https://orcid.org/0000-0002-4561-7288
Peer Review History
| Original SubmissionJune 9, 2021 |
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PONE-D-21-18979Insights on the historical biogeography of Philippine native pigs and its relationship with Continental domestic and wild boarsPLOS ONE Dear Dr. Layos, 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 Nov 16 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. Please include the following items when submitting your revised 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, Bi-Song Yue, 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 your Methods section, please provide additional location information, including geographic coordinates for the data set if available. 3. You indicated that you had ethical approval for your study. In your Methods section, please ensure you have also stated whether you obtained consent from owners of the domestic pigs included in the study or whether the research ethics committee or IRB specifically waived the need for their consent.""" 4. In your Methods section, please provide additional details regarding the wild pigs used in your study and ensure you have described the source. For more information regarding PLOS' policy on materials sharing and reporting, see https://journals.plos.org/plosone/s/materials-and-software-sharing#loc-sharing-materials. 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: Partly Reviewer #2: Yes Reviewer #3: Partly ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: 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 Reviewer #3: 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: No Reviewer #3: 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: The subject manuscript reports on a study evaluating the origin, dispersal, and level of genetic introgression in Philippine “native” pigs using mitochondrial DNA D-loop analysis. These genetic data are then compared to comparable mtDNA data from domestic pigs and Eurasian wild boar. While the stated goal of the study is straightforward, the exact composition of the pigs being investigated is not completely clear. There are no “native” Sus scrofa, either wild or domestic, in the Philippines. Meijaard and Melletti (2018) list the endemic (“native”) wild pigs that exist in the Philippine archipelago as including the following: Visayan warty pig (Sus cebifrons), Philippine warty pig (Sus philippensis), Mindoro warty pig (Sus oliveri), and Palawan bearded pig (Sus ahoenobarbus). Fossils of these Philippine wild pig species variously date as far back as the Pliocene through the late Pleistocene. The earliest documented archaeological remains of domestic pigs belonging to the species Sus scrofa in the Philippines were from a site in the Cagayan Valley dating back to 4000 BP (Heaney et al. 2016). Hybridization between domestic pigs (Sus scrofa) and Visayan warty pigs (Melletti et al. 2018), Philippine warty pigs (Meijaard and Melletti 2018), and Mindoro warty pigs (Tabaranza et al. 2018) in the Philippines has been documented. More specifically, such hybridization between domestic/feral Sus scrofa and Philippine warty pigs has been observed on Luzon, Minanao, Basilan and other islands in the archipelago (Heaney et al. 2005). All of that said, it solicits the question as to what were the pigs that this study was looking at. Given the comparisons to genetic data from known breeds of domestic pigs and Eurasian wild boar, the study would seem to be looking at only the introduced domestic pigs belonging to the species Sus scrofa. To that end, the manuscript needs to not use the modifier “native” for these domestic pigs, and these pigs should be specifically identified as “domestic” (or “local domestic”, “rural domestic”, or “local rural domestic” or something like that; the modifier “native” is misleading). On Line 113, it was noted that samples were also collected from Philippine “wild pigs”. Further, ID sample numbers P24 and P25 in Table S1 are listed as wild pigs from the Philippines. Accession No. MN625830 in Table S2 is listed as a “Philippine wild pig.” What were these Philippine wild pigs, feral Sus scrofa? There are no Eurasian wild boar present in the Philippines. Were these “wild pigs” in actuality warty pigs and not feral Sus scrofa? The two pigs illustrated in Fig. 1 A and G appear to be immature pure or hybrid warty pigs and not Sus scrofa. In a number of places in the manuscript the authors refer to “pigs”. This noun should be more specifically defined (e.g., “pigs, which includes both wild and domestic pigs” or “pigs, which includes only domestic pigs”). In most of these places, the reader is left guessing as to what types of pigs are being discussed. A single explanatory statement on this can be made in the introduction, which would then clarify the subsequent use of the noun “pig.” The authors also need to address the potential impacts of genetic introgression of warty pigs through hybridization with domestic Sus scrofa in the Philippines on their results. Is this something that was even considered in the analysis of the data? To my knowledge, this is the first study