PONE-D-22-31726Demystifying Cassiopea species identity in the Florida Keys: Cassiopea xamachana and Cassiopea andromeda coexist in shallow watersPLOS ONE

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Additional Editor Comments:

Dear Dr. Kaden Muffett,

I received feedback from three reviewers and both were very positive about your manuscript. In this way, I indicate that your manuscript can be accepted soon after making the specific modifications indicated by the reviewers. Please review the points listed and send us an updated version of your manuscript.

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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: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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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: dear authors,

the topic of your paper is very interesting and the paper opens a lot of questions on the species identification in that location where two different species coexist as well as past taxonomic misidentifications. All presented results seems to support the conclusion even if sometimes are a litlle bit confusing as stated along the manuscript file pdf attached.

all data of the manuscript are available. Please see the file attached for detailed comments

regards

Reviewer #2: General comments:

This is a very interesting paper about identifying species of Cassiopea in Florida. The study highlights the cryptic nature of Cassiopea and the importance of using molecular work for species identification. Additionally, it confirms that multiple species of Cassiopea can co-exist in the same area, and so location should not be used as a factor to identify species.

Overall, the paper is well written, and represents the results in a way that is easy to understand and interpret. However, I do have a couple of comments and questions that should be addressed in the paper. Mainly, the authors conclude that C. andromeda and C. xamachana are different species based off genetics and morphology. However, the authors also state that they did not complete any detailed morphological comparison between the two species. To be able to definitively conclude that there are two species occurring, especially as they so closely related, a detailed morphological comparison needs to be done before making such a conclusion. As a result, the authors need to tone back their conclusion that they are definitely different species and include another paragraph in the discussion discussing this further, along with strengthening their argument about why the authors concluded that there are two species based on genetics.

Specific comments:

Abstract:

Line 10: “upset multiple times” is unclear terminology. “Confused” may be a better term to use here

Introduction:

Line 26: “sampled broadly but shallowly” is confusing terminology. Do the authors mean shallow depth here? What depths do they define as shallow? These references refer to Cassiopea, which are typically found in shallow environments. Aurelia have been collected at depths of up to 18m though and so a clearer way of describing this could be close to shore.

Line 30: What other scyphozoan lineages?

Line 44: Is C. xamachana morphologically distinct from C. andromeda? They have often been confused taxonomically because they have similar morphological characteristics. Additionally, this is conflicting with the rest of the paper.

Line 61: I think the authors need to clarify that they did not look at deeper depths, where C. frondosa are known to occur. Cite the Fitt et al. 2021 paper.

Methods:

Line 69: What was measured? Their diameter?

Line 70: why were the samples put in ethanol rather than formalin for morphological analysis?

Results:

Line 136: Need references for previously published mitogenomes

Line 152: There are other sequences of C. xamachana on Genbank that are not in the Caribbean. Please see Stampar et al (2021) The puzzling occurrence of the upside-down jellyfish Cassiopea (Cnidaria: Scyphozoa) along the Brazilian coast: a result of several invasion events? And Gamero-Mora (2019) Regenerative capacity of the upside-down jellyfish Cassiopea xamachana.

Line 188: How shallow?

Line 190: How did the authors measure the density for each site? This is not included in the methods.

Line 194: Deeper sampling? What depths do they mean by this? Cassiopea frondosa has been sampled at deeper depths within the area so this needs to be clarified

Line 201: These stats for the difference between bell diameters needs to be included in the methods

Line 204: If no comparative morphological analysis could be done, line 198 needs to be revised. The authors shouldn’t state that there were no morphological differences between the two species if no detailed comparison was done

Line 211: A bit more detail needs to be provided here. Did the colour vary between species as well as between sites?

Discussion:

Line 214: Remove “dramatically”

Line 216: Remove “only”

Line 221: Hard to conclude that C. andromeda and C. xamachana are different species when they are in the same monophyletic group and this study did not do any morphological comparisons, but state that there was no morphological difference between species. This sentence needs to be revised as such as I don’t believe the authors can confidently state that C. andromeda and C. xamachana are different species without a proper morphological comparison. If the authors are going to state there are no morphological differences between the species, references need to be included to support this.

Expanding on above, I think the authors need to include a paragraph discussing how a proper morphological comparison needs to be done to support their findings that genetics shows that two species are occurring in Florida.

Line 265: Again, the authors state that there were no morphological differences between the two species, but have also acknowledged that they didn’t do a detailed morphological comparison.

Reviewer #3: The manuscript is well written, clear and easy to understand. Below are some specific observations/ suggestions.

Line 15 – Scientific names are commonly written out in full when they first appear in the abstract.

Lines 31, 42, 94, etc. – The names are again written out in full when they first appear after the abstract and are then abbreviated upon further use.

Line 43 -- Ecotype could replaced by species or taxon.

Line 65 – “through agreement >98% to either genome.”, which is the reference to those genomes?

Line 112 – For the multi-gene analysis (16S+COI), do the authors allowed individual models for the different genomic loci (genes or codon positions)? Why does the 28S dataset was not included in the combined analysis for tree generation?

Lines 140, 154, 160, 228, etc. – Mastigias papua, Versuriga anadyomene, Cassiopea andromeda, Cassiopea xamachana can be abbreviated (they were written out in full previously).

Some scientific names appear abbreviated at the beginning of sentences (e.g., line 176) while others were written out in full at the beginning of sentences (e.g., line 162), I suggest homogenizing the format.

Figure 3b could be improved by adding information about latitude and longitude (e.g., by adding, to the figure, an upper layer with a coordinate grid) and using a bigger font size for “Gulf of Mexico” and “Florida Keys ”

Figure 4 could be improved by coloring with two colors the circles that indicate the locations where both species were recorded (black and white as in figure three).

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Reviewer #1: No

Reviewer #2: No

Reviewer #3: No

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Attachments

Attachment

Submitted filename: PONE-D-22-31726_rev.pdf

Demystifying Cassiopea species identity in the Florida Keys: Cassiopea xamachana and Cassiopea andromeda coexist in shallow waters

PONE-D-22-31726R1

Dear Dr. Muffett,

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.

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Kind regards,

Sergio N. Stampar, Dr.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Dear authors,

After further evaluation by the reviewers, I am pleased to inform that the manuscript is ready for publication in Plos One.

Kind regards

Sergio Stampar

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

Reviewer #2: All comments have been addressed

Reviewer #3: All comments have been addressed

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: (No Response)

Reviewer #3: Yes

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

Reviewer #1: N/A

Reviewer #2: (No Response)

Reviewer #3: Yes

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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: (No Response)

Reviewer #3: Yes

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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: (No Response)

Reviewer #3: Yes

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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: dear authors, you have made the manuscript better by following the reviewers' comments. good for pubblication

Reviewer #2: (No Response)

Reviewer #3: (No Response)

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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: Yes: Edgar Gamero-Mora

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