Genetic polymorphisms in the serotonin, dopamine and opioid pathways influence social attention in rhesus macaques (Macaca mulatta)

Emmeline R. I. Howarth; Isabelle D. Szott; Claire L. Witham; Craig S. Wilding; Emily J. Bethell

doi:10.1371/journal.pone.0288108

Peer Review History

Original SubmissionMarch 9, 2023
18 Apr 2023 Decision Letter - Asem Surindro Singh, Editor PONE-D-23-06906Genetic polymorphisms in the serotonin, dopamine and opioid pathways influence social attention in rhesus macaques (Macaca mulatta)PLOS ONE Dear Dr. Bethell, 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. ============================== The manuscript is interesting as the report will be interested to many audience who are interested in understanding molecular mechanisms underlying social behavior. I would request the authors resubmit it after thoroughly revising considering the comments raised by the reviewers. I would also request the authors to insert some points on how the finding can reflect on humans with respect to those behaviors and what the future steps that can be taken up using your findings. ============================== Please submit your revised manuscript by Jun 02 2023 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. Please include the following items when submitting your revised manuscript: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols. We look forward to receiving your revised manuscript. Kind regards, Asem Surindro Singh, Ph.D Academic Editor PLOS ONE Journal Requirements: When submitting your revision, we need you to address these additional requirements. 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. In order to comply with PLOS ONE's guidelines for non-human primate experiments (http://journals.plos.org/plosone/s/submission-guidelines#loc-non-human-primates), please provide additional details regarding housing conditions, feeding regimens, environmental enrichment, and all relevant steps taken to alleviate suffering (anesthesia, analgesia, details about humane endpoints, euthanasia, etc.). Also indicate how often animal care staff monitored the health and well-being of the animals and the criteria used to make such assessments. Lastly, specify the disposition of animals at the end of the study (e.g. euthanasia, returned to home colony, etc.). If animals were euthanized following the study, please provide the method of sacrifice. 3. Thank you for stating the following financial disclosure: "This research was supported by NC3Rs grant NC/L000539/1to EJB. ERIH was supported by an LJMU PhD studentship." Please state what role the funders took in the study. If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. 4. Please expand the acronym “NC3Rs and LJMU” (as indicated in your financial disclosure) so that it states the name of your funders in full. This information should be included in your cover letter; we will change the online submission form on your behalf. 5. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. [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: No Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No Reviewer #2: Yes ****** 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: Major revision recommended, but I doubt that the authors can address my concerns. Although I've provided an opportunity to the authors to revise their paper based on my comments, I have little hope that the authors can properly address my statistical concerns, particularly because they are all non-statisticians. Reviewer #2: Very well planned study, executed meticulously with all necessary information. I did not find any major shortcomings in this article. It can be straight way go for publication. My best wishes to the authors. ****** 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: Plos1_Review_Report_Authors.pdf https://doi.org/10.1371/journal.pone.0288108.r001
Revision 1
1 Jun 2023 Author Response We thank the two anonymous Reviewers for their useful feedback on the manuscript. We hope we have addressed all comments adequately. Reviewer comments are addressed below in order. Review comments shown in bold. Response to Reviewer 1. We are pleased that Reviewer 1 concluded that ‘the article is well-written and contributes significantly to the existing literature on the effect of genetic polymorphism on the negative emotion and social behaviour of primates’. In addition, we would like to thank Reviewer 1 for their suggestions to improve the manuscript further. We trust we have addressed all the minor and major points thoroughly as follows: The name of the procedure implemented in this article is Bayesian MCMCglmm and it can mislead the reader. The author should use some alternative standard name for their procedure, for example, MCMC-based Bayesian GLMM. Note that the R package which implements MCMC based Bayesian GLMM method indeed is named “MCMCglmm”. However, the method should not be referred to as MCMCglmm. We have changed the text where this is referred to in two places. In the Abstract, the text now reads “Genetic data were then correlated with cognitive and observational measures of behaviour associated with wellbeing and survival using MCMC-based Bayesian GLMM in R to account for relatedness within the macaque population.” On page 21 (tracked changes version for all page numbers) we have changed the text to read “To account for relatedness between individuals, analyses were conducted using the animal model, in which pedigree was included as a random factor, using MCMC based Bayesian GLMM in R [134].” The abbreviation NHP (line 229) is used without clarification. Please clarify all the abbreviations carefully and introduce them in the right place in the article. Also, use abbreviations wherever possible. Use abbreviation instead of non-human primates at line 249. We have now deleted the use of NHP and changed this to simply primates (page 11) and checked through the manuscript for additional abbreviations which require clarification. We have made additional changes to clarify abbreviations for MRC and LJMU (page 12). We would like to highlight that abbreviations used in tables are included in the table footnotes. As the same data is used repeatedly to test the significance of genetic polymorphisms on different response variables using different models, so an adjusted p-value in place of an ordinary p-value should be reported. In that case, however, it seems that some of the significant discoveries would turn out to be false discoveries. This is a major concern and must be addressed carefully. We thank the reviewer for their concerns around this point and have re-stated the results focusing on credible intervals (the Bayesian form of confidence intervals) as they are more appropriate than P values for reporting Bayesian analysis. We have added a statement on page 22 to explain how we assessed significance: ‘Meaningful effects were evaluated based on whether the 95% credible interval of the estimate overlapped zero [140]’. We have replaced reported P values with CIs throughout the results section, and retained P values in the tables as additional information. We understand the point Reviewer 1 has raised about multiple testing. The purpose of this paper is to identify possible new polymorphisms of interest in the study of social attention. Therefore, as stated in the manuscript we have taken an exploratory approach, ensuring that we identify possible variants of interest. This is to help other researchers in identifying new genetic variants to focus future research efforts on. A more conservative approach would remove some of these variants from consideration. We trust the educated readership of PLOS ONE will understand this distinction and will be able to interpret the credible intervals in this light. We have clarified in the text on p22 that we provide P values as secondary information (e.g. for future meta analyses), and so it is not necessary to use adjusted P values as they are not used for significance testing. Regarding the use of separate models, these were informed by our previous work detailed in Howarth et al (2021). Therefore, the model parameters are prior justified. The discussion section is too long. It can be shortened by discarding lines like “When treated with mirtazapine, a noradrenergic and specific serotonergic antidepressant, individuals with the STin 12 allele showed a significant reduction in their Hamilton Depression Rating Scale score compared to individuals with the low expressing STin allele. Mirtazapine has also been used in the treatment of social anxiety [149] and social phobia [150].” We are attempting in this discussion not just to discuss these results as they pertain to macaque behaviour, but also with some reference to what is currently known about humans, and so the translational value of our findings. Thus, we do not believe that we can significantly shorten the discussion. However, the section reading “When treated with mirtazapine, a noradrenergic and specific serotonergic antidepressant, individuals with the STin 12 allele showed a significant reduction in their Hamilton Depression Rating Scale score compared to individuals with the low expressing STin allele. Mirtazapine has also been used in the treatment of social anxiety [149] and social phobia [150]” has been removed as the essence of this study is captured in the previous section. We have also made some edits to the previous paragraph on p30 as shown by track changes. Tuning MCMC is a challenging problem and improper selection of burn-in may lead to the incorrect posterior distribution, which in turn may incorrectly interpret a non-significant covariate to be significant. It would be better if the authors demonstrate some of the MCMC trace plots and posterior density as supplementary figures. We appreciate the opportunity to clarify our procedure here. As stated in the manuscript this is why we used an uninformative prior, and visually checked plots for effective burn-in and posterior density by eye. We have added clarification on p22: “With these parameters, absence of autocorrelation was assessed as below 0.1 for animal at 10000 lag in all cases and the chain was said to have mixed well”. We do not have access to the plots as they were inspected at the same time as running the models and not saved. The Pedantics R package has been archived meaning we cannot easily run this code again to re-generate the plots. That said I think the article is novel and after addressing the above-mentioned concerns it can be accepted for publication. We thank the referee for this summary and their pertinent feedback points. Response to Reviewer 2: We are pleased that Reviewer 2 found the research to be ‘well planned, executed meticulously with all necessary information … it can be straight way go for publication’. We feel this Reviewer understood the purpose of our paper in providing information that we trust will be of use for other researchers in identifying genes of interest in future studies. In particular, we feel the new knowledge about the potential role of genetic variants, STin, DRD4 and OXTR, in social attention in rhesus macaques, will facilitate new studies in this area. Attachments Attachment Submitted filename: Response to reviewers 20230530.docx https://doi.org/10.1371/journal.pone.0288108.r002
21 Jun 2023 Decision Letter - Asem Surindro Singh, Editor Genetic polymorphisms in the serotonin, dopamine and opioid pathways influence social attention in rhesus macaques (Macaca mulatta) PONE-D-23-06906R1 Dear Prof Al-Eitan, 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, Asem Surindro Singh, Ph.D Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0288108.r003
Formally Accepted
10 Jul 2023 Acceptance Letter - Asem Surindro Singh, Editor PONE-D-23-06906R1 Genetic polymorphisms in the serotonin, dopamine and opioid pathways influence social attention in rhesus macaques (Macaca mulatta). Dear Dr. Howarth: 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. Asem Surindro Singh Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0288108.r004

Open letter on the publication of peer review reports

PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.

We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.

Learn more at ASAPbio .