A new goniopholidid from the Upper Jurassic Morrison Formation, USA: novel insight into aquatic adaptation toward modern crocodylians

Goniopholididae is a group of basal neosuchian crocodyliforms closely related to Paralligatoridae and Eusuchia that lived during the Jurassic and Early Cretaceous. Goniopholidids have the long, flat snout and secondary palate of modern crocodylians, the acquisition of which is regarded as a key feature in the early evolution of crocodylian body plan and their aquatic adaptation. Here, we report a new species, Amphicotylus milesi, with the description from the best-preserved specimen to date of Goniopholididae from Wyoming, USA. Its posterior extension of the nasopharyngeal passage (pterygoid secondary palate) and the shortening and dorsal deflection of the ceratobranchial suggest that basal neosuchians could raise their gular valve to separate oral and pharyngeal cavities as in modern crocodylians. The anatomy of Amphicotylus milesi sheds light on the acquisition of this new respiratory system in the crocodyliform evolution and their early aquatic adaptation, leading to modern crocodylians.

Also, there is a completely different topology used for the R analyses in the SI… Where does it come from? Why are you not using the topology you analysed with the modified Andrade dataset?
New species As RSOS is an online-only journal can the authors make sure everything they do is done in accordance with the ICZN Code? That means ensuring at proof stage the ZooBank LSIDs for both the paper and the new species are present.
Anatomy and SI So, the anteriorly elongated internal nares. I can't see it in the figures. There are no close-ups, only interpretative line drawings. And from those, I would hesitate to say the morphology isn't purely post-mortem damage. To be honest, the description and figuring are what frustrate me most. As the authors say, this is the most complete known skeleton of a goniopholidid, and the description is largely in the SI and so are the figures. The complete description needs to be 'main text', there needs to be much more, and better figures.
I'm really sorry, but it's really not acceptable to 'hide away' the vast bulk of the description, and to give such limited figuring. There are some really good figures in the SI, but they are put into multi-element plates that reduce their size and quality (when you zoom in to double check the anatomy). The SI figures should be split into smaller units, and added into the main document.

Decision letter (RSOS-210320.R0)
We hope you are keeping well at this difficult and unusual time. We continue to value your support of the journal in these challenging circumstances. If Royal Society Open Science can assist you at all, please don't hesitate to let us know at the email address below.

Dear Dr Yoshida
The Editors assigned to your paper RSOS-210320 "A new goniopholidid from the Upper Jurassic Morrison Formation, USA: novel insight into aquatic adaptation toward modern crocodylians" have now received comments from reviewers and would like you to revise the paper in accordance with the reviewer comments and any comments from the Editors. Please note this decision does not guarantee eventual acceptance.
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Kind regards, Royal Society Open Science Editorial Office Royal Society Open Science openscience@royalsociety.org on behalf of Professor Peter Haynes (Subject Editor) openscience@royalsociety.org Associate Editor Comments to Author: Thank you for your patience while we secured the reviewer commentary below. Given the comments of reviewers 2 and 3, we recommend that you carefully review and revise the manuscript before resubmitting it for further consideration. Both reviewers note that the presentation of the manuscript can be much improved (and so value added to your work), and we would expect you to take these requests into account. Good luck and we'll look forward to seeing the revision in the near future.
Reviewer comments to Author: Reviewer: 1 Comments to the Author(s) Great work on a wonderful specimen.
Reviewer: 2 Comments to the Author(s) Dear authors, This is an impressive study and an essential contribution to our understanding of aquatic adaptations in neosuchian crocodylifroms. I placed my comments into the attached pdf, they are minor but given the number of them I recommended "major revision" . Overall, I suggest including a larger figure of the skull of the specimen. The material certainly deserves larger resolution photos and page restrictions no longer apply. Similarly, the authors could illustrate some of their observations derived from the disecting besides the schematic representation. I disagree with some details of the conclusions: given the instability of thalattosuchia in phylogenies and the poor sampling of ceratobranchials in the tree makes it difficult to trace the origin of the gular valve closing. Moreover, while the hypothesis of the authors regarding the function of the curved ceratobranchial makes perfect sense, it is a hypothesis not a fact (only a single event in the phylogeny) and the evolutionary implications should be proposed with less certainty. I am looking forward to see this excellent and essential work to be published! Reviewer: 3 Comments to the Author(s) First of all, I'd like to apologise for my review being late. Secondly, I do like the 'thrust' of this manuscript, I just think it requires major modifications to be acceptable for RSOS.
Odd statements There are some odd comments here and there, such as this from the introduction: "In the evolutionary history of crocodyliforms, the presence of the secondary palate is a key character for eusuchian crocodyliforms, and it appeared in the successive stem groups of Eusuchia such as paralligatorids and derived goniopholidids " All mesoeucrocodylians have a maxillopalatine secondary palate, and there is an independent maxillopalatine secondary palate in Shartegosuchoidea (even an independent acquisition of the 'pterygoid secondary palate'). I'm not entirely sure what the authors are meaning here.
Another one is: "Goniopholidids, which is a transitional group to Eusuchia," Goniopholidids aren't. It's an odd thing to say.
And there are more of these. I think the authors need to give a serious re-think to the tone of the manuscript. It reads very teleological, with neosuchian groups being 'pit-stops' on the road to Eusuchia. They weren't, many, such as goniopholidids, were evolutionary successful lineages that persisted for tens of millions of years.

Phylogeny
As the authors will no doubt be aware crocodylomorph phylogeny is chaotic in places. The position of major clades are in flux. So the comment: "Goniopholididae is a group of basal neosuchian crocodyliforms found in the in the northern hemisphere during the Jurassic and Early Cretaceous, and a sister clade to Paralligatoridae and Eusuchia" Needs to be better cited. I would simply state that Goniopholididae is a successful lineage of neosuchians outside of the Paralligatoridae + Eusuchia clade. That way, what you are saying doesn't require discussing competing phylogenetic hypotheses.
Also, there is a completely different topology used for the R analyses in the SI… Where does it come from? Why are you not using the topology you analysed with the modified Andrade dataset?
New species As RSOS is an online-only journal can the authors make sure everything they do is done in accordance with the ICZN Code? That means ensuring at proof stage the ZooBank LSIDs for both the paper and the new species are present.
Anatomy and SI So, the anteriorly elongated internal nares. I can't see it in the figures. There are no close-ups, only interpretative line drawings. And from those, I would hesitate to say the morphology isn't purely post-mortem damage. To be honest, the description and figuring are what frustrate me most. As the authors say, this is the most complete known skeleton of a goniopholidid, and the description is largely in the SI and so are the figures. The complete description needs to be 'main text', there needs to be much more, and better figures.
I'm really sorry, but it's really not acceptable to 'hide away' the vast bulk of the description, and to give such limited figuring. There are some really good figures in the SI, but they are put into multi-element plates that reduce their size and quality (when you zoom in to double check the anatomy). The SI figures should be split into smaller units, and added into the main document.

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Recommendation?
Accept with minor revision (please list in comments)

Comments to the Author(s) Dear authors,
Thank you for answering my comments and making the changes. I suggest specifying that the instable phylogenetic position of Thalattosuchia is not affecting the conclusions (if that is the case). think the manuscript is otherwise acceptable once minor improvements of the English are made here and there.

Do you have any ethical concerns with this paper? No
Have you any concerns about statistical analyses in this paper? No

Recommendation?
Accept as is

Comments to the Author(s)
Congratulations, your work is very interesting and valuable for crocodyliforms anatomy, especially the evolution from neosuchia to modern crocodylians.
Decision letter (RSOS-210320.R1) We hope you are keeping well at this difficult and unusual time. We continue to value your support of the journal in these challenging circumstances. If Royal Society Open Science can assist you at all, please don't hesitate to let us know at the email address below.

Dear Dr Yoshida
On behalf of the Editors, we are pleased to inform you that your Manuscript RSOS-210320.R1 "A new goniopholidid from the Upper Jurassic Morrison Formation, USA: novel insight into aquatic adaptation toward modern crocodylians" has been accepted for publication in Royal Society Open Science subject to minor revision in accordance with the referees' reports. Please find the referees' comments along with any feedback from the Editors below my signature.
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Kind regards, Royal Society Open Science Editorial Office Royal Society Open Science openscience@royalsociety.org on behalf of Peter Haynes (Subject Editor) openscience@royalsociety.org Associate Editor Comments to Author: Comments to the Author: The reviewers are largely satisfied that your paper is ready for acceptance -congratulations! There are a couple of (minor) suggestions made by reviewer 2 regarding some phrasing and a recommendation to check the language once more to help ensure the clarity of your message is maintained, but otherwise, good job on tackling the reviewer feedback and we'll look forward to seeing the paper in the journal after this final revision. All best.
Reviewer comments to Author: Reviewer: 2 Comments to the Author(s) Dear authors, Thank you for answering my comments and making the changes. I suggest specifying that the instable phylogenetic position of Thalattosuchia is not affecting the conclusions (if that is the case). think the manuscript is otherwise acceptable once minor improvements of the English are made here and there.
Reviewer: 4 Comments to the Author(s) Congratulations, your work is very interesting and valuable for crocodyliforms anatomy, especially the evolution from neosuchia to modern crocodylians.

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Author's Response to Decision Letter for (RSOS-210320.R1) Decision letter (RSOS-210320.R2) We hope you are keeping well at this difficult and unusual time. We continue to value your support of the journal in these challenging circumstances. If Royal Society Open Science can assist you at all, please don't hesitate to let us know at the email address below.
Dear Dr Yoshida, I am pleased to inform you that your manuscript entitled "A new goniopholidid from the Upper Jurassic Morrison Formation, USA: novel insight into aquatic adaptation toward modern crocodylians" is now accepted for publication in Royal Society Open Science.
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54
The most problematic group with regard to the composition of total group Chelonioidea 55 is Protostegidae [6]. Often recovered as highly derived chelonioids [7,8,9], the fossil occurrence     7,32,37,38,39,40]. Toxochelys was recovered here as a stem chelonioid and sister taxon to the 270 clade formed by Ctenochelyidae and crown group Chelonioidea. In contrast with many previous 271 analyses [8,9,11,37,41,42], Protostegidae is recovered as a clade of stem chelonioids supported Dashes indicate Bremer support values ≥ 6. MPTs = most parsimonious trees. (b) Gap Excess Ratio (GER) calculations for the topology of Americhelydian lineages recovered in the weighted parsimony analysis. The fossil occurrence of Allopleuron hofmanni is used as the maximum age constraint for Pan-Dermochelyidae. (c) GER calculations for the topology of Americhelydian lineages recovered in most previous analyses of fossil turtles. The fossil occurrence of Eosphargis breineri is used as the maximum age constraint for Pan-Dermochelyidae. In both GER calculations (b,c), the fossil occurrence of the oldest unambiguous pancheloniid, Euclastes weilandi, is used as the maximum age constraint for Pan-Cheloniidae. MIG = minimum implied gap; Gmax = maximum gap; Gmin = minimum gap. See electronic supplementary material for sources of fossil occurrence data.
170x137mm (300 x 300 DPI) Overall, I suggest including a larger figure of the skull of the specimen. The material certainly deserves larger resolution photos and page restrictions no longer apply.
As requested, we add a close-up view of the palatine-pterygoid region to provide details and our interpretation of the structure.
Similarly, the authors could illustrate some of their observations derived from the disecting besides the schematic representation.
Indeed. We add pictures of the dissected hyolingual musculoskeletal elements in the revised manuscript. Also, the sample size in this study is statistically large ( figure 6). In addition, as shown in figure S3, the similar scores of ceratobranchials among neosuchians suggest their synapomorphies, rather than convergence.
Moreover, while the hypothesis of the authors regarding the function of the curved ceratobranchial makes perfect sense, it is a hypothesis not a fact (only a single event in the phylogeny) and the evolutionary implications should be proposed with less certainty.
Although our explanation is convincing, we change the statement into the suggestive statement, as reviewer 2 pointed.
Reviewer 2 recommended us to rewrite "Sealed off from one another fold of the gular valve of the tongue".
Modern crocodylians actively raise the ventral fold of the gular valve to seal the narial and oral regions off, not by moving the dorsal fold. To highlight the form and function relationship between the ventral fold and hyoid, we wrote "These regions can be sealed off from each other by raising the ventral fold of gular valve at the base of a tongue to contact the dorsal fold at the posterior end of the palate." We rewrite "Therefore, the goniopholidid covered palate could have been common with modern crocodylians, which is similar with the other covered regions (suborbital fenestra and incisive foramen) by soft tissue in the palate." Synapomorphic? How can you establish the correlation between ceratobranchial and oral cavity? + note that Thalattosuchia is more basal in most other recent phylogenies.
We measure the mandible width which is a proxy for oral cavity.
Also, the phylogenetic positions of Thalattosuchia proposed by some recent papers are still in dispute and chaos although our data still supports that Thalattosuchia is a sister clade of Neosuchia. However, regardless of the recent phylogenetic instability of Thalattosuchia, neosuchians already have retained short ceratobranchials. Therefore, we rewrite "In thalattosuchians, the sister group of Neosuchia in this study, the ceratobranchial is short and straight (figure 6a), indicating that oral enlargement have already retained in Neosuchia or more basal clade (Thalattosuchia+Neosuchia)." Reviewer 2 recommended us to write "partially submerged and while the mouth being open under water" We rewrite "this taxon and other extinct neosuchians could have raised the ventral fold of the gular valve in a similar manner to modern crocodylians allowing them to breath while opening the mouth underwater when their external nares were above the water surface." Why Batrachomimus is excluded from this figure (figure 16)?
As mentioned in our discussion, Batrachomimus show dorsal deflection of ceratobranchial as in other neosuchians, but an outlier in the ratio of ceratobranchial length to mandible width among neosuchians, possibly due to its narrow mandible.

Reply to reviewer 3
There are some odd comments here and there, such as this from the introduction: We modify the statement into "In the evolutionary history of crocodyliforms, the pterygoid secondary palate is appeared in neosuchian crocodyliforms, such as Eusuchia, paralligatorids, and derived goniopholidids." Terminology of "secondary palate" is obscure in many of the previous papers, and as Reviewer 3 indicated, we use "pterygoid secondary palatine" for clarification.
"Goniopholidids, which is a transitional group to Eusuchia," Goniopholidids aren't. It's an odd thing to say. And there are more of these. I think the authors need to give a serious re-think to the tone of the manuscript. It reads very teleological, with neosuchian groups being 'pit-stops' on the road to Eusuchia. They weren't, many, such as goniopholidids, were evolutionary successful lineages that persisted for tens of millions of years.
…As the authors will no doubt be aware crocodylomorph phylogeny is chaotic in places. For visualization, we used heated trees in figures. Non-scored terminal taxa are pruned from our obtained tree, and then the topology is simplified. A tree in figure 16 comes from figure S1-3, and trees from figure S1-3 comes from our obtained tree (figure 13).
As RSOS is an online-only journal can the authors make sure everything they do is done in accordance with the ICZN Code? That means ensuring at proof stage the ZooBank LSIDs for both the paper and the new species are present.
We are ready now. Thank you. As reviewer 3 requested, we add the close-up view of internal choana and its