Posterior probabilities of membership of repertoires in acoustic clades

Hal Whitehead; Taylor A. Hersh

doi:10.1371/journal.pone.0267501

Peer Review History

Original SubmissionNovember 20, 2021
21 Mar 2022 Decision Letter - Christopher Nice, Editor PONE-D-21-36851Posterior probabilities of membership of repertoires in acoustic cladesPLOS ONE Dear Dr. Whitehead, 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 reviewers indicated that this is an interesting and important manuscript and I completely agree. The reviewers have a few minor comments that should be addressed by the authors. I am hoping these revisions can be made without much difficulty. Please submit your revised manuscript by May 05 2022 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. 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Reviewer #1: Partly 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: This is a cool paper that makes a “structure-like” model in order to identify groups that use the same call sets, in the way that Structure identifies sets of individuals with the same gene frequencies. (1) label the axes. Most structure plots are based on admixture model, so the x axis is estimated ancestry fraction. Here this is a no admixture model, so the axis corresponds to assignment probability. (2) several of the steps seem unclear. How is the posterior achieved? Structure uses MCMC but what is used here? It says that the model is non Bayesian. What is it instead? How is it decided which repertoires are not assigned to identity groups? It would be very instructive to compare to a fully structure like model (ie bayesian no admixure model) to justify these choices. (3) the statement this is somewhat circular is confusing. Presumably the logic is similar to the structure paper, ie where gene frequencies can be applied given population memberships and vice versa. If this is what is meant spell it out. (4) the approach would presumably be more powerful if IDcall and IDcallPP were combined together. It should be easier to identify different call signals given identityclade assignments. This possibility should at least be mentioned. Reviewer #2: The paper represents a fascinating development in analyzing population structure for species that use acoustic communication. It was well written and the findings clearly presented. I did find the italicizing of keywords to be distracting after a while so I recommend not doing that. One important point that was not emphasized in the Discussion is that their method will generally be much less invasive, and possibly less costly, than genetic methods to accomplish the same task. That said a comparison to a genetic study on the same populations would be informative validation of the approach. ****** 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. 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Revision 1
6 Apr 2022 Author Response Thank you for considering our manuscript “Posterior probabilities of membership of repertoires in acoustic clades” for publication in PLOS ONE. We are happy with the reviews and have revised the manuscript accordingly, as follows: Reviewer #1: This is a cool paper that makes a “structure-like” model in order to identify groups that use the same call sets, in the way that Structure identifies sets of individuals with the same gene frequencies. (1) label the axes. Most structure plots are based on admixture model, so the x axis is estimated ancestry fraction. Here this is a no admixture model, so the axis corresponds to assignment probability. � This is a good point. Labelling the y-axes would add to the complexity of the already complex plots, so we have added (in italics) to each of the captions for Figs 3-6: “The output from IDcallPP shows the posterior assignment probabilities of each repertoire…”, and also added (lines 216-7): “…, so the y-axes in Figs 3-6 are the posterior assignment probabilities." (2) several of the steps seem unclear. How is the posterior achieved? Structure uses MCMC but what is used here? It says that the model is non Bayesian. What is it instead? How is it decided which repertoires are not assigned to identity groups? It would be very instructive to compare to a fully structure like model (ie bayesian no admixure model) to justify these choices. � There is some confusion here. IDcall (the original Hersh et al. methodology) does not use Bayesian methods to find identity calls or identity clades, but the methodology used in the submitted paper (IDcallPP) to produce posterior probabilities does (equation 5 is Bayes’ theorem). In this case the calculation is straightforward, so methods like MCMC are not needed. To make this clearer, we have added (lines 205-6) “Although IDcallPP calculates posterior probabilities of identity clade membership using Bayes’ theorem (eq 5), the delineation of the identity clades by IDcall uses a non-Bayesian, and generally more conservative, method…” (3) the statement this is somewhat circular is confusing. Presumably the logic is similar to the structure paper, ie where gene frequencies can be applied given population memberships and vice versa. If this is what is meant spell it out. � We have spelled this out, adding (lines 73-75): “In other words, the calls heard in a repertoire are used to delineate identity clades, the very information that is used to calculate the posterior probability that the repertoire is a member of an identity clade. To remove this circularity, we omit repertoire R from the calculation…” (4) the approach would presumably be more powerful if IDcall and IDcallPP were combined together. It should be easier to identify different call signals given identity clade assignments. This possibility should at least be mentioned. � Yes, they are now combined. We have added (lines 242-3): “The IDcall and IDcallPP codes (in program language R) are under active development by the authors and can be accessed, along with the sperm whale datasets, through the Open Science Framework (https://osf.io/5fter/).” In the latest version of software, IDcall optionally calls IDcallPP. Reviewer #2: The paper represents a fascinating development in analyzing population structure for species that use acoustic communication. It was well written and the findings clearly presented. I did find the italicizing of keywords to be distracting after a while so I recommend not doing that. � We have removed the italicizing of key words as suggested by the reviewer. One important point that was not emphasized in the Discussion is that their method will generally be much less invasive, and possibly less costly, than genetic methods to accomplish the same task. That said a comparison to a genetic study on the same populations would be informative validation of the approach. � We have added (lines 237-241): “The collection and analysis of acoustic data to study population structure will often be less costly, and usually less invasive, than comparable genetic studies. Sometimes, as with our wren and cricket examples, the genetic and acoustic data can tell similar stories. In contrast, when acoustic repertoires are socially learned, as with sperm whales, the contrasting patterns of genetic and cultural inheritance may lead to complex population structures [18]. Thus, the analysis of acoustic data may be effective and/or essential if we are to understand population structures.” Attachments Attachment Submitted filename: Posterior_review_comments.docx https://doi.org/10.1371/journal.pone.0267501.r002
11 Apr 2022 Decision Letter - Christopher Nice, Editor Posterior probabilities of membership of repertoires in acoustic clades PONE-D-21-36851R1 Dear Dr. Whitehead, 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, Christopher Nice, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0267501.r003
Formally Accepted
14 Apr 2022 Acceptance Letter - Christopher Nice, Editor PONE-D-21-36851R1 Posterior probabilities of membership of repertoires in acoustic clades Dear Dr. Whitehead: 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. Christopher Nice Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0267501.r004

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