that has specifically looked at genetic composition as related to the anthropogenic origin of domestic pigs in the Philippines. As such, the data encompassed by the subject manuscript are both unique and important. Overall, the manuscript is well written. The editorial comments noted below are largely intended as suggested changes and should be used by the authors as deemed appropriate: • Line 1 – Does “Philippine native pigs” refer to wild or domestic pigs? There are no “native” domestic pigs in the Philippine islands. • Line 39 – Suggest changing “native” to “domestic” • Line 45 – Does this refer to domestic pigs or both domestic and wild pigs? • Line 51 - Does this refer to domestic pigs or both domestic and wild pigs? • Line 77 - I assume that this is referring to wild Sus scrofa (Yes?) • Line 78 - Suggest changing “exists” to “exist”; as a species, Sus scrofa would be a plural subject. • Lines 78-79 - Does “S. scrofa that exists in the Philippines today” mean the wild/feral or domestic Sus scrofa that exist in the Philippines today? • Lines 96-97 – Does “some modern and ancient Philippine pigs” refer to wild or domestic pigs or both? • Line 99 – Suggest changing “pigs” to “domestic pigs” • Line 103 - Suggest changing “Philippine pigs” to “Philippine domestic pigs” • Line 113 – Referring to “Philippine native pigs”, does this mean domestic pigs? If so, then use the modifier domestic and not native. Looking in the Supplemental tables, this must mean domestic pigs. • Line 139 – Suggest changing “Philippine native pigs” to “Philippine domestic pigs” • Line 177 – Does “Philippine pigs” refer to wild or domestic pigs or both? • Line 196 – Remove the extra space between “test” and “[39]” • Line 219 – Suggest changing “Philippine native pigs” to “Philippine domestic pigs” • Line 230 – The “native and domestic pigs” are both domestic pigs (Yes?) • Line 238 - Suggest changing “Philippine native pigs” to “Philippine domestic pigs” • Line 244 – Insert a comma after “0.01)” (0.01), which) • Line 254 - Suggest changing “Philippine native pigs” to “Philippine domestic pigs” • Line 261 - Suggest changing “Philippine native pigs” to “Philippine domestic pigs” • Line 272 - Suggest changing “Philippine native pigs” to “Philippine domestic pigs” • Line 272-273 – Should “Asian and European pigs” be changed to “Asian and European domestic pigs” or does that sample also include data from Eurasian wild boar? • Lines 293-299 - Could the animal discussed in this portion of the text in reality have been a warty pig and not a wild/feral Sus scrofa? This species difference might explain these genetic variances. Where is this animal (PHL21) listed in the Supplementary tables? • Line 301 - Suggest changing “Philippine native pigs” to “Philippine domestic pigs” • line 302 – Suggest changing “continental pigs and wild boar” to “continental domestic pigs and wild boar” • Line 304 – Suggest changing “Philippine pigs” to “Philippine domestic pigs” unless this includes both domestic and wild animals • Line 306 – What does “endemic Philippine wild pigs” refer to? Feral Sus scrofa? Native/endemic warty and/or bearded pigs? • Line 337 – Suggest changing “Philippine native pigs” to “Philippine domestic pigs” • Line 339 - Suggest changing “Philippine native pigs” to “Philippine domestic pigs” • Line 358 - Suggest changing “Philippine native pigs” to “Philippine domestic pigs” • Lines 369-370 - Suggest changing “Philippine native pigs” to “Philippine domestic pigs” • Line 382 - Suggest changing “Philippine native pigs” to “Philippine domestic pigs” • Line 384 – The acronym “NEA” needs to be defined • Line 385 – Suggest changing “Philippine pig genetic pool” to “Philippine domestic pig genetic pool” unless this includes both domestic and wild animals • Line 409 - Suggest changing “Philippine pig genetic pool” to “Philippine domestic pig genetic pool” • Line 410 - Suggest changing “Philippine native pigs” to “Philippine domestic pigs” • Line 411 – Suggest changing “Chinese pigs” to “Chinese domestic pigs” • Line 413 – Suggest changing “Philippine native pig” to “Philippine domestic pig” • Lines 414-415 - Suggest changing “Philippine native pigs” to “Philippine domestic pigs” • Line 418 – Suggest changing “domestic and native pigs” to “domestic pigs” • Line 422 - Suggest changing “Philippine native pigs” to “Philippine domestic pigs” • Lines 459-462 - Were the wild pigs referred to in this portion of the text referring to warty and/or bearded pigs or feral Sus scrofa? • Line 465 – Suggest changing “Philippine native pigs” to “Philippine domestic pigs” • Line 467 - Suggest changing “Philippine native pig” to “Philippine domestic pig” • Line 470 - Suggest changing “Philippine native pigs” to “Philippine domestic pigs” • Line 485 – Suggest changing “Philippine native pig” to “Philippine domestic pig” • Line 488 - Suggest changing “Philippine native pigs” to “Philippine domestic pigs” • Line 496 – Suggest changing “Philippine native pig” to “Philippine domestic pig” • Line 501 - Suggest changing “Philippine native pigs” to “Philippine domestic pigs” • line 547 - Suggest changing “Philippine native pigs” to “Philippine domestic pigs” • Line 593 – Change “2017” to “2018”; the copyright date of this book is 2018. Look at the page after the title page in the book. • Line 607 – “Sus” needs to be italicized • Line 630 - “Sus” needs to be italicized • Line 699 - “Sus scrofa” needs to be italicized • Line 712 - “Sus” needs to be italicized • Lines 764-765 - “Sus scrofa” needs to be italicized References: Heaney, L. R., D. S. Balete, G. V. Gee, et al. 2005. Preliminary report on the mammals of Balbasang, Kaling Province, Luzon. Sylvatrop: The Philippine Forest Research Journal 13:51-62. Heaney, L. R., D. S. Balete and E. A. Rickart. 