Peer Review History

Original SubmissionOctober 30, 2020
Decision Letter - Peter F. Biehl, Editor

PONE-D-20-34180

Insight into the introduction of domestic cattle and the process of Neolithization to the Spanish region Galicia by genetic evidence

PLOS ONE

Dear Dr. Hofreiter,

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.

All comments need to be addressed before re-submission.

Please submit your revised manuscript by Mar 15 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:

  • 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: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols

We look forward to receiving your revised manuscript.

Kind regards,

Peter F. Biehl, PhD

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 manuscript, please provide additional information regarding the specimens used in your study. Ensure that you have reported specimen numbers and complete repository information, including museum name and geographic location.

If permits were required, please ensure that you have provided details for all permits that were obtained, including the full name of the issuing authority, and add the following statement:

'All necessary permits were obtained for the described study, which complied with all relevant regulations.'

If no permits were required, please include the following statement:

'No permits were required for the described study, which complied with all relevant regulations.'

For more information on PLOS ONE's requirements for paleontology and archaeology research, see https://journals.plos.org/plosone/s/submission-guidelines#loc-paleontology-and-archaeology-research.

3. We note that you are reporting an analysis of a microarray, next-generation sequencing, or deep sequencing data set. PLOS requires that authors comply with field-specific standards for preparation, recording, and deposition of data in repositories appropriate to their field. Please upload these data to a stable, public repository (such as ArrayExpress, Gene Expression Omnibus (GEO), DNA Data Bank of Japan (DDBJ), NCBI GenBank, NCBI Sequence Read Archive, or EMBL Nucleotide Sequence Database (ENA)). In your revised cover letter, please provide the relevant accession numbers that may be used to access these data. For a full list of recommended repositories, see http://journals.plos.org/plosone/s/data-availability#loc-omics or http://journals.plos.org/plosone/s/data-availability#loc-sequencing.

4. Please amend the manuscript submission data (via Edit Submission) to include author Stefanie Hartmann.

5.We note that Figure(s) 1 in your submission contain map images which may be copyrighted. All PLOS content is published under the Creative Commons Attribution License (CC BY 4.0), which means that the manuscript, images, and Supporting Information files will be freely available online, and any third party is permitted to access, download, copy, distribute, and use these materials in any way, even commercially, with proper attribution. For these reasons, we cannot publish previously copyrighted maps or satellite images created using proprietary data, such as Google software (Google Maps, Street View, and Earth). For more information, see our copyright guidelines: http://journals.plos.org/plosone/s/licenses-and-copyright.

We require you to either (1) present written permission from the copyright holder to publish these figures specifically under the CC BY 4.0 license, or (2) remove the figures from your submission:

1) You may seek permission from the original copyright holder of Figure(s) 1 to publish the content specifically under the CC BY 4.0 license. 

We recommend that you contact the original copyright holder with the Content Permission Form (http://journals.plos.org/plosone/s/file?id=7c09/content-permission-form.pdf) and the following text:

“I request permission for the open-access journal PLOS ONE to publish XXX under the Creative Commons Attribution License (CCAL) CC BY 4.0 (http://creativecommons.org/licenses/by/4.0/). Please be aware that this license allows unrestricted use and distribution, even commercially, by third parties. Please reply and provide explicit written permission to publish XXX under a CC BY license and complete the attached form.”

Please upload the completed Content Permission Form or other proof of granted permissions as an "Other" file with your submission.

In the figure caption of the copyrighted figure, please include the following text: “Reprinted from [ref] under a CC BY license, with permission from [name of publisher], original copyright [original copyright year].”

b)  If you are unable to obtain permission from the original copyright holder to publish these figures under the CC BY 4.0 license or if the copyright holder’s requirements are incompatible with the CC BY 4.0 license, please either i) remove the figure or ii) supply a replacement figure that complies with the CC BY 4.0 license. Please check copyright information on all replacement figures and update the figure caption with source information. If applicable, please specify in the figure caption text when a figure is similar but not identical to the original image and is therefore for illustrative purposes only.

The following resources for replacing copyrighted map figures may be helpful:

USGS National Map Viewer (public domain): http://viewer.nationalmap.gov/viewer/

The Gateway to Astronaut Photography of Earth (public domain): http://eol.jsc.nasa.gov/sseop/clickmap/

Maps at the CIA (public domain): https://www.cia.gov/library/publications/the-world-factbook/index.html and https://www.cia.gov/library/publications/cia-maps-publications/index.html

NASA Earth Observatory (public domain): http://earthobservatory.nasa.gov/

Landsat: http://landsat.visibleearth.nasa.gov/

USGS EROS (Earth Resources Observatory and Science (EROS) Center) (public domain): http://eros.usgs.gov/#

Natural Earth (public domain): http://www.naturalearthdata.com/

6. 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.

Additional Editor Comments :

Please address the comments by reviewer 2 before re-submission.

[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: 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: The paper "Insight into the introduction of domestic cattle and the process of Neolithization to the Spanish region Galicia by genetic evidence" provide new and useful data about cattle population dynamics in a non-sampled region of the Iberian peninsula. This data is important for the knowledge of the world cattle phylogeny and evolution as well as to understand ancient human history. The paper is very well written and developed and the analyses are appropriate and correct. I don't have any changes to highlight.

Reviewer #2: This work describes the retrieval of mtDNA genome sequence from 11 ancient Iberian Bos specimens. The data, as described, is of good quality; many of the genomes are of high coverage, the methods are sound, the laboratory track record is excellent. I think these data are of interest - three very old wild ox specimens are included for example, and the phylogenetic placing of some of the domestic sequences at basal phylogenetic positions is notable. Therefore my overall recommendation is for acceptance.

However I have a few comments, line numbers are given

20. the founding population estimate should be quoted as a range rather than the central estimate of 81 females.

table 1. the % coverage of three samples: Bt_MR, Bt_C, Bt_AT_1600BP and one Mesolithic are much lower than others. This needs to be borne in mind when one discusses the phylogenetic positions of these. For example is Bt_MR basal in position rather than simply incompletely described for several mutations that would remove it from this position?

174 relating to this point above, Bt_MR is inferred as the central node - but is it?

268, same point. Are we sure these are basal.

Fig 2, the BEAST tree. This analysis has the facility to consider nodes with different time horizons. A strong aspect of the data here is that these samples have direct C14 dates. I suggest that a better or additional analysis might only use the best covered mtDNA genomes and time-stamp the ancient samples. It would be interesting if the topology of the tree changed in this circumstance.

The discussion is somewhat lengthy and could be abridged. For example, I think that the relevance/comparison to the aDNA analysis of human remains is over-discussed. The only point (and it is worth making) is the absence of T1.

323 An archaeologist might query the claim that this presents “ the first evidence that people with livestock migrated into that region from the European mainland.” Is there no other non aDNA evidence for this?

Data availibility: It is welcome that all raw fastq data will be deposited. This is because processed data (eg mtDNA sequences) are subject to local parameter choices and subsequent users may wish to process these slightly differently.

**********

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: Yes: Dan Bradley

[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 1

Dear Editor,

thank you and the reviewers for the comments to our manuscript entitled “Insight into the introduction of domestic cattle and the process of Neolithization to the Spanish region Galicia by genetic evidence.” As requested, we have revised our manuscript and include a version with tracked changes. The point-by-point responses to the reviewers’ comments are below.

Editor Comments:

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

Response: We have used the most current version of the LaTeX template, available at https://journals.plos.org/plosone/s/latex. This template appears to be more recent than the listed PDFs.

2. In your manuscript, please provide additional information regarding the specimens used in your study. Ensure that you have reported specimen numbers and complete repository information, including museum name and geographic location. If permits were required, please ensure that you have provided details for all permits that were obtained, including the full name of the issuing authority, and add the following statement: 'All necessary permits were obtained for the described study, which complied with all relevant regulations.' If no permits were required, please include the following statement: 'No permits were required for the described study, which complied with all relevant regulations.'

