The Phylogeny of Rays and Skates (Chondrichthyes: Elasmobranchii) Based on Morphological Characters Revisited

Round 1

Reviewer 1 Report

This is a lovely piece of work. I really like the detailed and clear diagrams that illustrate aspects of the morphological characters presented. This will make using the data set for further analyses easier and present a more accurate use of the characters outlined by the authors

There are some minor comments on the manuscripy

Comments for author File: Comments.pdf

Author Response

We thank the reviewer for taking the time to review our work, the minor typos and misspelling marked in the paper where corrected.

 

Reviewer 2 Report

Dear editors, authors,

It was my pleasure to read and review the paper by Villalobos-Segura et al., entitled ‘The phylogeny of Batomorphii (Chondrichthyes: Elasmobranchii) based on morphological characters revisited’.

This topic is very much of interest, especially in view of all the recent advances in the phylogeny of batomorph fishes, based on both molecular (modern) and morphological studies (modern, and fossil record). This is the first comprehensive (all-in-one) study since the last few years, and thus merits full attention. It seems that the methods have been applied as they should, and the general results seem OK. However, it felt that the manuscript was not yet ready for submission. It contains a lot of smaller mistakes and typo’s, and there are lots of inconsistensies in the details of the presentation. Moreover, I missed a good balance between the actual paper (only 5-6 pages of text) and the charachter discussion (60 pages). Finally, the introduction is not straightforward in the aim of the project, that is intra-relationships of batomorph fishes. Nearly all of the introduction, but also the larger part of the results, deals with relationships with other Chondrichthyes. Consequently, some parts need rewriting. I also advice to (re)consider the placement op the character discussion in the MS. If kept this way (and not transferred at the end as an appendix, or as suppl. information), it should be cleaned up, and consistent in every detail of its presentation. In conclusion, and that is difficult to say, especially because all authors are top-experts in this field, and the first and last author are even guest editors of this special volume, I feel obliged to suggest a major revision. 

In order to guide the authors in improving the MS, please allow me to address the main issues I encountered when reading the MS. For detailed comments, I refer to the annotaded MS (file attached).

 

0. Keywords

Several of the keywords are present in the title. I would suggest to select keywords that are different from the title.

 

1. Introduction

When I first read the introduction, it was not clear to me that authors wanted to address the relationships within batomorphs, i.e. batomorph intra-relationships. In fact, nearly all of the introduction deals with inter-relationships with other Chondrichthyan fishes (e.g., hypnosqualean hypothesis etc.). In this respect, the introduction is not straightforward, and rather confusing. In my opinion, the introduction would benefit a lot when started from batomorphs, and describing their diversity in terms of external morphology, ecology and distribution (both geographical and stratigraphical). What I really missed is the current state of knowledge on phylogeny within batomorphs. One could also address or illustrate some of the recent advances (and remaining problems), such as the merging of Pristiformes and Rhinobatiformes, and the position of Platyrhinidae that has seen considerable changes in the past few years (still within Torpediniformes in Weigmann, 2016). Because of this, I believe that the introduction needs rewriting. Of course, there is no problem to address also the relationship with other Chondrichthyan fishes in the introduction, but this should remain secondary. See also comments in annotated MS.

When addressing higher-level phylogeny in the introduction, I would suggest to add two references:

• De Carvalho, 1996 [91].
• Shirai, 1992 – Squalean phylogeny (even though authors copied several illustrations from this book, authors forgot to include it in the references; please note that the reference to Shirai, 1996 [3] in several of the Figures is erroneous – for details see annotated MS).

 

2. Materials and methods

The paper includes lots of taxa for both out- and ingroups. When listing the outgroup, authors present family names, whereas for the ingroup authors do not always provide family info. In my opinion, the presentation of the taxa included in the study can be made more transparant by adding family names where available (I understand that this might be difficult for fossil taxa), and/or by explicitely mentioning/highlighting the higher taxa that are not included in the analysis. At first sight, for modern selachimorphs, I only missed modern representatives of the order ‘Lamniformes’ in the outgroup? And the families ‘Anacanthobatidae’ and ‘Gurgesiellidae’ (both Rajiformes) for the ingroup?

Other comments are:

• Bathyraja is listed as a member of Rajidea, but is in fact a member of Arhynchobatidae.
• For the fossil record (both out- and ingroups), it seems (according to refs given in the introduction) that authors have mainly focussed on taxa that they studied themselves in the past. Although evident, it remains a pity that other skeletal specimens have not been included in the material/paper. E.g., amongst several examples, for the outgroup, the Cretaceous manta-like shark Aquilolamna (Vullo et al., 2021 – Science paper), and, e.g., for the ingroup, the Oligocene Weissobatis specimen (Hovestadt & Hovestadt-Euler, 1999). This is not a real critism, but rather missed opportunities.
• For the representation of chimaeroids, authors opted for the genera Chimaera and Harriotta, which is OK. However, when illustrating the condition of certain characters they often illustrate another genus and family, i.e. Callorhinchus (Callorhinchidae). If this other genus/family is just used to illustrate a particular state of a specific character, that might still be OK (however, not desirable), but if it is used to illustrate the condition in Chimaera and Harriotta, that is not (e.g., line 523). There are several ways to tackle this issue properly (delimit the use of the figures, opt for other illustrations, opt for other material,…). Please check if this problem also occurs for other taxa.
• About the numbering (chronology) of the characters, it is a pity that not all of them are grouped following the specific elements listed, e.g., the list starts with characters that are related tot he braincase, but also end (char. 142) with characters related to the braincase.
• Please try to be more consistent in the use of terminology throughout the MS, e.g., for the braincase, you now use many different terms such as cranium, neurocranium, chrondrocranium, … But also arrowheads vs. arrow marks, etc.

3. Results

Although the paper claims that it focusses on batomorph intra-relationships, more than half of the results (section 3) is dedicated to interrelations with other Chondrichthyes. Many results are stuck in the character discussion, per character, and not per node.

3.3. (sic) Character discussion

The section ‘character discussion’ (wrongly numbered as 3.3. in the MS) is the basis of the research project, but should not be the most important/prominent part in the presention/paper. The section covers 60 pages, whereas the actual paper only covers 5-6 pages of text. I am not (yet) convinced that this is the best way to present the results.

In similar research papers, characters are often listed at the end, in an appendix, or, if kept in the main part of the manuscript, listed more briefly. In the present manuscript, the characters are also complemented with Ptr rand MLtr results. In contrast, nodes are not explicitly discussed in the general part of the results/discussion. The presentation of the general results and discussion vs. the character discussion is, in my opinion, not well in balance.

The section ‘character discussion’ is also hard to read, and the character presentation looks messy in the details. There are lot’s of typo’s and smaller mistakes in this section, even duplicate characters (char. 7 and 9). If kept in the centre of the MS, this section needs a lot of cleaning up.

Please allow me to point to small details in the presentation as well:

• Please be more consistent in the way you present references after each character. Sometimes you only give a [ref], elsewhere you add the author’s name (with or without an ’s), preceded (or not) with the words ‘After…’, ‘Based on…’, ‘Modified from (:)….’, ‘New’…. but sometimes no reference/info is given at all. Especially the punctuation and the use of capital letters varies a lot in these sections, even for the same phrases. Just to give an example: (char x), (char. x), (charx), (Char. x), (new), (New),…. Try to stick to just a couple of phrases, the use of capitals and punctuations, and apply consistent throughout the MS.
• The same problem occurs in the captions to the Figures. They vary in their presentation, and puntucation. Moreover, the Figures are not consistent in the chronology of its individual parts. In some Figures (e.g., Figure 20, 21, 36, 39, 40, 43, 44), the chronology of the caption follows the different states (State 0 first, State 1 next, etc.) (this is the same chronology as in the text, and thus the most reader-friendly), but, many Figures are not (e.g., Figure 5: A=1, B=0, C=2, D=0). Also several typo’s or missing lettering occurs in the captions. In the beginning of the MS, I tried to highlight them, but I just gave up towards the end.
• The referencing from the text towards the Figures is OK, but the other way round is more difficult. The captions of the Figures often lack a clear reference to the exact character it illustrates. Perhaps the relevant character number can be given in the caption of all Figures? That would benefit the reader.

In my opinion, char. 6 (different morphologies of rostral cartilage) needs re-defining, or different coding as several other taxa present multiple types of cartilages in their rostrum.

For other comments, see annotated MS.

4. Discussion

The discussion is quite brief. One would expect discussion of the nodes (see comments above), and more detailed comparisons between previous studies. E.g., it would help if authors presented simplified phylogentic trees/cladograms of previous studies and of this paper (Ptr and MLtr) all on the same page, to visualise the similarities, differences, new insights and future research directives. Adding cladograms from previous studies would also benefit/support the introduction.

References

Check conformity with journal’s instructions. I highmighted a few issues, but did not check all.

Comments for author File: Comments.pdf

Author Response

We thank the reviewer for taking the time to review our work and we present the following reply to the comments provided.

Reviewer2 (Comment on Keywords): Several of the keywords are present in the title. I would suggest to select keywords that are different from the title.

Reply: We agree with the suggestion, and the paper now includes the following keywords: Character revision; phylogenetic analysis; morphology; Cretaceous; Jurassic; fossils.

