Investigating an Unknown Biodiversity: Evidence of Distinct Lineages of the Endemic Chola Guitarfish Pseudobatos percellens Walbaum, 1792 in the Western Atlantic Ocean
, Matheus M. Rotundo 2, PatrÃcia Charvet 3, Beatriz R. Boza 1, Bruno C. Souza 1, Najila N. C. D. Cerqueira 1, Claudio Oliveira 1, Rosângela Lessa 4 and Fausto Foresti 1Round 1
Reviewer 1 Report
Cruz et al.
Investigating an unknown biodiversity: evidence of distinct lineages of the endemic Chola Guitarfish Pseudobatos percellens Walbaum, 1792 in the Western Atlantic Ocean
L21: where they (no comma)
L45: unclear to which ‘standards’ refers
L49: that compromises
L55: late age
L72: marine environments have biological characteristics?? Recast
L81: why does this stand out??
L91: parts instead of points
L103: why these three regions specifically?
L109: “of the existence of a single lineage throughout its distributional range along”
L283: high instead of intense
L325: anecdotal
L358-363: How is this related to the present study??
L372-: if youre going to erect this hypothesis, then the reader needs more information about the temperature regions over which these samples were collected. This also should be mentioned in the introduction as a potential biogeographic boundary isolating populations. As is, there isn’t any real support mentioned in the manuscript.
L380: could there be a test of isolation by distance included in the pper? A simple mantel test with distance versus Fst (or a suitable linearized measure of genetic distance) would suffice. Included in this test, a multiple factor matrix mantel, could be other simple measures such currents etc.
L395: I think a lot of this belongs in the introduction and then brought up in a test in the results/discussion
L421: what other species, the two mentioned? What about other fishes beyond rays?
L431: provide a basis? Not sure what subsidies refers to here
L435: this refers to mtDNA and the data presented are SNPs, which I assume are biparental. The COI sequences aren’t terribly appropriate for population genetics, so what exactly is the point of this paragraph??
L442: are you suggesting that there is species-level divergences here? If so, where are the supporting data for this hypothesis? How exactly does these SNP data suggest that a taxonomic revision is required? It would really help if there is some context given regarding levels of divergence for other elasmobranchs.
Overall: This is an interesting paper that suggests large phylogeographic breaks with the study species. The manuscript would be better served if the hypotheses plus supporting data are clearly defined in the introduction. The manuscript could be shortened somewhat by deleting a lot of the barcoding analyses (and methods) since these data are used primarily for species identification. If they are retained, then it is worth mention how these data compare to the SNP data and whether it is even an appropriate locus to do this comparison. There are entirely way too many citations for such a short manuscript – I suggest that some extensive editing of these citations is necessary. Finally, the conclusions drawn are rather straightforward, but the ‘causal’ factors inadequately defined up front in the Introduction.
There is a real need for some extensive editing of the English and syntax
Author Response
Dear,
Please find enclosed the manuscript: “Investigating an unknown biodiversity: evidence of distinct lineages of the endemic Chola Guitarfish Pseudobatos percellens (Walbaum, 1792) in the Western Atlantic Ocean” by Cruz VP, Rotundo MM, Charvet P, Boza BR, Campos BS, Cerqueira NCND, Oliveira C, Lessa RP, Foresti F. We wish to have the manuscript considered for publication in the Diversity, in Special issue: "Wildlife Population Genetics, Evolution and Conservation: From Theory to Practice".
This manuscript is a revised version of our previous submitted manuscript with the number ID diversity-2196742.
I am submitting a new revised file, with the changes made highlighted using "track Changes” feature in Microsoft Word. Following your request, we have detailed our response for the reviewers in the following pages. In order to provide clarity, we have included the reviewer comments in italics and our answer just below in bold.
We believe that reviewers comments now have been adequately addressed through our responses. We thank you for your time towards improving this manuscript, which we hope is now acceptable for publication in Diversity.
All suggestions raised by the reviewers were accepted.
Furthermore, as required, the article was reviewed by a native English speaker.
Below are some comments on specific points.
#Review 1:
L81: why does this stand out??
Answer: P. percellens is a species still little investigated, and this information is an interesting data relating the size with the sex of the individuals.
L103: why these three regions specifically?
Answer: Because these two of these regions cover the extremes of the Brazilian coast, and a third for a better understanding.
L358-363: How is this related to the present study??
Answer: because we do not know if there was (or when) reproductive isolation over time in these species.
L380: could there be a test of isolation by distance included in the pper? A simple mantel test with distance versus Fst (or a suitable linearized measure of genetic distance) would suffice. Included in this test, a multiple factor matrix mantel, could be other simple measures such currents etc.
Answer: As suggested by the reviewer, it was inserted the simple mantel test with distance versus Fst.
L435: this refers to mtDNA and the data presented are SNPs, which I assume are biparental. The COI sequences aren’t terribly appropriate for population genetics, so what exactly is the point of this paragraph??
Answer: In line L435: we mentioned that many researchers considered P. percellens to be a widely distributed species, but we saw that in reality, this can present different lineages, with a resident behavior. We did not mention the DNA barcode, because in this study, we used the barcode only to confirm the molecular identification, therefore we did not carry out population analyzes with the COI.
L442: are you suggesting that there is species-level divergences here? If so, where are the supporting data for this hypothesis? How exactly does these SNP data suggest that a taxonomic revision is required? It would really help if there is some context given regarding levels of divergence for other elasmobranchs.
Answer: No. For better understanding we made a change in the writing, however here we highlight (once again) that the population results indicate the existence of two lineages of P. percellens distributed along the Brazilian coast.
Overall: This is an interesting paper that suggests large phylogeographic breaks with the study species. The manuscript would be better served if the hypotheses plus supporting data are clearly defined in the introduction. The manuscript could be shortened somewhat by deleting a lot of the barcoding analyses (and methods) since these data are used primarily for species identification. If they are retained, then it is worth mention how these data compare to the SNP data and whether it is even an appropriate locus to do this comparison. There are entirely way too many citations for such a short manuscript – I suggest that some extensive editing of these citations is necessary. Finally, the conclusions drawn are rather straightforward, but the ‘causal’ factors inadequately defined up front in the Introduction.
Answer: Obliged by considerations. However, the questions and hypotheses in this article are clearly stated at the end of the introduction. Regarding "shortened somewhat by deleting a lot of the barcoding analyzes (and methods)", it is not a good idea, since the readers will question it or the fact that individuals previously identified as P. percellens have actually been analyzed. And even about the number of quotes, it is relative, since it is an art that discusses the genetic results, associated with characteristics of the environment.
Author Response File: 
Author Response.pdf
Reviewer 2 Report
This is a well written and informative manuscript on a wide ranging but under studies elasmobranch, the Chola Guitarfish, Pseudobatos percellens. I appreciated the authors use of both DNA barcoding, an established and widely used method to genetically identify species, and the use of SNPs, a relatively new method with more power to determine genetic structure. I have no issues with the content, the analyses or the way the results were presented. Well done.
Author Response
Dear,
Please find enclosed the manuscript: “Investigating an unknown biodiversity: evidence of distinct lineages of the endemic Chola Guitarfish Pseudobatos percellens (Walbaum, 1792) in the Western Atlantic Ocean” by Cruz VP, Rotundo MM, Charvet P, Boza BR, Campos BS, Cerqueira NCND, Oliveira C, Lessa RP, Foresti F. We wish to have the manuscript considered for publication in the Diversity, in Special issue: "Wildlife Population Genetics, Evolution and Conservation: From Theory to Practice".
This manuscript is a revised version of our previous submitted manuscript with the number ID diversity-2196742.
I am submitting a new revised file, with the changes made highlighted using "track Changes” feature in Microsoft Word. Following your request, we have detailed our response for the reviewers in the following pages. In order to provide clarity, we have included the reviewer comments in italics and our answer just below in bold.
We believe that reviewers comments now have been adequately addressed through our responses. We thank you for your time towards improving this manuscript, which we hope is now acceptable for publication in Diversity.
All suggestions raised by the reviewers were accepted.
Furthermore, as required, the article was reviewed by a native English speaker.