Response: All specimens studied for our manuscript are housed in the "Instituto Universitario de Xeoloxía, Universidade da Coruña", the director of which is one of the co-authors (Aurora Maria Grandal D'Anglade). Therefore, no permits were required, and we have added the corresponding statement to the manuscript.

3. We note that you are reporting an analysis of a microarray, next-generation sequencing, or deep sequencing data set. PLOS requires that authors comply with field-specific standards for preparation, recording, and deposition of data in repositories appropriate to their field. Please upload these data to a stable, public repository (such as ArrayExpress, Gene Expression Omnibus (GEO), DNA Data Bank of Japan (DDBJ), NCBI GenBank, NCBI Sequence Read Archive, or EMBL Nucleotide Sequence Database (ENA)). In your revised cover letter, please provide the relevant accession numbers that may be used to access these data. For a full list of recommended repositories, see http://journals.plos.org/plosone/s/data-availability#loc-omics or http://journals.plos.org/plosone/s/data-availability#loc-sequencing.

Response: We deposited all raw sequence reads of this study in the NCBI Sequence Read Archive under BioProject accession number PRJNA705960. All generated mitochondrial genomes were deposited in NCBI GenBank. All accession numbers have now been included in the manuscript.

The samples Bt_MR_(3736BP) and Bt_CO_(60BP) cannot be made available at NCBI SRA (really – you mean GenBank, or? SRA should be fine), since the do not meet the GenBank submission criteria (less than 50 \\% ambiguous characters). These are available on request.

4. Please amend the manuscript submission data (via Edit Submission) to include author Stefanie Hartmann.

Response: The author Stefanie Hartmann is now included in the manuscript submission data.

5.We note that Figure(s) 1 in your submission contain map images which may be copyrighted. All PLOS content is published under the Creative Commons Attribution License (CC BY 4.0), which means that the manuscript, images, and Supporting Information files will be freely available online, and any third party is permitted to access, download, copy, distribute, and use these materials in any way, even commercially, with proper attribution. For these reasons, we cannot publish previously copyrighted maps or satellite images created using proprietary data, such as Google software (Google Maps, Street View, and Earth). For more information, see our copyright guidelines: \\url{http://journals.plos.org/plosone/s/licenses-and-copyright}.

Response: The map was created by coauthor Aurora Grandal-d'Anglade specifically for this study; it has not been used elsewhere. We have added this information to the legend of Figure 1 in our manuscript.

6. 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: \\url{http://journals.plos.org/plosone/s/supporting-information}.

Response: We reorganized the data of our supporting information into several different files that follow the PLOS ONE supporting information guidelines. Captions and in-text citations in our manuscript were updated as requested.

Reviewer 2 comments:

20. the founding population estimate should be quoted as a range rather than the central estimate of 81 females.

Response: We addressed this comment in line 20 of our manuscript. The sentence now reads: "Based on mitochondrial DNA data, a founding population of 29 to 783 females has been estimated for the beginning of the taurine cattle domestication in the Middle East [4, 17]"

table 1. the % coverage of three samples: Bt_MR, Bt_C, Bt_AT_1600BP and one Mesolithic are much lower than others. This needs to be borne in mind when one discusses the phylogenetic positions of these. For example is Bt_MR basal in position rather than simply incompletely described for several mutations that would remove it from this position?

Response: We agree with this comment, especially for the samples Bt_MR and Bt_CO. For both of them, we only were able to retrieve sequence information that covered less then 50% of the mitochondrial genome. Therefore, we added additional explanations for their placements in the phylogeny and the network in the discussion. Specifically, the following short sections were added.

line 271: "This is plausible for the older sample from A Tara, but not necessarily for the very young sample from Chan do Lindeiro. Its placement in the network, however, might be due to missing data in diagnostic regions of the mitochondrial genome due to its low mapping coverage."

line 277: "However, the lack of all diagnostic SNPs and the overall lower coverage of this sample make an inference of the haplotype impossible and question its placement in the network. Regions in its mitochondrial genome which we could not characterize in this study can have a large impact on the results of all our analyses for this sample."

174 relating to this point above, Bt_MR is inferred as the central node - but is it?

Response: This point is related to previous one, but is referring to a line in the results. Because in this line we only wanted to describe the samples placement in the network, we did not make any changes there. However, we do agree with the overall point that the central position of this sample might might be due to missing data at potentially important sections of the mitochondrial genome.

268, same point. Are we sure these are basal.

Response: We addressed this comment specifically with the changes made in the discussion at line 271, shown two comments above.

Fig 2, the BEAST tree. This analysis has the facility to consider nodes with different time horizons. A strong aspect of the data here is that these samples have direct C14 dates. I suggest that a better or additional analysis might only use the best covered mtDNA genomes and time-stamp the ancient samples. It would be interesting if the topology of the tree changed in this circumstance.

Response: We thank the reviewer for this suggestion and tried to implement it. Unfortunately, the BEAST analysis did no coalesce even after a very long run time (> 1 billion steps). Therefore, we assume that our data set does not contain enough temporal information for this type of analysis. Consequently, we have omitted it from the revisions.

The discussion is somewhat lengthy and could be abridged. For example, I think that the relevance/comparison to the aDNA analysis of human remains is over-discussed. The only point (and it is worth making) is the absence of T1.

Response: In order to abridge the discussion, we shortened the paragraph about the comparison with human remains. The new paragraph starts in line 282 of the manuscript and now reads as follows:

"Our cattle haplogroup assignments are in agreement with ancient DNA data of human remains from Spain, which showed that the transition from Mesolithic to Neolithic societies was mediated by demographic processes, involving admixture with pioneering farmers of Near Eastern origin [23, 24, 44, 45]. This genetic signal of Neolithic immigration in humans is consistent with the first appearance of cattle carrying the T3 haplotype, likely introduced by the incoming farmers. Noticeable, although recent studies have shown prehistoric gene flow between human population from African and southern/central Iberia around the Middle Neolithic/Bronze Age [24, 46], we found no evidence of African diversity in the domestic cattle analyzed in this study, as none of them was related to the African haplogroup T1."

323 An archaeologist might query the claim that this presents “ the first evidence that people with livestock migrated into that region from the European mainland.” Is there no other non aDNA evidence for this?

Response: We agree with this comment, as well, and changed the concerned line 315 accordingly. It now reads: "In accordance with human studies, we presented evidence that people with livestock migrated to that region from the European mainland."

Data availibility: It is welcome that all raw fastq data will be deposited. This is because processed data (eg mtDNA sequences) are subject to local parameter choices and subsequent users may wish to process these slightly differently.

Response: The raw fastq data is deposited in the NCBI Sequence Read Archive under BioProject accession number PRJNA705960. Accession numbers have now been included in the manuscript.

Other changes:

While the manuscript was in review, we received new C14 dating information for three samples of this study. The concerned samples are Bt_AT_strat, Bt_SA_strat_1, and Bt_SA_strat_2. Their sample names were changed accordingly to Bt_AT_3370BP, Bt_SA_1200BP_1, and BT_SA_1290BP_2. Due to the new samples names, we made changes in Figure 2 and Figure 3 and also changed the names in the manuscript and Table 1.

Yours sincerely,

Marie Gurke, on behalf of all co-authors

Decision Letter - Peter F. Biehl, Editor

Insight into the introduction of domestic cattle and the process of Neolithization to the Spanish region Galicia by genetic evidence

PONE-D-20-34180R1

Dear Dr. Hofreiter,

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,

Peter F. Biehl, PhD

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Formally Accepted
Acceptance Letter - Peter F. Biehl, Editor

PONE-D-20-34180R1

Insight into the introduction of domestic cattle and the process of Neolithization to the Spanish region Galicia by genetic evidence

Dear Dr. Hofreiter:

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. Peter F. Biehl

Academic Editor

PLOS ONE

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 .