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  1. Evaluation Summary:

    This manuscript will be of strong interest to scientists studying the development of early jawed vertebrates, in particular the extent and structure of their dermal skeleton, but it will also interest a broader audience, given how it connects modern-day morphological techniques to paleobiology. The authors provide the most complete account to date of the body scales of an antiarch stem-group gnathostome; this is the first work to model in 3-D the entire scale cover of such a fossil fish. The authors show that the body scales are varied in form, regionalized and that they comprise two main tissue layers. Based on this they argue that these conditions are plesiomorphic for antiarchs and the gnathostome crown group.

    (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #3 agreed to share their name with the authors.)

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  2. Reviewer #1 (Public Review):

    The authors have 3D-modelled the whole squamation of one of the most basal gnathostomes as the basis for establishing the distribution of scale forms over the body, showing that the squamation was highly regionalized. Based on the structure of the scales they hypothesize that a bipartite structure of scales could be a plesiomorphic character of jawed vertebrates.

    The high-resolution CT scanning results are very impressive, and well figured out and described. This investigation is the first to use this method to reproduce a whole squamation, and as such has produced information not previously possible based on visual examination of articulated fossils. I see no weaknesses in their methods, and their results support their major conclusions. It is unfortunate that thin sectioning of scales was not more informative, but this is a preservation, not a preparative issue. Whether the study supports one of the authors' conclusions - that the development of a scale middle layer is accompanied by the complexity of the crown sculpture - is contentious.

    No doubt this 3D scanning method will be used in the future on other whole squamations of early vertebrates, testing the hypothesis that a highly regionalized squamation is a plesiomorphic gnathostome feature - or the other possibility, that the limits of previous investigations based on a visual assessment of variation in squamation over an animal could not provide the same wealth of detail, resulting in underassessment of regionality.

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  3. Reviewer #2 (Public Review):

    Wang and Zhu investigated the squamation and scale morphology of Parayunnanolepis xitunensis using x-ray computed tomography. They present a thorough analysis of the squamation and individual histological scale structure across the body of an individual holotype specimen. Through this investigation, the authors provide evidence that yunnanolepidoid scales, which have a bipartite histological structure and a regionalized squamation pattern, might be plesiomorphic for jawed vertebrates. These data add to the ongoing investigation of the morphological variation of dermal scales throughout evolutionary time.

    The conclusions of this paper are mostly well supported by data, but some aspects of data presentation and discussion could be extended.

    1. The study provided three-dimensional data from the scales of one articulated individual specimen, which is an amazing contribution to the literature. However, there was no discussion about the size or maturity of the specimen. There is some mention in the literature of how dermal scales change throughout ontogeny. Although in this case it would be quite difficult to obtain multiple specimens of different sizes, there was no discussion about how the morphology of the scales might be different depending on the maturity of the specimen. Additionally, there was no discussion about developing scales. For example, there are a few scales presented in the manuscript that do not fit into any of the scale categories described. Perhaps these scales are regenerating or developing, depending on the age of the specimen.

    2. The authors use data throughout the text based on measurements of individual scales from Parayunnanolepis xitunensis to provide some general quantitative comparisons across scales on the body. However, none of this data is provided or summarized in the manuscript. There is evidence from dermal denticles in modern sharks demonstrating the same morphological differences across the body. The inclusion of this data would provide quantitative comparative metrics that could be used to study changes in scale morphology across evolutionary time.

    3. Although the figures document the various scale categories well, more detail should be included for the figures to stand alone. In many cases, the reader needs information from the text to understand the figure.

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  4. Reviewer #3 (Public Review):

    Wang and Zhu use a combination of computed tomographic methods and thin sectioning to provide what I think is the most complete characterisation of the articulated squamation of a stem-group gnathostome yet published. They use computed tomography to characterise body scale morphologies across the body of the antiarch placoderm Parayunnanolepis xitunensis, identifying 13 regionalised morphotypes of scale. Thin sectioning of isolated scales from the same locality, assigned to Parayunnanolepis on the basis of these morphotypes, shows that they lack a spongy middle layer, a structural characteristic of antiarch's dermal head armour as well as the dermal skeletons of many other Palaeozoic vertebrates. Based on their inferred position for yunnanolepids, as early-branching members of the antiarchs, themselves the sister-group to all other mandibulate jawed vertebrates, they interpret this data to mean that this absence of a spongy middle layer and regionalised squamation are plesiomorphic both for antiarchs and for mandibulate stem-gnathostomes more generally.

    The methods provide a detailed overview of the material the authors describe, and the authors' interpretation of that data is on the whole justified. The real strength of the paper is in identifying all of these morphotypes on an articulated fossil, which preserves the head skeleton, and sufficient phylogenetic information to be able to place confidently in the early vertebrate tree. I'm sure that this will ensure it becomes a key reference work for those interested in the dermal skeleton of Palaeozoic fishes.

    The weaknesses mainly lie with the comparison of this data more broadly amongst Palaeozoic jawed vertebrates. There's a conspicuous absence of comparison to jawless stem-group gnathostomes other than osteostracans which would help inform plesiomorphic gnathostome states, despite there being published data on their body squamations. The manuscript would also benefit from considering alternative phylogenetic placements for antiarchs, and the effect that this would have on their conclusions.

    The information they provide will doubtless be of great use to other workers interested in the anatomy of placoderm body squamations and in identifying isolated parayunnanolepid scales. As touched on above the fact that this data comes from an animal that is commonly incorporated into phylogenetic analyses means that this new data will be used by those scoring characters for these analyses and perhaps to help formulate new body squamation characters. This means that this new information will also indirectly feed into major areas of investigation in early jawed vertebrate palaeontology such as the evolution of jaws.

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