Author Response File: Author Response.pdf
Reviewer 3 Report
General Comments
1. The subject matter of the manuscript is suitable for the journal Animal Diversity and is a valuable contribution to the literature. I recommend its publication following revision based on the specific comments (mostly editorial suggestions) below.
Specific comments
1. Line 27. Note that the reader is not yet familiar with the acronym “DAPC”.
2. Line 31. “specie” should be ‘species’.
3. Line 43. “, however,” should be ‘; however,’.
4. Line 51. “in face of” should be ‘in the face of’.
5. Line 54. “, this because” should be ‘; this is because’.
6. Line 55. I suggest altering “age of maturity late” to ‘late age at maturity’.
7. Line 58. “ecosystems” should be ‘ecosystem’.
8. Lines 65‒66. The statement “Stingrays of the family Rhinobatidae comprise three genera: Acroteriobatus, Pseudobatos, and Rhinobatos” is not correct. The genera of Rhinobatidae are guitarfish, not stingrays.
9. Line 83. Alter “using mito-“ to ‘using a mito-‘.
10. Line 97. Consider altering “by-catch” to ‘byproduct’ or ‘non-targeted catch’. “By-catch” is usually considered ‘discarded catch’.
11. Line 135. I suggest altering the expression “The tree was tested” to ‘The phylogenetic tree was tested’ to ensure that the general scientific reader understands the subsequent use of the term “tree”.
12. Line 150. I suspect “reduced in” should be ‘reduced by’.
13. Line 166. “the concentration” should be ‘a concentration’.
14. Line 175. I suspect “reads” should be ‘readings’.
15. Line 176. “are processed” should be ‘were processed’ to be consistent with the past tense of the rest of the methods.
16. Line 185. Alter “analisys” to ‘analysis’.
17. Line 214. “50.000.000” should be ‘50,000,000’ or ‘50 million’.
18. Line 224. “Maximum Likelihood” should be ‘The Maximum Likelihood’.
19. Line 225. “other” should be ‘the other’.
20. Line 228. I suggest a comma after “finally”.
21. Line 274. I am confused by “Figure A3b”.
22. Line 294. “Same color” should be ‘The same color’.
23. Line 296. I suggest altering “about” to ‘for’ or ‘of’.
24. Lines 386 and 390. I suspect the expression “hyaline barrier’ should be ‘haline barrier’.
25. Line 395. I suggest altering “in the Brazil-“ to ‘on the Brazil-‘.
26. Line 417. I suspect that the expression “being that all of them present an amphi-American distribution” should be ‘such that together they present as an amphi-American distribution’.
27. Line 418. “that include” should be ‘that includes’.
28. Line 427. I suggest altering “such” to ‘such as’.
29. Line 440. Alter “the the existence” to ‘the existence’.
30. Line 449. Alter the expression “in the Brazillian coast and consequently,” to ‘on the Brazillian coast and, consequently,’.
Author Response
Dear editor,
Please find enclosed the manuscript: “Investigating an unknown biodiversity: evidence of distinct lineages of the endemic Chola Guitarfish Pseudobatos percellens (Walbaum, 1792) in the Western Atlantic Ocean” by Cruz VP, Rotundo MM, Charvet P, Boza BR, Campos BS, Cerqueira NCND, Oliveira C, Lessa RP, Foresti F. We wish to have the manuscript considered for publication in the Diversity, in Special issue: "Wildlife Population Genetics, Evolution and Conservation: From Theory to Practice".
This manuscript is a revised version of our previous submitted manuscript with the number ID diversity-2196742.
I am submitting a new revised file, with the changes made highlighted using "track Changes” feature in Microsoft Word. Following your request, we have detailed our response for the reviewers in the following pages. In order to provide clarity, we have included the reviewer comments in italics and our answer just below in bold.
We believe that reviewers comments now have been adequately addressed through our responses. We thank you for your time towards improving this manuscript, which we hope is now acceptable for publication in Diversity.
#Review 3:
All suggestions raised by the reviewers were accepted.
Furthermore, as required, the article was reviewed by a native English speaker.
Author Response File: Author Response.pdf
Round 2
Reviewer 1 Report
Admirable job of editing apparent in this revision