2016. The mammals of Luzon Island: biogeography and natural history of a Philippine fauna. Johns Hopkins University Press, Baltimore, Maryland, USA. 304 pp. Melletti, M., and E. Meijaard (editors). 2018. Ecology, Evolution and Management of Wild Pigs and Peccaries: Implications for Conservation. Cambridge University Press, United Kingdom. 480 pp. Meijaard, E., and M. Melletti. 2018. Philippine warty pig Sus philippensis (Nehring, 1886). pp. 157-161. in Ecology, Evolution and Management of Wild Pigs and Peccaries: Implications for Conservation. (M. Melletti and E. Meijaard, eds.). Cambridge University Press, United Kingdom. 480 pp. Melletti, M., E. Meijaard, and L. Przybylska. 2018. Visayan warty pig Sus cebifrons (Heude, 1888). pp. 150-156. in Ecology, Evolution and Management of Wild Pigs and Peccaries: Implications for Conservation. (M. Melletti and E. Meijaard, eds.). Cambridge University Press, United Kingdom. 480 pp. Tabaranza, D. G. E., E. Schütz, J. C. T. Gonzalez, L. M. Espiritu-Afuang. 2018. Mindoro warty pig Sus oliveri (Groves, 1997). pp. 162-169. in Ecology, Evolution and Management of Wild Pigs and Peccaries: Implications for Conservation. (M. Melletti and E. Meijaard, eds.). Cambridge University Press, United Kingdom. 480 pp. Reviewer #2: The authors produce some interesting results that should be of interest to PLOS ONE readership. It is original research that has been ethically conducted with robust statistical methods. They contributed their genetic samples to GenBank and provided all of their supplemental materials for download. I believe if someone was so inclined they would be able to reproduce their research which is the hallmark of sound science. The only thing that sticks out to me is that English is not their first language. There are no outright errors, it just doesn't flow well. If they could find a native English speaker to polish it a bit then it would be fantastic. My recommendation is a minor revision. Reviewer #3: This manuscript is an important contribution to the discussion of human and human-mediated plant/animal global dispersion. I feel that the manuscript could benefit from some re-organization, refinement, and a bit more detail in the introduction. - Line 48 - What is the D7 haplogroup? I’m not sure the authors can refer to this without describing what it is. - LINE 50 - What is the significance of a D2 haplogroup how would the reader know what these are? - Line 54-56 - It seems like a sentence may be missing or the phrasing is off. Perhaps another sentence concluding the significance of the work is needed. - Introduction: - The authors should consider breaking the introduction up into more paragraphs to help the reader. - The authors should also consider adding in some discussion of the D-type haplogroups as it plays a very important role later on in the manuscript, but is not described at all until the Discussion. - For example, lines 370-378 may be more appropriate for the introduction so the reader has some sense as to why, in the results section, there is reference to “D-type” haplotypes. - Furthermore, which D cluster refers to Asian Phologeographic vs. European?? (See line 380) - Line 222 - S4 appendix does not appear in the manuscript that the review has access to. - Line 276 - It is not clear to me in Fig 2 the two distinct core lineages. Suggest that the authors revise Fig 2 to clearly indicate the “asian” and “European” core lineages. - Line 281 - The authors make it very difficult to follow the groupings by creating multiple different short-hand methods to describe geographic groupings. In line 281, the authors refer to MTSEA as D7. Suggest sticking to one of these classifications. - S2 Fig - It would be helpful to have the countries labeled in this map so that the reader can refer to their specific locations when reviewing Table 1 as well as the introduction, specifically lines 78-86 - Line 384 - What is “NEA”? I don’t see it defined anywhere else. The number of acronyms and confusing usage of them has mad reading this manuscript very challenging. Strongly suggest removing all acronyms or simplifying significantly. - Line 397 - Perhaps the authors should consider introducing the importance of the “D” haplotypes to their results in the introduction so that the reader may understand the classification - Line 393-398 - Seems like a key finding of the study, but it is buried in the middle of a large paragraph. - Perhaps the map could also include the geographic origins of the D-type haplotype clusters. The phylogenetic tree might also - I’m having some trouble understanding how the philippine “native” pigs that were presumably dispersed by humans (whether from Taiwan or otherwise) can be considered “native” and would want the authors to define what they consider to be native and at what point of genetic mixing would the animal no longer be classified as native? Further, in line 459 the authors refer to “wild” Philippine pigs. Are these different than “native” pigs? - The authors might consider bringing an abridged summary of lines 443-458 into the introduction to further help the reader understand the context of this manuscript. ********** 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 Reviewer #3: 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". 