Dear Dr. Pecnik,

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.

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Even providing valuable information on dairy feeding habits of Scythians, the study may suffer from lack of robustness and possible insufficient number of individuals tested, as commented by reviewers. Possible risk of contamination was also mentioned as a considerable problem and the authors should meticulously address this issue. Several other methodological omissions are noted by Reviewer #2.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

Reviewer #1: Yes

Reviewer #2: Partly

Reviewer #3: Yes

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2. Has the statistical analysis been performed appropriately and rigorously? -->?>

Reviewer #1: N/A

Reviewer #2: No

Reviewer #3: N/A

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3. Have the authors made all data underlying the findings in their manuscript fully available??>

The PLOS Data policy

Reviewer #1: Yes

Reviewer #2: No

Reviewer #3: Yes

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4. Is the manuscript presented in an intelligible fashion and written in standard English??>

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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Reviewer #1: This paper presents original research on palaeo-proteomic analysis of human dental calculus to assess reliance on dairy products. Previous research presented in the paper have provided a broad picture of subsistence practices among the Scythian culture and the use of palaeo-proteomic analysis to assess specific contents of the diet is particularly useful as a complementary element of research.

The study provides evidence for the first palaeo-proteomic evidence of BTNS1A1 from dental calculus, a nice result that will encourage additional research by demonstrating additional potential questions.

While the sample size is small, this is the result of assessing the reliability of samples through oral signature assessment. It is more desirable for researchers to present small, pilot samples of solid data rather than inflate sample size with inadequate results. In addition, while the sample size is small, the proteomic data is well integrated with previous isotope and ceramic residue data to strengthen interpretations. The interpretation and conclusions presented in the paper are not overstated. The suggestion of limited access to horse milk consumption is presented as a possibility with a specific call for further assessment. The final paragraph of the conclusion focuses specifically on additional methods to further expand the initial patterns presented here.

I have only one correction - line 185, The sentence should start "As such"

Reviewer #2: This study analyzes 43 dental calculus samples from Scythian individuals and successfully identifies milk proteins in six individuals, including horse-derived milk proteins in one case. The results are archaeologically significant and offer important insights into subsistence strategies. However, several methodological and analytical aspects need more clarification or improvement.

1. High exclusion rate of dental calculus samples and possible contamination

Only 11 out of 43 samples passed the oral signature assessment, resulting in a very high exclusion rate. The authors should clearly address why so many samples failed to meet the criteria. For example, the following possibilities are candidates:

・Poor preservation of dental calculus

・Effects of post-excavation treatment or consolidation (e.g., glue from adhesives or stabilizers)

・Differences in burial environments or soil conditions at the archaeological sites

At present, it is unclear whether the low success rate reflects limitations of the proteomic protocol or issues related to sample integrity or handling.

2. Incomplete adherence to established reliability criteria in paleoproteomics

While the study reports the use of thresholds such as PSM ≥ 2, protein-level FDR < 5%, and peptide-level FDR < 2%, it does not employ stricter commonly used standards such as unique peptides ≥ 2 and FDR < 1%.

For example, the following publication supports the use of "unique peptide ≥ 2" to reduce false positives:

Peng et al., 2003, Journal of Proteome Research

https://doi.org/10.1021/pr025556v

Given the implications for reproducibility and interpretive confidence, the authors should explain why these stringent thresholds were not used, and what additional steps (if any) were taken to control the FDR. If such rationale cannot be sufficiently justified, the authors should consider reanalyzing the dataset using these established criteria.

3. Omission of deamidation analysis

Deamidation is one of the most commonly used indicators of authenticity in ancient protein studies. The authors should calculate the deamidation rates and show them in the manuscript. The authors mentioned Ramsøe et al. (2021) and other papers to justify the exclusion of deamidation analysis, bbut the previous study does not argue against calculating the deamidation rate. Instead, it highlights variability of deamidation rate of dental calculus across individuals and samples, and suggests that deamidation should be used in combination with multiple lines of evidence to authenticate ancient protein data. Given the high exclusion rate of calculus samples in this study, it would be especially valuable to report deamidation rates to support the authenticity of the peptide identifications.

4. Minor comments

・Integration with ancient genomics: The authors should discuss ancient genome of Scythians, particularly lactase persistence-related variants. Such genetic data could help to consider about the dietary interpretations.

・Equine protein spectra: Since the identification of equine milk consumption is discussed in detail, it would strengthen the study to show the MS2 spectra of the relevant peptides, particularly those assigned to Equus.

Reviewer #3: This manuscript presents a relevant study on an important topic: the history of dairying. The authors apply a relatively recent analytical approach to examine dental calculus contents and successfully retrieve dietary information of Scythian populations in present-day Ukraine, contributing to the growing body of literature about these Iron Age societies.

