PONE-D-25-33066Pathways at the Iberian Crossroads: Dynamic

Modeling of the Middle–Upper Paleolithic TransitionPLOS ONE

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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?

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

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

Reviewer #1: Yes

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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: No

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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

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: This paper presents a new constrained agent-based model incorporating biological, cultural and dispersal processes to simulation Neanderthal and modern human population distributions in Iberia during the Middle to Upper Paleolithic transition (MUPT). Building on previously published Human Existence Potential (HEP) models by Klein et al (2023), the authors explore population movement out of centers of occupation and across the Iberian Peninsula. Key contributions include the identification of potential dispersal routes into and within Iberia, a hypothesized location for Neanderthal-modern human interbreeding, and support for a coupled demographic-climate model for Neanderthal extinction.

While the constrained ABM is generally well-explained and justified, the absence of code access and the lack of sensitivity analyses addressing key assumptions limit the reproducibility and robustness of the results. For these reasons, I recommend major revisions.

Major comments:

The paper assumes that the HEP model provides a reasonable estimate of suitable places for Neanderthal and modern human occupation. While the HEP is robust based on training methods, its reliability might be compromised by limiting the training data to sites from the Iberian Peninsula (Barr and Wood, 2024). Have the authors tested whether excluding sites from the broader European continent significantly alters the results? The authors’ own prior paper (Shao et al 2021) shows different HEP for the Iberian Peninsula interstadial periods when using a pan-European site list. The influence of site inclusion is also evident in this paper’s results – adding the Picareiro changed model results and interpretations. The authors should either: 1) justify restricting the site list to the Iberian Peninsula or 2) demonstrate that using a broader dataset would not significantly affect model results.

The inclusion of Châtelperronian sites in the Middle Paleolithic sample representing Neanderthal presence is problematic given unresolved debates about authorship (Gravina et al., 2018; Djakovic et al., 2024). The discussion of the Châtelperronian in the introduction is too brief consider the debates surrounding this industry. The authors should make clear here how they are treating the Châtelperronian sites because the way it is currently written seems to suggest that these sites would be the location of “mixed” populations. Additionally, same as the above point, the authors should demonstrate that removing the Châtelperronian sites would not change model results.

Neanderthal simulations begin from four geographic points, but no rationale is provided for these locations. Presumably, these correspond to archaeological sites, but this should be explicitly stated. Further, the authors should test how variation in number, location, and distribution of seed sites affects results.

The use of N0 = 1000 for Neanderthals is not explained or tested. Although the authors dismiss 2000-3000 individuals as too large a population in their results section, this contradicts effective population size estimates (e.g. Lalueza-Fox et al., 2005; Bocquet-Appel and Degioanni, 2013; Prüfer et al., 2014), where 1000 individuals is on the lower end. The authors should justify this parameter using archaeological and/or genetic data. The authors should also test the sensitivity of the model to different N0 values. The same applies to modern human initial population size, which is left unexplained and untested.

Minor comments:

• The introduction references network formation but this is only considered in population growth (equation 8). If true network dynamics are not modeled, either remove this framing or expand on how networks function in the simulation.

• Description of the HEP variants is fragmented. Their mathematical derivation appears under population growth but would be clearer if presented with the initial definitions. Additionally, I suggest reorganizing Sections 2.4 and 2.5 (input data for HEP calculations) to precede the growth and mobility models, so that the logic flows from environmental modeling to demographic modeling to mobility modeling to model parameter values.

• Modern human seeding is taken from the results of a previous paper, but that study used a different dispersal model. The justification for using this location should be clarified and supported.

• The interbreeding dynamics should be clarified: do admixed individuals reproduce independently, or only through additional interbreeding events?

• The ending feels abrupt. Consider adding a statement about why this kind of modeling is relevant or future directions for empirical validation.

• Some main text references point to Supplement figures/tables. These should be clearly annotated.

• There are a few equations where variables are not defined in the text: for example, no definition of rB for equation 7, no definition of m for equation 15.

• In Supplementary Material:

In Section 8.1, should the results for T be plotted somewhere?

In Section 8.2, should the cb be alpha?

In site table, it would be good to specify what sites have MP vs CHÂT.

References:

Barr, W.A., Wood, B., 2024. Spatial sampling bias influences our understanding of early hominin evolution in eastern Africa. Nature Ecology & Evolution.

Bocquet-Appel, J.-P., Degioanni, A., 2013. Neanderthal Demographic Estimates. Current Anthropology. 54, S202–S213.

Djakovic, I., Roussel, M., Soressi, M., 2024. Stone Tools in Shifting Sands: Past, Present, and Future Perspectives on the Châtelperronian Stone Tool Industry. Journal of Paleolithic Archaeology. 7, 29.

Gravina, B., Bachellerie, F., Caux, S., Discamps, E., Faivre, J.-P., Galland, A., Michel, A., Teyssandier, N., Bordes, J.-G., 2018. No Reliable Evidence for a Neanderthal-Châtelperronian Association at La Roche-à-Pierrot, Saint-Césaire. Scientific Reports. 8, 15134.

Lalueza-Fox, C., Sampietro, M.L., Caramelli, D., Puder, Y., Lari, M., Calafell, F., Martínez-Maza, C., Bastir, M., Fortea, J., Rasilla, M. de la, Bertranpetit, J., Rosas, A., 2005. Neandertal Evolutionary Genetics: Mitochondrial DNA Data from the Iberian Peninsula. Molecular Biology and Evolution. 22, 1077–1081.

Prüfer, K., Racimo, F., Patterson, N., Jay, F., Sankararaman, S., Sawyer, S., Heinze, A., Renaud, G., Sudmant, P.H., de Filippo, C., Li, H., Mallick, S., Dannemann, M., Fu, Q., Kircher, M., Kuhlwilm, M., Lachmann, M., Meyer, M., Ongyerth, M., Siebauer, M., Theunert, C., Tandon, A., Moorjani, P., Pickrell, J., Mullikin, J.C., Vohr, S.H., Green, R.E., Hellmann, I., Johnson, P.L.F., Blanche, H., Cann, H., Kitzman, J.O., Shendure, J., Eichler, E.E., Lein, E.S., Bakken, T.E., Golovanova, L.V., Doronichev, V.B., Shunkov, M.V., Derevianko, A.P., Viola, B., Slatkin, M., Reich, D., Kelso, J., Pääbo, S., 2014. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature. 505, 43–49.

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Pathways at the Iberian Crossroads: Dynamic

Modeling of the Middle–Upper Paleolithic Transition

PONE-D-25-33066R1

Dear Dr. Shao,

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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Kind regards,

Marco Peresani

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

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: All comments have been addressed

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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: (No Response)

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

Reviewer #1: (No Response)

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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: (No Response)

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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: (No Response)

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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: Thank you to the authors for taking the time to address all the comments in detail. The addition of new sensitivity analyses as well as specific reference to the results of all the sensitivity testing in the manuscript clearly demonstrate the robustness of the results. This allows the authors to offer interesting new hypotheses about Neanderthal and modern human population distributions and dispersal in Iberia that can be further tested with archaeological data.

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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

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