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| Revision 1 |
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PONE-D-21-18979R1Insights on the historical biogeography of Philippine domestic pigs and its relationship with continental domestic pigs and wild boarsPLOS ONE Dear Dr. Layos, Thank you for submitting your manuscript to PLOS ONE and for your patience as we worked to find reviewers who could provide a meaningful evaluation of your work. After careful consideration, we feel that your revised submission would be of interest to the PLOS ONE community but it 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. Both reviewers 1 and 4 feel your study helps to expand understanding of the origin and genetic composition of domesticated pigs in the Philippines. In your revision, please address the suggestions and comments both reviewers have provided to help improve the clarity and impact of the manuscript. Please also address reviewer 4's questions regarding similarity between this manuscript and another currently in review in another journal. As per PLOS ONE's publication policy, articles will not be accepted for publication if they have already been published "in whole or par, elsewhere in the peer-reviewed literature". And, all figures should be original and not published elsewhere. Please make sure to keep these policies in mind when responding to reviewer 4 and drafting your revision. Please submit your revised manuscript by Mar 03 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. 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:
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, Jeffrey A. Eble, Ph.D. Academic Editor PLOS ONE Journal Requirements: Please review your reference list to ensure that it is complete and correct. 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. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #1: (No Response) Reviewer #4: (No Response) ********** 2. 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 #4: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #4: Yes ********** 4. 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 #4: Yes ********** 5. 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 #4: Yes ********** 6. 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: The subject revised manuscript reports on a study evaluating the origin, dispersal, and level of genetic introgression in Philippine domestic pigs using mitochondrial DNA D-loop analysis. These genetic data are then compared to comparable mtDNA data from domestic pigs and Eurasian wild boar. This revision is much improved over the earlier draft. Again, to my knowledge, this is the first study that has specifically looked at genetic composition as related to the anthropogenic origin of domestic pigs in the Philippines. As such, the data encompassed by the subject manuscript are both unique and important. Overall, the manuscript is well written. The editorial comments noted below are largely intended as suggested changes and should be used by the authors as deemed appropriate: • Lines 43-44 – Suggest changing “the history of pig dispersal” to “the history of domestic pig (Sus scrofa) dispersal”. • Line 45 – Suggest changing “associated with some human migration events” to “associated with human migration events” • Line 47 – Suggest changing “wild boars” to “wild boar” • Line 55 – Suggest changing “Philippine pig haplotypes” to “Philippine domestic pig haplotypes” • Line 67 – Suggest changing “The wild boar (Sus scrofa L.)” to “The Eurasian wild boar (Sus scrofa L.)” • Lines 86-87 – Suggest changing “an exceptionally high levels of endemism” to “an exceptionally high level of endemism” • Line 87 – Suggest changing “The Philippines has repeatedly” to “The Philippines have repeatedly” • Line 89 - Suggest changing “four endemic wild pigs such as the Philippine” to “four endemic wild pigs including the Philippine” • Line 91 – Suggest changing “as well as one native shared with Sundaic” to “as well as one native species shared with the Sundaic” • Line 94 – Suggest changing “ubiquitous wild boar S. scrofa was not considered native” to “ubiquitous Eurasian wild boar S. scrofa is not native” • Lines 111-112 – Suggest changing “For this reason, [27] excluded” to “For this reason, Larson et al. [27] excluded” • Line 128 – Suggest changing “an introduced pig breed” to “an introduced