The analyses appear careful and methodologically rigorous, and the authors acknowledge the interpretive limitations of their data. They also clearly outline future research directions that could address the gaps and hypotheses raised in the discussion of the manuscript.

Their results provide evidence of mixed dairy pastoralism in the Scythian era, supporting previous isotopic and archaeological findings. Another important contribution of this study is the identification of horse milk protein in the dental calculus of one of the analyzed individuals, marking the first direct evidence of milk consumption from this species by the Scythians. This finding aligns with historical records of Scythian practices and adds a valuable layer of molecular data to our understanding of their dietary habits.

Furthermore, the identification of BTN1A1 (a MFGM peptide) in dental calculus represents a novel contribution to paleo-proteomics, as this marker had previously only been detected in archaeological artifacts (ceramic vessels and woven baskets) and ancient preserved cheese. This adds methodological value to the study and could influence future research in the field.

Limitations and Suggestions:

Despite the merits outlined above, the study is limited by its small sample size. Only two archaeological sites are represented, and out of 43 calculus samples collected, only samples from 11 individuals yielded proteomes that passed the criteria for dietary analysis in the “assessment of oral signature for sample authentication”. Moreover, milk protein was detected in only 6 individuals (3 per site), and horse milk was identified in just one case.

As the authors correctly acknowledge, generalizations based on such a small dataset should be cautiously approached. While the challenges of working with bioarchaeological material are well-known, and limited sample sizes are not uncommon, the study’s interpretive reach should be kept proportionate to the available evidence.

Based on the scarcity of horse milk protein in the samples, the authors suggest that access to horse milk may have varied within Scythian society, potentially reflecting hierarchical divisions. While this is a plausible hypothesis, it remains speculative given the data. Moreover, the absence of a dietary marker (such as horse milk protein) does not necessarily imply non-consumption, due to the fact that several factors affect calculus formation and the preservation of exogenous remains in its matrix.

The authors are commendably transparent about these caveats and argue that “further archaeological and biomolecular data from a wider portion of Scythian-era populations” could complement the investigations and fill the gaps left. Adding to this discussion, I would also suggest incorporating, whenever feasible, a multi-proxy approach in future analyses of dental calculus, combining, for example, protein, aDNA, and plant and other microremains data from samples (or subsamples) of the same individuals and contexts. This could strengthen interpretations and allow for a broader reconstruction of ancient diets.

In addition, I think it would be beneficial to include other bioarchaeological or bioanthropological data (if available) from the analyzed individuals, particularly the one with evidence of horse milk consumption. Such data could help assess whether status-related differences in diet are supported by other lines of evidence.

Specific observations:

• The authors state that “no other dietary proteins at distinct taxonomic levels were detected” but do not clarify whether this results from methodological limitations, database constraints, or a genuine absence of other dietary proteins. A brief explanation would be helpful.

• The section titled “Background and Workflow” is more appropriately categorized as a methodological description rather than a result. I suggest merging it with the “Methods” section for consistency and clarity.

• Line 118: The term “replication”, referring to five calculus samples, is unclear. Does this mean multiple samples from the same individual, or sub-sampling of a single calculus deposit? If the former, the authors should explain why additional samples were taken. Since the techniques used to access the dental calculus contents are typically destructive, it is important to note whether efforts were made to conserve material for future analysis and to document (by photographing and recording macroscopic aspects) the calculus deposits before its detachment. This is particularly relevant given the growing value of calculus as a multi-proxy resource.

Text revision:

Finally, the manuscript is clear and generally well written. However, it would benefit from some revisions and careful proofreading. Below are some issues I have identified in both the main text and the “Supplementary Information”:

Main Text:

• Line 68: “...easily accessible to water sources…” → Remove “to”: “easily accessible water sources.”

• Line 84: Replace “microfossil” with “micro-remains,” which is now the preferred and more accurate term in the context of dental calculus studies.

• Lines 87–88: The publication year for Soncin et al. is repeated. Please, revise for accuracy.

• Line 93: The map (Figure 1) should be cited earlier in the text, ideally when the archaeological sites are first introduced. I suggest replacing “see Supplementary Information” with “see Figure 1.”

• Lines 145–150: The sentence beginning with “While the ruminant assignments…” is unclear and needs rephrasing.

• Page 16: The URL provided for Geber et al. (2019) appears to be incorrect. Please verify and correct the citation.

Supplementary Information:

The section titled “Scythian settlements and cemeteries” would be better integrated into the manuscript’s Introduction and requires grammatical editing. For example:

- Lines 27–30: “As two important political and economic centres, the Scythian inhabitants engaged in agro-pastoralism, industrial workmanship, and trading, evidenced by historical records, (bio)archaeological findings, and multi-isotope analyses.” → This sentence should be restructured for clarity.

- Lines 34 & 52: Revise to “Bel’sk is located in northeastern Ukraine” and “in south-central Ukraine,” respectively.

- Line 66: In Supplementary Figure 2, “represent” should be corrected to “represents.”

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Reviewer #1: No

Reviewer #2: No

Reviewer #3: No

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Dear Dr. Pecnik,

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.

Several additional clarifications should be made, according to Reviewer #4.

Please submit your revised manuscript by Jan 10 2026 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org . When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

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Academic Editor

PLOS ONE

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

Reviewer #2: All comments have been addressed

Reviewer #4: (No Response)

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2. Is the manuscript technically sound, and do the data support the conclusions??>

Reviewer #2: Partly

Reviewer #4: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously? -->?>

Reviewer #2: N/A

Reviewer #4: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available??>

The PLOS Data policy

Reviewer #2: Yes

Reviewer #4: Yes

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5. Is the manuscript presented in an intelligible fashion and written in standard English??>

Reviewer #2: Yes

Reviewer #4: Yes

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Reviewer #2: (No Response)

Reviewer #4: I enjoyed reading and assessing this manuscript on the palaeoproteomics of Scythian dental calculus. The topic addressed is important for understanding the occurrence and diversity of dairy use in the Iron Age steppe context. The study is clearly written and appears to be methodologically careful, particularly following the recent manuscript revisions. The identification of BTN1A1 is an interesting and valuable aspect of the work. The reports of horse milk assignment are quite well supported. Overall, this is a well-conducted and interesting contribution, and I have only a few comments that should be straightforward to address.

Sample size

The sample size is small but carefully filtered, which is entirely appropriate. This approach is preferable to inflating n with data of uncertain or poor quality, and it reflects a commendable level of caution in data selection.

Clarification from the response to Reviewer 2

In the response to Reviewer 2, the authors state that “the high failure rate is interpreted as reflecting variable preservation rather than laboratory contamination, as no consolidants were used and blanks were clear.” This is a reasonable explanation, but it is not clear whether this statement appears explicitly in the main text. If not, it would be good to include a brief mention of this rationale in the manuscript itself for transparency.

Title and framing

The title emphasises milk as a staple through the word “reliance.” While this is an engaging framing, it might be a little strong given that the dataset comprises only six samples with milk proteins from two sites. This represents solid direct evidence for dairy consumption, and likely regular consumption, but “reliance” may somewhat overstate the strength of the direct data unless the authors’ argument is that these proteomic findings confirm or complement historical accounts of horse milk use among Scythian groups. Some slight moderation or clarification of this framing could be considered.

Threshold at 0.5

The choice of a pass threshold at 0.5 “based on inspection” could benefit from a brief justification in the Methods section. For instance, was this threshold selected because it effectively distinguishes between highly contaminated samples and oral-rich proteomes? A short explanatory sentence would help readers understand how this decision was made and improve methodological clarity.

Deamidation

The inclusion of deamidation assessment in the revised manuscript is reassuring and significantly strengthens confidence in the authenticity of the results. This is a valuable addition.

Protein naming consistency

There appear to be inconsistencies in the naming of BTN1A1 / BTNS1A1 / BTS1A1. These should be standardised throughout the manuscript for clarity and accuracy.

Data availability

In the tracked version, the following statement appears:

“Mass spectrometry proteomics data have been deposited on MassIVE (massive.ucsd.edu; MSV000092635). For reviewer access use the username: MSV000092635_reviewer and the password: Scythian-Paper!.”

This is perfectly acceptable during peer review but would raise a minor concern if carried into the published version, as it suggests the repository may not yet be fully public. PLOS will expect the dataset to be completely open (no login required) upon publication.

In the final version, the Data Availability statement should therefore read simply:

“Mass spectrometry proteomics data are available on MassIVE (MSV000092635).”

No usernames or passwords should be included.

Table 1 – Locality of individual (Sr)

In Table 1, the column “Locality of individual (Sr)” includes the entry “born outside and moved as a child.” I understand this derives from a previous study, but it remains an interpretation rather than a directly observed result. While it may be a strong inference, it is still an inference. The column heading or note should make clear that this is an interpretive statement rather than a direct measurement.

Overall, this is a thoughtful and well-constructed study that makes a meaningful contribution to the growing field of ancient proteomics. With a few minor clarifications and adjustments as suggested above, it will make a solid addition to the literature.

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Reviewer #2: No

Reviewer #4: Yes:  Robert C. Power

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Paleo-proteomic analysis of Iron Age dental calculus provides direct evidence of Scythian reliance on ruminant dairy

PONE-D-25-05635R2

Dear Dr. Pecnik,

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.

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PLOS One

Additional Editor Comments (optional):

Reviewers' comments: