Late middle Miocene caviomorph rodents from Tarapoto, Peruvian Amazonia

Myriam Boivin; Laurent Marivaux; Walter Aguirre-Diaz; Aldo Benites-Palomino; Guillaume Billet; François Pujos; Rodolfo Salas-Gismondi; Narla S. Stutz; Julia V. Tejada-Lara; Rafael M. Varas-Malca; Anne H. Walton; Pierre-Olivier Antoine

doi:10.1371/journal.pone.0258455

Peer Review History

Original SubmissionJuly 19, 2021
8 Sep 2021 Decision Letter - Jürgen Kriwet, Editor PONE-D-21-23419Late middle Miocene caviomorph rodents from Tarapoto, Peruvian AmazoniaPLOS ONE Dear Dr. Boivin, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by Oct 23 2021 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. 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If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. Additional Editor Comments (if provided): Dear Authors: Thank you very much again for submitting this manuscript to Plos One. Both reviewers commented on the manuscript and agree with your conclusions. They both find it a very valuable work that solves severl long-lasting taxonomic issues. There are however some minor issues that I'd like you to take care of before the manuscript can be accepted for publication. Kind regards, Jürgen Kriwet [Note: HTML markup is below. Please do not edit.] 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 ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: I Don't Know ****** 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 ****** 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 ****** 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: In this work, the anatomy of dozens of newly collected specimens from Perú was exhaustively described (and illustrated), using up-to-date caviomorph dental terminology. The information provided in this study is pretty valuable as it resolves long-term uncertainties about several caviomorph taxa informally described 30 years ago in northern South America, a region much less studied than middle and high latitudes. I find this manuscript very interesting, competent, and methodologically sound and recommend it be published. Please, see the annotated manuscript file attached here for some specific minor comments and suggestions. Although my native language is not English, I cannot advise or detect severe mistakes in the manuscript. In addition, the figures, cites, tables, and analyses are adequate, as far as I can tell. Reviewer #2: The manuscript is an impressive piece of work in describing not only the new late middle Miocene caviomorphs from Tarapoto but also offering a detailed formal description of the contemporaneous caviomorph rodents from La Venta so that the scientific names for these taxa finally become available for science. The comparisons are extensive and the paper shows the author’s deep knowledge of this systematic group in the South American Miocene. The paper is well organized; the descriptions clear and the figures and tables all are well executed and necessary. However, I stumbled over one statement in the materials and Methods section where the authors say that “The description and comparison of this material [from La Venta] in the present work is based on published photos and drawings” (lines 195/196). Why did the authors not analyze the actual materials described by Walton? Were they not possible to loan for some reason? Maybe adding an explaining sentence would be advisable. There are some comments/corrections in the annotated PDF, which all should be easy to accommodate by the authors. I recommend publication of this manuscript after very minor revisions. ****** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. 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 [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. Attachments Attachment Submitted filename: PONE-D-21-23419_reviewer+AS.pdf Attachment Submitted filename: PONE-D-21-23419_reviewer-with comments.pdf https://doi.org/10.1371/journal.pone.0258455.r001
Revision 1
21 Sep 2021 Author Response JOURNAL REQUIREMENTS: EMAIL: 08/09/2021 1. We revised all elements so that our manuscript meets PLOS ONE's style requirements. Compared to PLOS ONE style templates, we noted and changed some minor style mistakes about the Headings 1 and 2, the Figure Citations and the place of the legend of some figures in the text. Moreover, we modified the file names following the indications of the Editor’s mail. 2. Yes, we modified in the Acknowledgments: ‘We gratefully thank the E. Beucler, O. Bourgeois (LPG, Nantes, France) and the ‘Thème Terre’ of LPG in order to have covered the costs of a journey in Montpellier.’ by ‘We gratefully thank the E. Beucler and O. Bourgeois (LPG, Nantes, France) in order to have allowed MB realizing a journey in Montpellier.’ Moreover, we added the Laboratoire de Planétologie et de Géodynamique de Nantes to the list of our funds. 