-->PONE-D-25-63578-->-->Functional morphology of the Cambrian archaeocyath sponge Yukonensis-->-->PLOS One

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Shamim Ahmad, PhD

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Additional Editor Comments:

Dear Author,

The reviewer finds the application of computational fluid dynamics (CFD) to Archaeocyathus yukonensis yukonensis to be innovative and potentially valuable. However, they raise substantial concerns that currently undermine the interpretability and robustness of the study, necessitating a major revision before further consideration.

The primary concern relates to the organization and clarity of the manuscript. At present, the biological morphology of Yukonensis is insufficiently described and visualized before the introduction of modeling parameters. This makes it difficult for readers particularly paleontologists to understand how the numerical geometry relates to the fossil organism. A clearer, more systematic morphological description, supported by figures that explicitly illustrate key structures (e.g., corolla morphology, spine arrangement, chamber architecture), should precede the CFD methodology.

More critically, the reviewer identifies fundamental discrepancies between the fossil morphology and the geometry used in the simulations, which may significantly affect the validity of the flow results:

• The absence of the inner wall in the CFD model is problematic given the sponge-grade organization of archaeocyaths, where flow dynamics are governed by pressure gradients across the intervallum. The rationale provided for excluding the inner wall is insufficient, and its omission likely alters internal flow resistance in a way that compromises interpretations of feeding strategy.

• The representation of the thorny corolla as two-dimensional, zero-thickness planes oversimplifies structures that are described and illustrated as thick, three-dimensional spines. Such simplification removes surface rugosity and turbulence effects that are likely critical for flow mixing and pore-scale dynamics.

• The simplification of curved, hollow spines into straight cones eliminates the very geometric features that could plausibly redirect flow, which is a central hypothesis of the study.

• The reduction of chamber number in the full-body model (four chambers versus at least six observed in specimens) raises concerns about boundary effects and whether the reported “dead zones” reflect biological reality or model artifacts. Justification or sensitivity testing is required.

Because of these geometric simplifications, the reviewer cautions that the conclusion—interpreting Yukonensis as an active feeder based on stagnant passive flow—may be model-dependent rather than biologically driven. The conclusions should therefore be significantly softened, clearly acknowledging that passive flow inefficiency applies only under the specific modeled constraints.

In addition, the reviewer notes specific technical issues that must be addressed:

• The reported Young’s modulus value for spines appears inconsistent with known values for calcite and may represent a typographical error.

• There are discrepancies between spine spacing measurements in Table 2 and those used in the model, which require verification against the fossil material.

Overall, while the study has promise, substantial revisions to manuscript structure, morphological fidelity, modeling justification, and interpretive claims are required. Addressing these points carefully will significantly strengthen the manuscript.

With warm Regards,

Dr S Ahmad

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Reviewer #1: Partly

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Reviewer #1: N/A

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Reviewer #1: Yes

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Reviewer #1: Yes

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Reviewer #1: This manuscript employs computational fluid dynamics modeling to test feeding strategies and structural stability in the enigmatic archaeocyath Yukonensis yukonensis. While the application of numerical modeling to this unique morphology is valuable, I have significant concerns regarding 1) the structure of the article, and 2) critical discrepancies between the actual fossil morphology and the geometry used for the simulation. I therefore suggest a major revision for the manuscript before publication. Of note, although I am familiar with archaeocyath, I am not a specialist in this specific taxon nor in functional morphology modeling, so I invite the authors to correct me if my interpretation of the model setup is mistaken.

1. It is difficult to follow the morphology of Yukonensis based on the current figures and text structure. Fig 1B, C does not clearly show the spine structure, yet the text describes model parameters before adequately visualizing the biological structure. As a reader, I found it confusing to reconcile the "wide" vs. "narrow" corolla descriptions (Fig 1A vs 1D) with the single species description. As a paleontologist, I believe it is necessary to fully describe the reconstructed biological structure of Yukonensis before introducing the modeling parameters, a step that is currently missing in the manuscript.

2. There are critical discrepancies between the organism described in the text/images and the 3D geometry used for the simulations, which likely compromise the validity of the flow model results.

- The characteristic double-walled structure of archaeocyaths is clearly visible in the photomicrographs (Fig 1E, F) and the diagram (Fig 1C). However, the model (Fig 1B) lacks an inner wall entirely. The authors state this was done to "focus solely on the external structure" (lines 183-184), but for a sponge-grade organism, flow is dictated by the pressure gradient across the intervallum (Savarese, 1992). Removing the inner wall would fundamentally alter the internal flow resistance. This is particularly important given that the authors are interpreting the organism as an active filter feeder.

- The authors model the complex thorny corolla as "two-dimensional planes with no thickness" (Lines 182-183). However, the text describes the corolla as an "inverted umbrella" with distinct spines, and the authors note spines are up to 0.5 mm in diameter (Line 158, Fig. 1E). Modeling such large structures with zero thickness treats the corolla as a smooth baffle. In reality, thick spines would create surface rugosity and turbulence, potentially mixing flow into the pores, a mechanism completely lost in the simplified model.

- While the text acknowledges "curved, hollow spines" (and Fig 1E shows a clavate/club-like shape), the methodology simplifies them into straight cones. Given that the study aims to test flow redirection, straightening a curved feature removes the very trait (curvature) that would most likely redirect fluid.

- The full-body model uses only four chambers, whereas Fig. 1A shows at least six. The flow results (Fig 2) show significant differences between the top and bottom chambers. The authors should justify why four chambers are sufficient to represent a mature organism or conduct a sensitivity test with more chambers to ensure the observed "dead zone" is not simply an inlet/outlet boundary artifact.

- The authors conclude Yukonensis was an active feeder because the passive model resulted in stagnant flow. However, as discussed above, because the model oversimplifies the morphology of the organism, this result may be an artifact of the geometry rather than the biology. The conclusion should be softened to state that passive flow is inefficient under these specific geometric constraints.

3. Minor Comments

- Line 179 lists the Young’s Modulus of the spine as 8897 GPa. The Young’s Modulus of calcite is typically ~70–80 GPa. Is this a typo for 88.97 GPa?

- Table 2 states the distance between spines is 4.8–6.6 mm, with 13 to 16 spines. This seems disproportionately large compared to the chamber size and differs significantly from the dimensions used in the model (1.105–1.358 mm). Please verify if these dimensions are correct relative to the fossil specimens.

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Reviewer #1: Yes: Jeong-Hyun Lee

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Functional morphology of the Cambrian archaeocyath sponge Yukonensis

PONE-D-25-63578R1

Dear Mr. Zaid Ahmed Qureshi,

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,

Shamim Ahmad, PhD

Academic Editor

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Additional Editor Comments (optional):

Dear Author,

The revised manuscript reflects a strong and commendable effort to address reviewer concerns, resulting in a significantly improved and more coherent study. The restructuring of the manuscript, particularly the clearer introduction of morphological features prior to model implementation, has greatly enhanced readability. The revised figures are notably improved and now more effectively communicate the anatomical complexity of Yukonensis yukonensis, especially with respect to the corolla and spine structures. The methodological refinements are also appreciated. The transition from simplified two-dimensional representations to more realistic three-dimensional geometries, along with the inclusion of curved and hollow spines, represents a meaningful advancement in the modeling approach. Additionally, the decision to temper the conclusions regarding feeding mechanisms demonstrates appropriate scientific caution and strengthens the credibility of the study.

That said, one important limitation persists. The absence of the inner wall in the computational model remains a significant simplification given the fundamental role of the intervallum in archaeocyathan fluid dynamics. While your explanation and acknowledgment of this constraint are clear and appropriate, the lack of this feature still limits the biological fidelity of the simulations. If incorporating the inner wall is not feasible, it would be beneficial to further emphasize this limitation in the discussion and explicitly frame the results as representative of a simplified external-flow scenario rather than a complete organismal system. Minor issues, including previously noted inconsistencies in material properties and morphometric parameters, appear to have been satisfactorily resolved.

In summary, the manuscript is now substantially improved and scientifically more robust. With careful framing of the remaining limitation, it is well-positioned for publication.

with best wishes,

Dr Shamim Ahmad

Reviewers' comments: