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Congratulations! This final version has addressed all the referees' comments succesfully. From my point of view, the reviewing process has been very important, and has improved the quality of your paper and strengthened the results. A very clear guiding thread is present, and all the sections are very well explained. Thanks for your time and patience in the reviewing process.
I have made a last reading, and I have noted some minor typographical errors. I detail them below. Please, correct them in the fully typeset publication proofs, together with others that you can identify in them, before final publication.
I wish you all the best in your research projects and career.
Cheers,
PhD Blanca Moncunill-Solé
Minor typographical changes:Line 27. Change “ma” to “Ma”.
Line 44. Change the “n5” to “n = 5”. The same for the rest of the samples.
Line 97. Add “(France)” following “Sansan”.
Line 138. Change “(2013), figure 3” to “(2013, fig. 3)”.
Line 198. Delete one of the “Cf.”.
Line 220. Change “cf.” to “Cf.”.
Line 222. Change “Equus” to “E.”.
Line 231. Add a blank space between “E.” and “caballus”.
Line 243. Delete a blank space before “Cf. A.”.
Line 300. Change “2010” to “(2010)”.
Line 321. Change “Anchitherium” to “A.”
Line 375. Change “Hyopsodus” to “Hy.”.
Line 382. Add a blank space between “model” and “(Ekdale, 2013)”.
Line 389. Delete a blank space after “(82.2º)”.
Line 415. Delete one of the “cf.”.
Line 437. Change “Anchitherium” to “A.”
Line 443-444. “E. caballus” should be in italics.
Line 481. Change “Hipparion” to “H.” in both cases of the sentence.
Line 496, 540, 622, 675, 680, 681, 714, 765 Change “Equus” to “E.”.
Line 667. Change “et al” to “et al.”
Line 694. Change “(Fig12A. 13A)” to “(Fig. 12A, 13A)”
Line 752. Change “Cf.” to “cf.” before “Equus”.
Line 757. Change “Cf.” to “cf.” before “Hipparion” and “H.”.
Line 775. Change “Anchitherium” to “A.”
Line 1032. This reference is not alphabetically ordered.
Figure captions. Some “cf.” are in capital letters. Correct it.
Figure 5 and 6. Add a blank space between “Concud” and “3”.
[# PeerJ Staff Note - this decision was reviewed and approved by Kenneth De Baets, a PeerJ Section Editor covering this Section #]
Dear authors,
I would like to congratulate you for the great effort made in the first round of revisions. After reviewing the new version of the manuscript, I agree with the referees that there are still some minor issues that should be addressed prior to publication. I have noticed a few typo errors, and I also believe that, as suggested by Reviewer 2, the article would gain in strength if some terms were made more specific.
I kindly invite you to carefully review the referees’ comments, as well as the attached PDF files. Please take into them to improve the manuscript. If you choose not to implement certain suggestions, be sure to provide a clear and well-reasoned justification in your rebuttal letter.
I hope you can address these points promptly. Thank you for your time, dedication, and patience throughout the review process.
Best regards,
Dr. Blanca Moncunill-Solé
[# PeerJ Staff Note: Reviewer 2 declared a potential Conflict of Interest, and the Editor was aware of this when making their decision #]
The article meets the journal's standards of basic reporting.
I have no concerns with the experimental design.
The conclusions and interpretations in the paper are valid.
I appreciate the authors' care in addressing all of my original concerns. I am satisfied with their revision.
This manuscript is much improved from its previous version, but there are still some typos and odd turns of phrase that should be corrected. I have indicated these in an annotated PDF. In addition, I found a few sources that are cited in the text but are not referenced in the bibliography. I have also indicated these in the PDF, and all of them should be very quick fixes. I also found that, in Supplementary File 2 Character 16, the word "petrosal" is misspelled. This is the only typo I found in the supplementary files.
In my last round of review, I requested that the authors update their text descriptions to provide more detail and better match the features labeled in their figures. They have updated their descriptions quite a bit, and I greatly appreciate the effort they put into doing so. They have chosen not to describe as many features as I would personally have liked because they felt that "Describing all features, for all specimens, would have been redundant in most cases and uninformative." It appears that we may have a slight philosophical difference in how to approach a morphological description, but I respect the authors' choice and have no wish to force my preferences on their work, so I would consider the current level of description to be sufficient aside from one potential instance that I note in "Additional comments". Overall, I would like to emphasize how much this manuscript has been enhanced since the first submission thanks to the work of the authors.
As with the Basic Reporting, I would first like to say that the authors have done a wonderful job of updating their experimental design, including finding some errors that us reviewers did not catch. I would also like to admit that my request for them to report their PAUP* settings was unnecessary given that the exhaustive search function does not have any analytically relevant settings to adjust. However, the authors’ response to my comment on this has left me a little puzzled. They state that “all parameters are already included in the Nexus file”, but the Nexus file that was submitted does not include a PAUP* block and it appears that the file was generated outside of PAUP*—it includes all equally parsimonious trees but no record of how they were produced. Given that the authors indicated that the Nexus file should contain this information, I would ask them to double-check that the correct Nexus file was submitted.
I previously requested that the authors elaborate on their use of MeshLab to make measurements. They have done so for most of the measurements, but they do not explain how they determined the angles between the semicircular canals, which is a measurement that I asked them to explain in the last round of review. Given that they also did not address it in their response, it is possible that my request was simply missed, and if so, I would like to reiterate it here. In my experience, there are a lot of ways that people go about measuring these angles, so it is important to specify which technique was used.
I have very little to say here because the authors have thoroughly addressed my concerns, including creating a supplemental file mapping their characters to those of previous analysis, and a table of bony labyrinth measurements. The only improvement I would like to suggest is including the measurements of the angles between the semicircular canals in said table. The authors do not give specific angles in the text, only stating that the canals are at right angles or obtuse angles, so having the actual values in the table would be of great assistance and improve the reporting of the underlying data.
I would once again like to say that the authors have by-and-large fixed everything that I flagged last time, and the manuscript is in a very good state. There are just two specific things that I would like to mention because they do affect the scientific contents of the manuscript. I apologize for the length of my explanations.
1. In two of their descriptions (Lines 259-260 and 333-334), the authors state that the basicapsular groove is along the dorsal margin of the petrosal. I expressed concern about this last time because the basicapsular groove is a ventrally located structure, which is supported by their figures. The authors responded saying that “We believe that there may be a misunderstanding, as the basicapsular groove is actually dorsal in Hipparion depereti (figure 3), as in Equus caballus (see O’Leary 2010 : figure 114) and almost all equids. This ventral or dorsal position of this groove is also one character from their matrix that we use, which confirms that it can be dorsal.” I agree with them that there has been a misunderstanding, but it seems that the problem lies in how O'Leary's character is being interpreted and described. The authors are correct that O’Leary presents two character states: dorsal and ventral. However, if you look at the relevant figures, you will see that the groove is not on the dorsal surface of the petrosal, which is generally the area of the tegmen tympani and mastoid region. The basicapsular groove of H. deperti and E. caballus (and the cetaceans described by O’Leary) is on the dorsomedial surface of the petrosal i.e., the endocranial surface. This makes a big difference, and indeed, on the endocranial surface, the groove is along the ventral margin, not the dorsal margin. It just so happens that the other position of the basicapsular groove is on the ventromedial surface. While I would not presume to know the mind of another, I would guess that O’Leary chose the "dorsal" and "ventral" character states because one location is dorsomedial and the other is ventromedial, and these got simplified to dorsal and ventral. The authors have coded the character correctly in their matrix because the groove is indeed on the dorsomedial face of the petrosal (i.e., the dorsal character state), but their description is inaccurate because they say that the groove is on the dorsal margin of the petrosal. This implies that the groove is dorsal to the internal acoustic meatus and the subarcuate depression, which it very clearly is not. To avoid this confusion, I would suggest describing the position of the groove in relation to surrounding structures and avoid using the term “dorsal” without proper contextualization.
2. In the last round of review, I suggested that the authors describe the sacculus and utriculus of the bony labyrinth of Hipparion concudense because the specimen is well-enough preserved for these features to be visible. The authors’ response was that they “…refrain from describing those structures, as they are unknown to us and do not seem to have been previously described in the literature that we know of.” This seems to be an error in communication given that at least one author has extensively published on bony labyrinths, including identification of the sacculus and utriculus. It is possible that the authors meant they are unaware of published descriptions specific to perissodactyls, but if so, I would argue that this is an even better reason for the authors to describe these features in their current paper, even if it is just one sentence saying that they are well-defined and giving their general shape/proportions. I have provided a couple of references that should be familiar to the authors and might help them in their identification and description of the structures:
Costeur, L., Valli, A., Beaudouin, C., & MenneCart, B. (2018). On some ruminant petrosal bones and their bony labyrinth from Senèze (Villafranchian, France). Revue de Paleobiologie, 37(2), 443–456. https://doi.org/10.5281/zenodo.2545101
Ekdale, E. G. (2013). Comparative anatomy of the bony labyrinth (inner ear) of placental mammals. PLoS ONE, 8(6), 1–100. https://doi.org/10.1371/journal.pone.0066624
Mennecart, B., & Costeur, L. (2016). A Dorcatherium (Mammalia, Ruminantia, middle Miocene) petrosal bone and the tragulid ear region. Journal of Vertebrate Paleontology, 36(6), e1211665. https://doi.org/10.1080/02724634.2016.1211665
Mennecart, B., & Costeur, L. (2016). Shape variation and ontogeny of the ruminant bony labyrinth, an example in Tragulidae. Journal of Anatomy, 229(3), 422–435. https://doi.org/10.1111/joa.12487
Mennecart, B., Rössner, G. E., Métais, G., DeMiguel, D., Schulz, G., Müller, B., & Costeur, L. (2016). The petrosal bone and bony labyrinth of early to middle Miocene European deer (Mammalia, Cervidae) reveal their phylogeny. Journal of Morphology, 277(10), 1329–1338. https://doi.org/10.1002/jmor.20579
Dear authors,
Thank you very much for your contribution. After the reviewers' evaluation and reading the manuscript myself, I agree with them that the study is of great interest and generally well structured, with a clear narrative. However, some details should be revised before publication to improve the overall quality of the article, its reproducibility, and to strengthen the results:
Formatting: In several sections, the language, grammar, and structure need to be reviewed.
Materials and Methods: There is a lack of scanning parameters and measurement details. Both referees note issues with anatomical terminology. Additionally, there is no information regarding the phylogenetic analysis methodology.
Results: Missing measurement tables and lack of detail in the phylogenetic analysis. In some parts, more detailed descriptions are needed (some anatomical elements are described for certain taxa but not for others, although they are later used in the matrix). There are inconsistencies in the number and code of characters in your matrix and the sources cited.
Figures: It is necessary to add orientation indicators for the elements, as well as some anatomical structures referenced in the text.
Furthermore, the reviewers have raised some specific issues regarding the material descriptions, which you can consult in the attached PDFs. Please take into account all the comments, suggestions, and recommendations provided by the referees to improve the manuscript. If you choose not to implement certain suggestions, be sure to provide a clear and well-reasoned justification in your rebuttal letter.
I look forward to reviewing the revised version of your manuscript.
Thank you again for your valuable contribution.
Best regards,
Dr. Blanca Moncunill-Solé
**PeerJ Staff Note:** It is PeerJ policy that additional references suggested during the peer-review process should only be included if the authors agree that they are relevant and useful.
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I found this paper to be very interesting. As with the authors, I have always found it surprising that the ear region of perissodactyls is so understudied, especially given how many detailed studies there are for other mammal clades, as well as the intensity of studies of perissodactyl dentitions and interest in perissodactyl paleontology. Thus, I was excited to see this paper. Overall, I find it to be well written and I don’t have much to quibble on the anatomical identifications. However, I do have several general and specific comments that I think would improve the manuscript.
The figures look very nice. I would recommend including directional arrows in the figures or some sort of directional information (e.g., which way is anterior? Or dorsal) in the figure captions for readers who may not be familiar with ear anatomy.
Under Materials & Methods, it would help to list the scanning parameters such as voxel dimensions, inter-slice spacing, number of slices through the ear region, etc. This is important information for the reproducibility of the study and independent assessment of the image data. This could be included in a table (e.g., an expanded Table 1), unless the information is the same for every specimen.
Regarding the Measurements section of Materials & Methods, I think that the authors could be more explicit about their measurements. Are they following methods of previous studies, or do they have their own protocol? Again, this is essential for the reproducibility of the study, as well as the utility in comparing the results presented here to those in published (or yet-to-be published) literature.
A table with some of the bony labyrinth measurements (e.g., some of those included in some of the cited papers such as angles between canals) would be useful and greatly enhance the paper. If nothing else, including even just cochlear turns in Table 1 would be beneficial.
In the description of the bony labyrinth of Hipparion depereti (NMB.A.Mo.655), specifically line 263, it is stated that the “shape of the fenestrae cannot be described due to preservation”. Which fenestrae are these? It appears that the fenestrae cochleae and vestibuli are intact in Fig. 3B, but I could be mistaken.
“Vestibula" isn’t commonly used, is it? I would prefer either vestibule or to a lesser extent vestibulum, although this might be a matter of taste. “Vestibula” just seems like an odd usage to me.
On line 345, I think that the plural form of tegmen tympani is tegmina tympani.
Is there a secondary bony lamina observed in Equus stenonis (NMB.V.A.2753), or is it absent in everything? It looks like there might be a faint lamina in Fig. 9, but it is a little difficult to see. If the lamina is absent in everything, then it wouldn’t hurt to mention that for each taxon.
On line 378, I wonder if there is a better term than “hinge”. Perhaps inflection or deflection? Also, I don’t understand what is meant by “The cochlea is few detached from the vestibula” here and elsewhere. What is meant by “few detached” should be clarified.
The last paragraph before the Conclusions is nice to see! It is important to think about allometric and ontogenetic variation, or lack thereof in the basicranium and ear region.
Lines 547-548 state that the petrosal “lacks precision for generic level distinctions considering its inability or recover the monophyly of the genus Hipparion.” That assumes that Hipparion is actually monophyletic…I am not suggesting that it is not, this suggests that there is homoplasy someplace, if not in the ear region than in other regions of the anatomy.
~E.G. Ekdale
There are some areas in which the language, grammar, and sentence structure need revision to improve clarity. I have flagged some of these in the annotated PDF, and I believe that any I have missed can be fixed during copy-editing. There are also some problems with anatomical terminology that I have commented on in the annotated PDF, such as the identity of the hiatus Fallopii, but these are easily corrected and, in some cases, are open to debate. Your introduction and background provide good context, and the literature is well referenced and cited. The figures are relevant and well labeled, and I only have minor suggestions for the figure captions (see annotated PDF), although I do think the manuscript would benefit from more frequent references to the figures in the descriptions.
The petrosal and bony labyrinth are very challenging to describe, and I applaud you for describing five taxa in one paper. You have provided some excellent figures to support your descriptions, but the descriptions themselves could be more detailed. There are many prominent anatomical features labeled in the figures that are not mentioned in the text, and the features that are mentioned are sometimes only discussed for one or two specimens. It can be challenging to interpret anatomy from figures alone, so having your description of these features helps readers understand the morphology of the petrosal, particularly when some of these features are also coded in a phylogenetic matrix. For example, the fossa for the muscularis tensor tympani is coded as present for all five taxa, but it is only described for Equus senezensis. I also notice that some features, such as the fossa for the muscularis tensor tympani, are not labeled in the figures. I have not been able to flag all anatomical features that lack descriptions and/or figures, but I hope that you will be able to review your manuscript and identify what parts are missing. In general, the descriptions, figures, and matrix should all present the same information in different formats.
Your research question is well defined, relevant, and meaningful, and it has undergone rigorous investigation. The methods associated with your phylogenetic analysis appear to be sound, but they are not described sufficiently to be fully replicable. For example, you do not report what settings you used in PAUP*, other than that you conducted an exhaustive search. Your analysis also does not include measures of tree stability, such as Bremer support or Bootstrap values, which would make your analysis more rigorous. I would recommend that such measures be reported and included in the discussion of your results as they are quite helpful when evaluating the results of parsimony analyses.
You also mention that you used MeshLab to take measurements of your models, but you do not elaborate on what tools were used in MeshLab to take these measurements. It may be obvious to someone who uses MeshLab regularly, but if a reader is trying to replicate your measurement protocol, they would likely find it challenging without more explicit instructions, especially for some of the more challenging measurements such as the angles between the semicircular canals.
You provide the necessary Nexus file, and you explain where your characters come from in general terms, but it would be helpful if you were able to provide a text document linking each character in your matrix to the study it came from as an additional piece of underlying data. This becomes important because some of your characters are from multiple sources, such as the depth of the subarcuate fossa, which comes from both Spaulding et al. (2009) and Mateus (2018). You report how many characters you took from each source, but because of these duplications, your character counts do not fully line up. For example, you say that you used 34 characters from Spaulding et al. (2009) and 9 from Mateus (2018), but that adds up to 43 petrosal characters, whereas you report that you have 44 petrosal characters (line 122). Having a document that maps where you got each character could help avoid this confusion for both you and your readers. Additionally, you talk about characters from particular studies, but you do not identify which characters these are (e.g., lines 509-510, you say “For all the other variable characters from Mateus (2018),…”), making it challenging to look at your matrix and know which characters you are discussing. Having a reference document would greatly improve the clarity of these statements.
Another piece of underlying data that is currently unavailable is a table reporting your bony labyrinth measurements. In your methods, you talk about taking the height and width of the cochlea and the height, length, and width of the semicircular canals, but you do not report these values. This makes it challenging to understand what data were used to produce some of your results. A supplementary file with these measurements would improve the replicability of your study and allow other researchers to incorporate these data into their own studies.
This is a solid piece of research that tests previously proposed hypotheses of equid relationships using data from the petrosal bone, the bony labyrinth, and the stapes. The otic region is morphologically complex, and you have done a good job of describing the anatomy and providing clear figures to support your descriptions. The work you have done is inspiring and will hopefully lead to more research in this area. Along with the comments I have made above, I have some other suggestions for how you can improve your manuscript. These are presented in the order that I encountered them during reading:
1) From my understanding, most of your specimens are isolated petrosals. For isolated petrosals, it is best practice to provide an explanation as to why the bone is referable to the species you have identified it as. This will help other researchers who may also be working with isolated petrosals, and it will help prevent concerns that your specimens are misidentified. An explanation would fit well into your first paragraph of description and comparison for each taxon.
2) Some parts of your descriptions, particularly for the bony labyrinth, appear to be copy-and-pasted among the different taxa. I realize it can be frustrating describing similar morphologies multiple times, but I would suggest rephrasing your descriptions so that they are not verbatim repeats of each other. This will improve the quality of your manuscript, and it will prevent readers from having an unexpected sense of déjà vu.
3) I worry that I have found some errors in the coding of your matrix that may affect your results. In particular, for Anchitherium, the ventrolateral tuberosity is coded as absent but you describe it as present and you label it in the relevant figure. Because you have Anchitherium coded as absent, this character is one of the ten parsimony informative characters in your analysis. If the character state is changed to present for Anchitherium, which appears to be correct based on your description and figure, this character would no longer be parsimony informative. I am also confused why you have Hyopsodus coded as inapplicable for this character instead of unknown or absent. The presence of the ventrolateral tuberosity is not dependent on a different character in your matrix, so an inapplicable coding does not make sense to me.
Additionally, I think you may have accidentally calculated the cochlear aspect ratio incorrectly for some of your specimens, although I cannot be certain without seeing your width and height measurements. All I can say is that I tried calculating the aspect ratio of Equus senezensis based on the models you provided, and I got ratios much lower than what you report. My ratios are as low as 0.53, which would place the specimen in the “low aspect ratio” category, while your lowest ratio is 0.65. Based on your data, you have rightfully coded your specimens as having a high aspect ratio, but I am struggling to understand how you got ratios ranging from 0.65 to 0.82 from the models. If there is a problem with this character coding, it may be less of an issue than that of the ventrolateral tuberosity character because this character is currently not parsimony informative (only Tapirus is coded as having a low aspect ratio). Even so, if some of your specimens have a low aspect ratio, it would change the optimization of the character on the tree, and it might actually render the character parsimony informative. I hope that I am wrong about the calculations and that your current values are correct, but I think it would be worth double-checking given that this character features in your discussion as a synapomorphy of Equidae. There are a few other instances of potential miscodings that I have commented on in the annotated PDF, but these are the two that are most likely to affect the results of your analysis.
I realize this is a lot to process at once, and I do apologize for requesting so many changes, but it is my belief that these revisions will greatly enhance the content and accessibility of your manuscript. I very much enjoyed reading your work, and I look forward to seeing this paper published.
Dr. Selina Viktor Robson
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