3. We request the permission to Elsevier for using of the Figure 1 in Antoine et al. (2021) and the Figures 1 and 2 in Marivaux et al. (2020). These articles are not licensed under CC BY 4.0. They are Rightslink enabled. So, we replaced the maps (A, B) for new ones and deleted the stratigraphic log (C), as it is was recently published (Marivaux et al. 2020). We cited instead the fig. 2 in Marivaux et al. (2020). REVIEWER 1 COMMENTS: pdf file Please see Solórzano et al (2020). Late early Miocene caviomorph rodents from Laguna del Laja (~ 37° S), Cura-Mallín Formation, south-central Chile. Journal of South American Earth Sciences, 102, 102658. Yes, exactly. Thank you. We changed ‘(Laguna del Laja and Pampa Castillo)’ by ‘(e.g., Laguna del Laja and Pampa Castillo)’. (line 79) Despite its much lower diversity the Urumaco rodent fauna (Venezuela) is also interesting... Yes, clearly the fauna from Urumaco Formation is very interesting and important in paleontological view. Here we had considered the most diverse caviomorph faunas at low latitudes of South America. As far we know, this fauna includes six caviomorph taxa (Sánchez-Villagra, 2012; Carrillo & Sánchez-Villagra, 2015), while some Peruvian faunas include equal number of taxa or more (e.g., 8 from Fitzcarrald Arch; Tejada-Lara et al. 2015). It is the reason why we preferred to not add it to our list, but we changed the sentence for more clarity: ‘At low latitudes of South America, two remarkable and species-rich local faunas are known, La Venta in Colombia (Honda Group; late middle Miocene) [18] and Acre in Brazil (Solimões Fm. [Formation]; late Miocene; see [19]).’ by ‘At low latitudes of South America, two remarkable and very species-rich caviomorph faunas are known, La Venta in Colombia (Honda Group; late middle Miocene) [18] and Acre in Brazil (Solimões Fm. [Formation]; late Miocene; see [19]).’ (lines 79-82) Sorry, but compare with what? We delete “and compare”. (line 106) I believe this is part of your novel and interesting results. If that is the case, you should be a little more clear in this sentence. We changed the sentence by ‘This locality shares taxa or closely related taxa with La Venta fauna described by one of us (AHW) in the framework of her PhD [37]: Microsteiromys, Ricardomys, and Microscleromys.’. (lines 107-109) I am not sure why you stated "Colloncuran". In above paragrahs you considered the studied rodent assemblage from Peru to be Laventan. We tentatively assigned to Nuyuyomys chinqaska the erethizontoid material from MD-67. According to Antoine et al. (2013, 2016), MD-67 is early middle Miocene (i.e., Colloncuran-Laventan SALMA). To clarify it, we added a sentence in the material and methods: ‘Three isolated teeth from MD-67 locality in Peru (MUSM 1974, 1975, and 4298; early middle Miocene) were originally attributed to cf. Microsteiromys sp [31]. They are reassigned here in light of the new material from Tarapoto.’. (lines 238-240) but also some doubts abouth the cogeneric afinities betweenn Scleromys spp. in northern and southern South America Yes, clearly. We added a sentence with respect to this point: ‘Moreover, some doubts were expressed about the cogeneric afinities between Scleromys spp. from northern versus southern South America [18,71].’. (lines 2784-2786). Moreover, we decided to follow the notation “Scleromys” proposed by Walton (1997) for our taxon and the other northern species of Scleromys and modified consequently the manuscript, Table 2, S1 Table and S2 Table. I think this paragraph fits better in the "paleobiogeographical implcations" section Yes clearly. We put it in the “paleobiogeographical implcations" section. In this section, we changed the paragraph: ‘The moderate or strong faunal similarities between MD-67, Fitzcarrald fauna, CTA-44 Top, TAR-31, and La Venta ([33,34,36] and see this work) suggest that the Eastern Cordillera of the North Andes and Pebas System would have not constituted barriers for mammals dispersals during the middle and earliest late Miocene at least for a region close to the Andes (Western Corridor) [36,44].’ by ‘With our results, the geographical ranges of Ricardomys longidens, Microscleromys paradoxalis and M. cribriphilus are now extended southerly to Peruvian Amazonia for the Laventan interval. More generally, strong taxonomic affinities between the vertebrate assemblages of La Venta (Colombia) and Fitzcarrald, Madre de Dios (MD-67), Iquitos, Contamana, and TAR-31 in Peruvian Amazonia support the existence of a single “Pebasian” biome throughout the middle–earliest late Miocene, and more specifically during the Laventan SALMA, as shown by their terrestrial and aquatic components (crocodylomorphs, chelonians, marsupials, rodents, primates, notoungulates, astrapotheres, litopterns, sirenians, and/or cetaceans; [21,26,31-34,36,158-160] and see this work). These moderate or strong faunal similarities suggest that the Eastern Cordillera of the North Andes and Pebas System would have not constituted barriers for mammalian dispersals during this interval at least for a region close to the Andes (Western Corridor) [36,44].’ (lines 2869-2880) We changed the order of the concerned citations in the bibliography section and in the manuscript (ex-159 and 160 after ex-177). This section appears to contradict with those stated above (also highlighted). With your available data I thing there is not much support for this ideas. Alternatively, you can stated that the idea it is just a plausible scenario that deserve further scrutiny. Yes, we agree, we deleted this part and the citations associated in the bibliography section. We thank very much the reviewer 1 for his comments. REVIEWER 2 COMMENTS: The description and comparison of this material [from La Venta] in the present work is based on published photos and drawings” (lines 195/196). Why did the authors not analyze the actual materials described by Walton? Were they not possible to loan for some reason? Maybe adding an explaining sentence would be advisable. Yes, it is very important point. Our original project was that two of our co-authors, Dr. Susan Walton (Springfield Technical Community College, USA) and Myriam Boivin (INECOA, Argentina), meet in USA or France (where the material from Tarapoto was studied before being returned to Peru) with original and/or casts of the material from La Venta and Tarapoto, respectively, in order to study all the material together. However, the covid pandemic and the confinement did not allow to manage it, to make and send casts to each other, or to loan request to the concerned Museums. Therefore, we decided to work from the pictures and drawings from Walton (1990, 1997). We added a sentence in the Material and Methods section (La Venta paragraph) to clarify this point: “For reasons related to the covid pandemic and confinement, the original material from La Venta could not be directly observed.”. (lines 194-195) Main comments in the pdf in chronological order: I think you mixed up the descriptions for (B) and (C)? Please double check the respective cross references in the text. Yes, thank you. We had mixed up in the legend. Moreover, we had mistake in the citation of the holotype of Microsteiromys jacobsi using the field number (FMNH PM 54677) instead of the collection number (FMNH PM 54672) in the manuscript. We checked and corrected each citation. I suggest to mark the holotype specimen, e.g., with an asterisk symbol I suggest to use the same symbol in the figures to mark the holotype specimens. We changed the mention ‘holotype’ by three asterisks and we added the sentence ‘The asterisks appoint the holotype material.’ in all legends of figures with a holotype. We thank very much the reviewer 2 for his comments. MAIN PERSONNAL MODIFICATIONS: We registered our manuscript and the new taxon names on ZooBank and put the associated links on the manuscript body text. We deeply apologize because we had made three errors in the statistical part in the original version of our manuscript (S1 and S2 Files). Noteworthily, these changes do not have implications for the taxonomic assignment of specimens of Microscleromys or for broader systematic conclusions. 1. We had calculated the correlation coefficient of Spearman between len and wid for all loci in the first version of our manuscript. However, these variables are normal or not depending on the locus. The correlation coefficient of Spearman is non-parametric and is generally used when two continuous variables have a distribution not normal or if one of them is not normal (Schober et al., 2018). Conversely, the correlation coefficient of Pearson is used in case of two normal continuous variables. Thus, we applied the Pearson coefficient when we had two normal variables. We modified the Table S1A (S1 File) and the scripts (S2 File). 2. For the tests of average comparison, we deleted the results of non-parametric tests keeping only those of the parametric tests in case of normal variables. We modified the Table S1B,C (S1 File) and the scripts (S2 File). 3. We had made a mistake in the figure names in the S1 File. We modified it. For example, for Table S3A, we put Table S1A. Attachments Attachment Submitted filename: Response to Reviewers_3.doc https://doi.org/10.1371/journal.pone.0258455.r002
28 Sep 2021 Decision Letter - Jürgen Kriwet, Editor Late middle Miocene caviomorph rodents from Tarapoto, Peruvian Amazonia PONE-D-21-23419R1 Dear Dr. Boivin, 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. An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Jürgen Kriwet Academic Editor PLOS ONE Additional Editor Comments (optional): Dear authors: Thank you very much for carefully considering all comments and suggestions posed by the reviewers. And alsomthank you for checking your statistical analyses and to correct the errors you found. Kind regards, Jürgen Reviewers' comments: https://doi.org/10.1371/journal.pone.0258455.r003
Formally Accepted
7 Oct 2021 Acceptance Letter - Jürgen Kriwet, Editor PONE-D-21-23419R1 Late middle Miocene caviomorph rodents from Tarapoto, Peruvian Amazonia Dear Dr. Boivin: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Jürgen Kriwet Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0258455.r004

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