 Reviewer2 (Comment on introduction): When I first read the introduction, it was not clear to me that authors wanted to address the relationships within batomorphs, i.e. batomorph intra-relationships. In fact, nearly all of the introduction deals with inter-relationships with other Chondrichthyan fishes (e.g., hypnosqualean hypothesis etc.). In this respect, the introduction is not straightforward, and rather confusing. In my opinion, the introduction would benefit a lot when started from batomorphs, and describing their diversity in terms of external morphology, ecology and distribution (both geographical and stratigraphical). What I really missed is the current state of knowledge on phylogeny within batomorphs. One could also address or illustrate some of the recent advances (and remaining problems), such as the merging of Pristiformes and Rhinobatiformes, and the position of Platyrhinidae that has seen considerable changes in the past few years (still within Torpediniformes in Weigmann, 2016). Because of this, I believe that the introduction needs rewriting. Of course, there is no problem to address also the relationship with other Chondrichthyan fishes in the introduction, but this should remain secondary. See also comments in annotated MS.

Reviewer2 (Comment on introduction): When addressing higher-level phylogeny in the introduction, I would suggest to add two references:

• De Carvalho, 1996 [91].
• Shirai, 1992 – Squalean phylogeny (even though authors copied several illustrations from this book, authors forgot to include it in the references; please note that the reference to Shirai, 1996 [3] in several of the Figures is erroneous – for details see annotated MS).

Reply: The introduction and other relevant parts were changed to better to follow all aims of the present work, including the several phylogenetic analyses carried on the batomoprhs from both perspectives (molecular and morphological) and the topological differences (higher-level and lower-level) recovered in different studies among the different data types and within the data types. While and important focus on the present study are batoid intra-relationships, we also aimed to provide a wider context for them (i.e., within chondrichthyans) which is an aspect not well explored in most batomoroph papers. Shirai 1992 – Squalean phylogeny- is now added to the references and along with de Carvalho 1996 work is also included in this section.

Reviewer2 (Comment on materials and methods): The paper includes lots of taxa for both out- and ingroups. When listing the outgroup, authors present family names, whereas for the ingroup authors do not always provide family info. In my opinion, the presentation of the taxa included in the study can be made more transparant by adding family names where available (I understand that this might be difficult for fossil taxa), and/or by explicitely mentioning/highlighting the higher taxa that are not included in the analysis. At first sight, for modern selachimorphs, I only missed modern representatives of the order ‘Lamniformes’ in the outgroup? And the families ‘Anacanthobatidae’ and ‘Gurgesiellidae’ (both Rajiformes) for the ingroup?

Reply: We added an explicit statement on why some taxa were not included. However, there is no obscure plan regarding the inclusion or exclusion of taxa in the present analysis. In all cases responded to the availability of material to be reviewed in detail during the pandemic, this is the case for Carchariniformes, Lamniformes, Anacanthobatidae’, Gurgesiellidae’.

Reviewer2 (Comment on materials and methods): Bathyraja is listed as a member of Rajidea, but is in fact a member of Arhynchobatidae.

            Reply: The correct taxonomic affiliation is now provided

Reviewer2 (Comment on materials and methods): For the fossil record (both out- and ingroups), it seems (according to refs given in the introduction) that authors have mainly focussed on taxa that they studied themselves in the past. Although evident, it remains a pity that other skeletal specimens have not been included in the material/paper. E.g., amongst several examples, for the outgroup, the Cretaceous manta-like shark Aquilolamna (Vullo et al., 2021 – Science paper), and, e.g., for the ingroup, the Oligocene Weissobatis specimen (Hovestadt & Hovestadt-Euler, 1999). This is not a real critism, but rather missed opportunities.

            Reply: Again, this goes back to the material that we had available during the pandemic. Regarding the Aquilolamna, while the specimen is an excellent piece of exhibition, little to no phylogenetic features are present in the specimen (JK, per. obser.).

Reviewer2 (Comment on materials and methods): For the representation of chimaeroids, authors opted for the genera Chimaera and Harriotta, which is OK. However, when illustrating the condition of certain characters, they often illustrate another genus and family, i.e. Callorhinchus (Callorhinchidae). If this other genus/family is just used to illustrate a particular state of a specific character, that might still be OK (however, not desirable), but if it is used to illustrate the condition in Chimaera and Harriotta, that is not (e.g., line 523).

Reply: While it is not desirable to use a taxa that is not included in the matrix to illustrate a state. I really do not see an issue if the state is the same in the taxa in the matrix and the species in the illustrations is mentioned (EVS, per. obser.). However the issue was  corrected by using Chimaera to illustrate the character state.

Reviewer2 (Comment on materials and methods): Please try to be more consistent in the use of terminology throughout the MS, e.g., for the braincase, you now use many different terms such as cranium, neurocranium, chrondrocranium, … But also arrowheads vs. arrow marks, etc.

Reply: Terminology was reviewed and kept consistent.

 

Reviewer2 (Comment on results): Although the paper claims that it focusses on batomorph intra-relationships, more than half of the results (section 3) is dedicated to interrelations with other Chondrichthyes. Many results are stuck in the character discussion, per character, and not per node 

Reply: This section was also changed making clear that we are focusing on batomorphs phylogenetic relations at both higher-level and lower-level. The special focus on the interrelations with other condrichthyans is because we consider is an aspect not explored in most papers.

 

Reviewer2 (Comment on materials and methods): About the numbering (chronology) of the characters, it is a pity that not all of them are grouped following the specific elements listed, e.g., the list starts with characters that are related to the braincase, but also end (char. 142) with characters related to the braincase.

Reviewer2 (Comment on results): The section ‘character discussion’ (wrongly numbered as 3.3. in the MS) is the basis of the research project, but should not be the most important/prominent part in the presention/paper. The section covers 60 pages, whereas the actual paper only covers 5-6 pages of text. I am not (yet) convinced that this is the best way to present the results. In similar research papers, characters are often listed at the end, in an appendix, or, if kept in the main part of the manuscript, listed more briefly. In the present manuscript, the characters are also complemented with Ptr rand MLtr results. In contrast, nodes are not explicitly discussed in the general part of the results/discussion. The presentation of the general results and discussion vs. the character discussion is, in my opinion, not well in balance.

loss most of its original significance and impact GM, per. comm.

 

Reviewer2 (Comment on results): nodes are not explicitly discussed in the general part of the results/discussion. The presentation of the general results and discussion vs. the character discussion is, in my opinion, not well in balance.

 

Reviewer2 (Comment on results): Please allow me to point to small details in the presentation as well:

• Please be more consistent in the way you present references after each character. Sometimes you only give a [ref], elsewhere you add the author’s name (with or without an ’s), preceded (or not) with the words ‘After…’, ‘Based on…’, ‘Modified from (:)….’, ‘New’…. but sometimes no reference/info is given at all. Especially the punctuation and the use of capital letters varies a lot in these sections, even for the same phrases. Just to give an example: (char x), (char. x), (charx), (Char. x), (new), (New),…. Try to stick to just a couple of phrases, the use of capitals and punctuations, and apply consistent throughout the MS.
• The same problem occurs in the captions to the Figures. They vary in their presentation, and puntucation. Moreover, the Figures are not consistent in the chronology of its individual parts. In some Figures (e.g., Figure 20, 21, 36, 39, 40, 43, 44), the chronology of the caption follows the different states (State 0 first, State 1 next, etc.) (this is the same chronology as in the text, and thus the most reader-friendly), but, many Figures are not (e.g., Figure 5: A=1, B=0, C=2, D=0). Also several typo’s or missing lettering occurs in the captions. In the beginning of the MS, I tried to highlight them, but I just gave up towards the end.
• The referencing from the text towards the Figures is OK, but the other way round is more difficult. The captions of the Figures often lack a clear reference to the exact character it illustrates. Perhaps the relevant character number can be given in the caption of all Figures? That would benefit the reader.

Reviewer2 (Comment on results): In my opinion, char. 6 (different morphologies of rostral cartilage) needs re-defining, or different coding as several other taxa present multiple types of cartilages in their rostrum.

Reviewer2 (Comment on discussion): The discussion is quite brief. One would expect discussion of the nodes (see comments above), and more detailed comparisons between previous studies. E.g., it would help if authors presented simplified phylogenetic trees/cladograms of previous studies and of this paper (Ptr and MLtr) all on the same page, to visualise the similarities, differences, new insights and future research directives. Adding cladograms from previous studies would also benefit/support the introduction.

 

Round 2

Reviewer 2 Report

Dear editors, authors,

It was my pleasure to receive the revised version of your MS.

When having read the MS again, it is clear that authors took all comments from the first revision very serious. All issues mentionned in my first review seem properly dealt with, such as the new keywords, the new introduction, the way that the charachter-part has translocated in front of the true results and discussion, the addition of the institutional abbreviations, the addition of the simplified trees in the discussion, etc. I also appreciate the re-organisation of many Figures so that the chronology of the items in each Figure follows the chronology of the states (0-1-2). It is quite an accomplishment that all of these changes have been made by the authors in such a short period of time.

There are just a few small, new issues I would like to point at: see the annotated MS attached. The most important one is that the numbers of some of the characters have changed? Please check carefully my annotations throughout the entire MS, so that each character has the correct number attached to it. I also suggest the authors to go through the entire MS once again to check all cross-references for Figures, lettering etc. In this second round, I could not check all, and it is clear that some small errors remain, which is normal in view of all the changes that had to be made in such short period of time.

Looking forward to seeing this paper published.

Comments for author File: Comments.pdf

Author Response

We thank the reviewer for the input and effort on these rounds of corrections.

The minor typos and mistakes were corrected.

The character number were checked against and the numeration was corrected in the cases were it was needed.