupy Undisturbed Forest, Forest in Regeneration, and Areas Whose Original Features Have Been Changed need to be classified as a separate category from those that occupy only one of these areas or any other combination of these habitats.

Also, perhaps a supplementary table that describes the correlations of the variables to the dimensions would be clarifying?

We have added the table with the values as supplementary material.

It is not clear what are differences between Euclidian and Gower distances. That should be explained in the text. Also, both NMDS and the Procrustes analyses should be better explained. For instance, I’m familiar with using Procrustes analysis to derive shape variables, and then use these shape variables as response variables in phylogenetic regressions.

We used Euclidean distance for continuous variables and Gower distance for categorical variables. Regarding NMDS and Procrustes analysis, we performed a non-metric multidimensional scaling (NMDS) analysis to identify patterns in the datasets and used the first five factors as variables to conduct the Procrustes analysis, which allowed us to assess the correlation between the datasets. We have added this information to the relevant section.

All the matrices discussed should be shown as supplementary tables or even data.

We add this information as a supplementary table.

The RDA should also be explained in more detail so that readers can better follow the logic of the analysis.

We have added this information to the section.

Finally, is there a way to incorporate the relatedness among species in the analysis? After all, species means are not independent data and species more closely related may also be more similar in ecology because of phylogenetic effects. At least using a phylogenetic PCA (Revell 2009) for morphology would be good, and then using species scores on the PCs in subsequent analyses that have ecological axes as predictors. The species are likely all sampled in the phylogeny of Portik et al. 2023.

Revell, L. J. (2009). Size-correction and principal components for interspecific comparative studies. Evolution, 63(12), 3258-3268.

Portik, D. M., Streicher, J. W., & Wiens, J. J. (2023). Frog phylogeny: a time-calibrated, species-level tree based on hundreds of loci and 5,242 species. Molecular Phylogenetics and Evolution, 188, 107907.

We appreciate the submission of the references and have incorporated the phylogenetic signal by adding the species as a covariate in the analyses.

Results

It is important to also describe morphological PC2.

We have added this information to the section.

Figure 1A and 1B can be plotted in the same panel, the species as points and the variables as arrows in which the length indicates how much the variable contributes to the axes.

We appreciate your suggestion, but we prefer to keep the figures separate for better interpretation of the results. However, we have rearranged the acronyms to avoid any overlap.

The same for Figure 2A and 2B. Also, there should be no overlap on the acronyms for the categorical variables in the plots.

We appreciate your suggestion, but we insist on keeping the figures separate for better interpretation of the results. However, we have rearranged the acronyms to avoid any overlap.

All figures: The captions need much more information than what is currently there. For instance, the acronyms should be described.

We have made modifications and improvements.

When describing NMDS results, it is not clear what the percentages mean.

The percentage refers to the correlation between the ordinations. We have clarified this in the text.

Figure 3: Should there actually be a morphological RDA1 and RDA2 and an ecological RDA1 and RDA2? Given that there are PC axes to describe morphology, why not perform a regression between morphological PCs and ecological RDA axes? Even better if PCs could come from a phylogenetic PCA.

The RDA already represents the correlation between the morphological and ecological variables, so no further analysis is necessary. We have improved the explanation in the text.

Discussion

It is important to try to connect the results with the desiccation hypothesis. Is there empirical evidence to support the hypothesis?

All the data presented in our study are empirical, collected during fieldwork.

The lack of a phylogenetic context for the analyses makes it hard to understand the relative roles of phylogeny and ecology to explain the patterns found.

We appreciate the suggestion regarding phylogeny, but in this study, our aim was to relate morphological measurements with species' habit and habitat characteristics, without addressing phylogenetic retention or synapomorphies. Therefore, we included species as covariates and treated them as sampling units. However, in future work, we plan to investigate the retention of these traits in relation to phylogeny, inferring the relationship between phylogenetic signal and morphological adaptations to impacted environments.