domestic pig breed” • Line 133 - Suggest changing “diversity and structure exhibits a signature” to “diversity and structure exhibit a signature” • Line 217 - Suggest changing “described by [4] with six clades” to “described by Larson et al. [4] with six clades” • Line 218 – Suggest changing “proposed by [10] were used” to “proposed by Tanaka et al. [10] were used” • Line 287 – Suggest changing “most pigs in the populations studies” to “most pigs in the population studies” • Line 320 - Suggest changing “D7 haplogroup which accounted” to “D7 haplogroup, which accounted” • Line 324 – Suggest changing “what [5] recognized” to “what Scandura et al. [5] recognized” • Lines 333-334 – Suggest changing “the previous researches.” to “the previous research.” • Line 340 – Suggest changing “wild boars” to “wild boar” • Line 361 - Suggest changing “contrast, domestic pigs in MSEA combined revealed” to “contrast, combined domestic pigs in MSEA revealed” • Line 404 - Suggest changing “Philippine pigs” to “Philippine domestic pigs” • Line 437 - Suggest changing “Before the European arrived in the Philippines” to “Before the Europeans arrived in the Philippines” • Line 442 – Suggest changing “which exhibited” to “which is exhibited” • Line 446 - Suggest changing “was minimal, which accounted for only” to “was minimal, accounting for only” • Line 464 - Suggest changing “Chinese pigs, therefore this precluded the origin of these haplogroup” to “Chinese pigs, which precludes the origin of this haplogroup” • Line 480 – Suggest changing “populations despite shared haplotypes could” to “populations, despite shared haplotypes, could” • Lines 490-497 – What “Philippine wild pigs” are being referred to here? The Philippine wild pigs that Bill Oliver was referring to in the IBEX article cited are not Sus scrofa, and in fact are all separate species from either domestic or wild Sus scrofa. Without identifying the species of the Philippine wild pigs that you are referring to, I’m not sure of the value of this paragraph to the rest of the study. • Lines 510-511 - Suggest changing “In addition, [72] have previously discussed” to “In addition, Scandura et al. [72] have previously discussed” • Line 525 – Suggest changing “distributions which represent” to “distributions that represent” • Line 560 - Suggest changing “reported by [54]” to “reported by Frantz et al. [54]” • Line 566 – Suggest changing “exchange of pigs” to “exchange of domestic pigs” • Line 574 – What is the name “native pig populations” referring to here, domestic or wild pigs? There are no “native” domestic pig populations in the Philippines. John J. Mayer, Ph.D. Savannah River National Laboratory Battelle Savannah River Alliance Aiken, SC 29808 (803) 819-8404 Reviewer #4: This manuscript aimed to present the origin and distribution of Philippine domestic pigs based on partial mitochondrial D-loop sequences analysis. The results showed the genetic connection between the Philippine domestic and continental pigs, supporting the Neolithic-Austronesian expansion model and proposing the possible alternative migration route. The data and analyses presented in the manuscript are appropriate, and the results support the key messages. The sequences under accessions MN625805-MN625830 are searchable; however, the sequences under accessions MW924902-MW92973 could not be found in the GenBank database. I am reviewing another manuscript submitted to a different journal. In that manuscript, some pictures of pigs looked the same as all sub-figures in Fig. 2, except Fig. 2F. In addition, some contents in the introduction section of that manuscript were very similar, if not the same, as some parts of the introduction of this manuscript; for example, the content on Page 4, Line 96-103 starts with the words "To date." However, more Philippine pig samples were included, and some analyses applied on mitochondrial D-loop sequences in that manuscript differed from this manuscript. In addition, the conclusion in that manuscript could be considered as an answer of the future direction of this manuscript mentioned on Page 23, Line 567-569, that " a more thorough investigation should be conducted to relate the possible ancestral diffusion that occurred from MSEA to the Philippines via Sundaland. Despite the concerns in the previous paragraph, the following comments should be addressed before accepting publication. Page 2, Line 61-62: Regarding the sentence on these lines, what is the population showing sudden decline? The population name, such as Philippine pigs, Mainland Southeast Asian pigs, should be specified. In my opinion, both Bayesian skyline plots (Fig. 7) did not clearly show a sudden decline, so I am wondering what result supported this statement? This comment also applied to the statement "The sudden population decline occurred approximately 25,000 years before present (BP)" on Page 15, Line 377-378 and "The underlying sudden population decline as predicted in the BSP markedly followed the LGM period" on Page 23, Line 571-572. Page 8-9, Line 214-216: The statement "This method calculates the net divergence of each taxon from all other taxa as the