Author Response File: Author Response.docx

Reviewer 2 Report

Comments and Suggestions for Authors

Dear authors,

This work is interesting because it aims to analyze a community of Amazonian toads, trying to connect morphological and ecological variation. Yet, I found some major issues with analyses that must be addressed by the authors to make the work more robust. Below are my specific comments.

Introduction

I think the hypothesis stated at the end of the introduction is interesting, but then it is good to have a paragraph on water balance in frogs, maybe touching on the water conservation hypothesis, to make the predictions more connected with theory and previous work.

Material and Methods

General comment: If the hypothesis is about risk of desiccation, why not use climatic variables, such as precipitation, as relevant ecological variables to relate with morphology?

Section 2.1 How many species were analyzed and what was the average sample size per species? This is written in the Results but should be moved up to this section.

Section 2.2 I did not have access to the supplementary tables, but there should be a supplementary table that shows the classification for each ecological variable for every species. It would be important to know if a single species lives in more than one forest type for example.

Section 2.3 I’m not familiar with MCA, however, the authors should better explain what this analysis does in general terms. From Table 2, I understood that it combines variables in single dimensions. Yet, why are there dimensions with several levels of the categorical variable grouped (e.g., PPxSFxAA) but also dimensions with just one single level of the categorical variable (e.g., just PP) for vegetation type, environment and spawning environment?

Also, perhaps a supplementary table that describes the correlations of the variables to the dimensions would be clarifying?

It is not clear what are differences between Euclidian and Gower distances. That should be explained in the text. Also, both NMDS and the Procrustes analyses should be better explained. For instance, I’m familiar with using Procrustes analysis to derive shape variables, and then use these shape variables as response variables in phylogenetic regressions.

All the matrices discussed should be shown as supplementary tables or even data.

The RDA should also be explained in more detail so that readers can better follow the logic of the analysis.

Finally, is there a way to incorporate the relatedness among species in the analysis? After all, species means are not independent data and species more closely related may also be more similar in ecology because of phylogenetic effects. At least using a phylogenetic PCA (Revell 2009) for morphology would be good, and then using species scores on the PCs in subsequent analyses that have ecological axes as predictors. The species are likely all sampled in the phylogeny of Portik et al. 2023.

Revell, L. J. (2009). Size-correction and principal components for interspecific comparative studies. Evolution, 63(12), 3258-3268.

Portik, D. M., Streicher, J. W., & Wiens, J. J. (2023). Frog phylogeny: a time-calibrated, species-level tree based on hundreds of loci and 5,242 species. Molecular Phylogenetics and Evolution, 188, 107907.

Results

It is important to also describe morphological PC2.

Figure 1A and 1B can be plotted in the same panel, the species as points and the variables as arrows in which the length indicates how much the variable contributes to the axes. The same for Figure 2A and 2B. Also, there should be no overlap on the acronyms for the categorical variables in the plots.

All figures: The captions need much more information than what is currently there. For instance, the acronyms should be described.

When describing NMDS results, it is not clear what the percentages mean.

Figure 3: Should there actually be a morphological RDA1 and RDA2 and an ecological RDA1 and RDA2? Given that there are PC axes to describe morphology, why not perform a regression between morphological PCs and ecological RDA axes? Even better if PCs could come from a phylogenetic PCA.

Discussion

It is important to try to connect the results with the desiccation hypothesis. Is there empirical evidence to support the hypothesis?

The lack of a phylogenetic context for the analyses makes it hard to understand the relative roles of phylogeny and ecology to explain the patterns found.

Comments on the Quality of English Language

The English should be improved to enhance comprehension.

Author Response

Altamira, Brazil, November 22, 2024

Ms. Bojana Radonjic

Section Managing Editor

Dear Bojana Radonjic,

We are pleased to resubmit our revised manuscript entitled “Can the morphological variation of Amazonian Bufonidae (Amphibia, Anura) be predicted by their habits and habitats?” (Previous submission ID: jzbg-3318899).

We sincerely appreciate the time and effort that you and the reviewers have dedicated to evaluating our manuscript. The insightful comments provided have significantly enhanced the quality of our work, and we have carefully addressed each of them in this revised version. At the conclusion of this letter, we outline the specific points raised by the reviewers (in bold) and detail the corresponding changes and justifications.

We remain open to further suggestions for improvement, should the reviewers require additional revisions, and we would be happy to continue refining the manuscript as necessary. We look forward to your feedback and hope the revised manuscript is now suitable for publication in Journal of Zoological and Botanical Gardens.

Sincerely,

The Authors

 

Comments and Suggestions for Authors

The manuscript titled “Can the morphological variation of Amazonian Bufonidae (Amphibia, Anura) be predicted by their habits and habitats?” is in a good presentation and contains a very relevant study. All the finds were minuncialy detailed and provides important data for the understanding of herpetofauna patterns of morphology, habits and habitats, specifically, to the Bufonidae family. So, I accept the manuscript with minor reviews described below.

Line 21: We aimed to identify in this work the existence of morphological patterns in habitat use and diurnal or nocturnal habits of Bufonidae in the Brazilian Amazon.

Better use: We aimed to identify in this work the existence of morphological patterns related to habitat use and diurnal or nocturnal habits of Bufonidae in the Brazilian Amazon.

Thank you for your suggestion. We have made the changes, and we believe the manuscript is now improved.

Line 179: Which is the limit in each size, “large, medium, and small” ?

We have added the information regarding the values for large, medium, and small sizes.

In results you could represent on the figures, the Three group you ant to represent. It turns better to understand.

We have added the information regarding the values for large, medium, and small sizes in the figure.

Comments and Suggestions for Authors

Dear authors,

This work is interesting because it aims to analyze a community of Amazonian toads, trying to connect morphological and ecological variation. Yet, I found some major issues with analyses that must be addressed by the authors to make the work more robust. Below are my specific comments.

Introduction

I think the hypothesis stated at the end of the introduction is interesting, but then it is good to have a paragraph on water balance in frogs, maybe touching on the water conservation hypothesis, to make the predictions more connected with theory and previous work.

Thank you for your valuable comment. We have added a paragraph on the proposed topic, incorporating relevant studies.

Material and Methods

General comment: If the hypothesis is about risk of desiccation, why not use climatic variables, such as precipitation, as relevant ecological variables to relate with morphology?

We thank the reviewer for the suggestion. However, in our case, the use of this metric would not be feasible, as the climatic variables would be the same for all points, and the study area would be too small for this test. Nonetheless, we appreciate the idea and plan to implement it in a new manuscript aimed at testing the precipitation gradient and body size.

Section 2.1 How many species were analyzed and what was the average sample size per species? This is written in the Results but should be moved up to this section.

We have added the requested information.

Section 2.2 I did not have access to the supplementary tables, but there should be a supplementary table that shows the classification for each ecological variable for every species. It would be important to know if a single species lives in more than one forest type for example.

Depending on the variable studied, a species can indeed be included in more than one category, such as species that can occupy upland, wetland, and riparian areas. This information is quite complex to assess by simply looking at the table; therefore, we conducted a Multiple Correspondence Analysis (MCA), which is like PCA but designed for categorical data. The relationship between species and habitat types was summarized through the MCA and is presented in Supplementary Table 03. Additionally, we can provide the original data upon request and subject to usage conditions.  

Section 2.3 I’m not familiar with MCA, however, the authors should better explain what this analysis does in general terms. From Table 2, I understood that it combines variables in single dimensions. Yet, why are there dimensions with several levels of the categorical variable grouped (e.g., PPxSFxAA) but also dimensions with just one single level of the categorical variable (e.g., just PP) for vegetation type, environment and spawning environment?

The combinations were necessary due to the presence of species that occupy more than one category. For example, species that occupy Undisturbed Forest, Forest in Regeneration, and Areas Whose Original Features Have Been Changed need to be classified as a separate category from those that occupy only one of these areas or any other combination of these habitats.

Also, perhaps a supplementary table that describes the correlations of the variables to the dimensions would be clarifying?

We have added the table with the values as supplementary material.

It is not clear what are differences between Euclidian and Gower distances. That should be explained in the text. Also, both NMDS and the Procrustes analyses should be better explained. For instance, I’m familiar with using Procrustes analysis to derive shape variables, and then use these shape variables as response variables in phylogenetic regressions.

We used Euclidean distance for continuous variables and Gower distance for categorical variables. Regarding NMDS and Procrustes analysis, we performed a non-metric multidimensional scaling (NMDS) analysis to identify patterns in the datasets and used the first five factors as variables to conduct the Procrustes analysis, which allowed us to assess the correlation between the datasets. We have added this information to the relevant section.

All the matrices discussed should be shown as supplementary tables or even data.

We add this information as a supplementary table.

The RDA should also be explained in more detail so that readers can better follow the logic of the analysis.

We have added this information to the section.

Finally, is there a way to incorporate the relatedness among species in the analysis? After all, species means are not independent data and species more closely related may also be more similar in ecology because of phylogenetic effects. At least using a phylogenetic PCA (Revell 2009) for morphology would be good, and then using species scores on the PCs in subsequent analyses that have ecological axes as predictors. The species are likely all sampled in the phylogeny of Portik et al. 2023.

Revell, L. J. (2009). Size-correction and principal components for interspecific comparative studies. Evolution, 63(12), 3258-3268.

Portik, D. M., Streicher, J. W., & Wiens, J. J. (2023). Frog phylogeny: a time-calibrated, species-level tree based on hundreds of loci and 5,242 species. Molecular Phylogenetics and Evolution, 188, 107907.

We appreciate the submission of the references and have incorporated the phylogenetic signal by adding the species as a covariate in the analyses.

Results

It is important to also describe morphological PC2.

We have added this information to the section.

Figure 1A and 1B can be plotted in the same panel, the species as points and the variables as arrows in which the length indicates how much the variable contributes to the axes.

We appreciate your suggestion, but we prefer to keep the figures separate for better interpretation of the results. However, we have rearranged the acronyms to avoid any overlap.

The same for Figure 2A and 2B. Also, there should be no overlap on the acronyms for the categorical variables in the plots.

We appreciate your suggestion, but we insist on keeping the figures separate for better interpretation of the results. However, we have rearranged the acronyms to avoid any overlap.

All figures: The captions need much more information than what is currently there. For instance, the acronyms should be described.

We have made modifications and improvements.

When describing NMDS results, it is not clear what the percentages mean.

The percentage refers to the correlation between the ordinations. We have clarified this in the text.

Figure 3: Should there actually be a morphological RDA1 and RDA2 and an ecological RDA1 and RDA2? Given that there are PC axes to describe morphology, why not perform a regression between morphological PCs and ecological RDA axes? Even better if PCs could come from a phylogenetic PCA.

The RDA already represents the correlation between the morphological and ecological variables, so no further analysis is necessary. We have improved the explanation in the text.

Discussion

It is important to try to connect the results with the desiccation hypothesis. Is there empirical evidence to support the hypothesis?

All the data presented in our study are empirical, collected during fieldwork.

The lack of a phylogenetic context for the analyses makes it hard to understand the relative roles of phylogeny and ecology to explain the patterns found.

We appreciate the suggestion regarding phylogeny, but in this study, our aim was to relate morphological measurements with species' habit and habitat characteristics, without addressing phylogenetic retention or synapomorphies. Therefore, we included species as covariates and treated them as sampling units. However, in future work, we plan to investigate the retention of these traits in relation to phylogeny, inferring the relationship between phylogenetic signal and morphological adaptations to impacted environments.

Author Response File: Author Response.docx