sum of the individual distances from variance within and among groups of Philippine pigs and comparison sequences." should be revised. It was not whether the net divergence of each taxon was the sum of the individual distance, and the distance was calculated from within and between groups variance. In addition, is the term "variance" the statistical variance or the sequence differences? Page 11, Line 262-264: How many haplotypes were found in total? The summation of the number of PHL, Cambodia, Bhutan, Laos, Myanmar, and Vietnam haplotypes was 74, but the sentence on Line 264 stated that "these sequences collapsed when pooled from 76 to 57 haplotypes. Page 11, Line 265: Would the 26 haplotypes be found in 26 samples? If this is correct, should "a single sequence" be changed to "a single sample"? Page 12, Line 285: The (Figs 2 and 3) should be changed to (Fig. 3 and 4). Page 14, Line 335-337: Why would the presence of unique haplotypes, such as PHL21, in Philippine wild pigs suggest the presence of new subspecies of wild pigs? I think carrying the distinct mtDNA haplotype defined based on partial D-loop sequence is insufficient to suggest that the sample is the new subspecies. Page 16, Line 409-412: What was the result supporting the statement "The distribution of the haplotype frequencies did not indicate equilibrium."? In addition, would the genetic connection to the continental pigs shown by phylogeny and haplotype network suggest the multiple ancestors of Philippine domestic pigs? Page 18, Line 447-449: The citation should be added to the sentence "This observation is consistent with the situation in domestic pigs in the MSEA, where the mtDNA of European pigs has a negligible impact on the maternal origin of domestic pigs." Page 20, Line 494-497: Due to the limited sequences available and included in this study, do you have enough evidence to suggest that the Philippine wild pigs were descended from the indigenous wild pigs? Page 47: Would it be possible to expand the network on Fig. 4, especially for haplogroup D2 and D7, to present the connection between haplotypes? ********** 7. 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| Revision 2 |
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PONE-D-21-18979R2Insights on the historical biogeography of Philippine domestic pigs and its relationship with continental domestic pigs and wild boarsPLOS ONE Dear Dr. Layos, Thank you for submitting your manuscript to PLOS ONE. After careful consideration of the revised manuscript, we feel that it has merit; however, some additional revisions are needed to meet PLOS ONE’s publication criteria. We invite you to submit a revised version of the manuscript that addresses my comments listed below. Line 55: "collapsed with" is unclear. If the intent is to highlight the prevalence of D7 haplogroup in the Philippines perhaps "included" would be more appropriate. Lines 63-64: Which finding highlights an important challenge managing Philippine pig genetic resources and what is the challenge? Lines 202-204: The description of Arlequin AMOVA fixation indices is inaccurate and needs to be revised. As noted in the Arlequin user manual (Excoffier et al. 2005), PhiST tests for deviations from panmixia within the full sample, PhiCT tests the significance of designated population groupings, and PhiSC tests for differences among populations within groups.Excoffier, L., Laval, G., & Schneider, S. (2005). Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evolutionary bioinformatics, 1, 117693430500100003.Lines 220-252: My feeling is that population demographic analyses as presented may be inaccurate because groupings include historically isolated populations. This violates model assumptions and can bias results by reflecting changes in the degree of structure rather than changes in population size (eg. Heller et al. 2013). Given this, I think the impact of the paper could be improved by leaving out demographic analyses and placing the focus more clearly on phylogenetic and phylogeographic results. However, if you decide to retain demographic analyses please include a caveat highlighting the potential impact of historic population subdivision on demographic estimates.Heller, R., Chikhi, L., & Siegismund, H. R. (2013). The confounding effect of population structure on Bayesian skyline plot inferences of demographic history. PloS one, 8(5), e62992.Line 264-265: The sentence starting with "Twenty-six..." is unclear. Line 284: Because PhiST reflects the average contribution of population subdivision to deviation from panmixia, significance is possible even if some populations comparisons are not significantly different. Given this, please change "at all geographic locations examined" to something like "indicating significant genetic structure among the geographic locations examined."Table 2: Please revise the "source of variation" column and related notes below the table to more accurately reflect Arlequin fixation indices. Specifically, PhiSC is more accurately described as "among populations within groups". Table 3: Is pairwise Fst or PhiST presented here? If genetic distance between haplotypes was included in the analysis then PhiST would be correct.Line 333: "nomenclature quotation" is unclear. Line 507: Is "Fst" a typo? If not, some clarification in the methods is needed. Line 507: "individuals" seems to be a typo. Please correct.Figure S1: There are no indels so the the definition of the "minus" symbol can be deletedFigure S1: D7 is not included in the figure. Figure 1: Please enlarge the haplotype key to ensure readability.Figure 5-7: If demographic analyses are retained these figures should be moved to Supplemental data. Please submit your revised manuscript by Mar 19 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. 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:
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, Jeffrey A. Eble, Ph.D. Academic Editor PLOS ONE Journal Requirements: Please review your reference list to ensure that it is complete and correct. 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. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: [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. |
| Revision 3 |
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PONE-D-21-18979R3Insights on the historical biogeography of Philippine domestic pigs and its relationship with continental domestic pigs and wild boarsPLOS ONE Dear Dr. Layos, Thank you for submitting your manuscript to PLOS ONE. We very much appreciate your careful attention to reviewer and editor comments throughout the review process; however, we feel one additional revision with a focus on grammar and punctuation is needed to fully meet PLOS ONE’s publication criteria. Therefore, we invite you to submit a revised version of the manuscript that addresses the points listed below and includes a final close review of the manuscript for grammatical and formatting errors. Line 48- delete "a" in "revealed a considerable"Line 50- add comma between "analysis with" AND delete comma between "(5.10%), harboringLine 55- delete "with"Line 59-61- This sentence is unclear and should be revised.Line 132- delete "even"Line 202- delete "namely"Line 212- what was Fst used for pairwise analyses while PHIst was used for AMOVA? If a mutational model was included in pairwise comparisons then PHIst should be used. If genetic distance was not included then Fst is the accurate parameter, but if that is the case then I think a brief justification is needed to help readers understand why genetic distance was included in one set of analyses and not the other.Line 297- is "(Fst values, p<0.01)" a typo? Did you mean to include the range of Fst values here?Line 336- delete "A" in "A widespread Asian ancestry"Line 422- "underlies as a genetic basis" is unclear. Please reviseLine 427- what "equilibrium" are you referencing?Lines 435-437- Please revise for clarity and grammar. For example... "Thus, these events may have paved the way for the introduction of multiple distinct lineages of domestic pigs to the Philippines, as has been documented for chickens [56] and goats [57]."Lines 443-446- Please revise for clarity and grammar. Line 446- replace "the preliminary studies that revealed" with "preliminary genetic studies revealed"Line 449- add "in the Philippines" after "D2 haplotypes"Line 458- change "precisely evident as shown by" to "supported by"Line 461- change "a crucial" to "an important"Lines 471-474- This sentence is unclear, please revise.Line 500- replace "and the consequent" with ", and subsequentLines 500-503- This sentence is unclear, please revise.Line 503- is "founder" a typo? If I understand your point then "founder event" would be more accurate.Line 504- "population" should be pluralLine 568- "sound impact" is unclear, please revise.Line 569- delete "the" before "changes"Line 570- delete "the" before "population size"Line 578-580- This sentence is unclear, please revise.Line 583- delete "flow" Please submit your revised manuscript by Apr 14 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. 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:
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, Jeffrey A. Eble, Ph.D. Academic Editor PLOS ONE Journal Requirements: Please review your reference list to ensure that it is complete and correct. 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. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: [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. |
| Revision 4 |
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Insights on the historical biogeography of Philippine domestic pigs and its relationship with continental domestic pigs and wild boars PONE-D-21-18979R4 Dear Dr. Layos, 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, Jeffrey A. Eble, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: |
| Formally Accepted |
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PONE-D-21-18979R4 Insights on the historical biogeography of Philippine domestic pigs and its relationship with continental domestic pigs and wild boars Dear Dr. Layos: 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. Jeffrey A. Eble Academic Editor PLOS ONE |
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