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The manuscript has been significantly improved after the revisions. A number of the reviewers’ comments were addressed thoroughly, which contributed to enhancing the quality of the manuscript. After the second review, the reviewers positively noted the updates and the results.
[# PeerJ Staff Note - this decision was reviewed and approved by Ann Hedrick, a PeerJ Section Editor covering this Section #]
No issues found
This data set is rather exceptional
Thoroughly addressed.
The authors have adequately addressed my comments and provided a thorough rebuttal. I commend the authors on the thorough documentation that they have provided with the model, it's extremely detailed, relevant, and laid out in quite a logical format.
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The authors have done a good job in addressing and responding to the issues raised in the first round of revision. The text flow and readability have been improved, and more clarification on the model structure has been provided.
The submitted manuscript contains a significant amount of relevant data and materials related to the assessment of organic matter stocks in complex marine food chains. Overall, the manuscript is well suited to the theme of the PeerJ journal. After a detailed review of the manuscript, the reviewers made a number of recommendations for its improvement. Please respond to them or provide your comments.
**PeerJ Staff Note:** Please ensure that all review, editorial, and staff comments are addressed in a response letter and that any edits or clarifications mentioned in the letter are also inserted into the revised manuscript where appropriate.
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See attached PDF for comments
The manuscript by Shea et al. presents a Bayesian framework for modelling the contribution of organic matter sources to consumers, based on ẟ15N values measured in individual amino acids. The model is flexible, allowing the use of other tracers, such as ẟ13C values in amino acids, and provides a robust approach for estimating source contributions. For model implementation, it requires tracer data for the potential organic matter sources, one or more consumer samples, and information on the trophic discrimination for each of the tracers applied in the model. The model offers several advantages as it allows the use of not only “source” amino acids (which differentiate very little between each trophic step), but also the “trophic” amino acids, to estimate source contribution to a mixture, while accounting for the different trophic discrimination occurring in protozoan versus metazoan trophic steps. The manuscript is well-written, and detailed description of the model’s development and implementation will be useful to readers interested in applying this method. The use of tracers, particularly ẟ15N in amino acids, is becoming increasingly relevant in food web ecology, making this work of considerable interest to the “stable isotope ecology” community. However, I believe some clarifications regarding model implementation and improvements in text structure are needed to enhance readability before this manuscript can be accepted for publication.
Model clarification (Section 2.1, model description): In Part 3 of the Process Model (Mixing Model, 3A in Figure 1), the model uses tracer values (e.g., ẟ15N in amino acids) to estimate the tracer values of the base of the food web (the mixture of organic matter sources). These values are estimated based on the proportional contribution (mixing coefficients) of each organic source to that mixture. However, there are two unknowns: 1) the tracer values of the mixture (the base of the food web) that we aim to estimate (and for which we need for the trophic discrimination model in 3B); and 2) the sources’ contribution to the mixture (mixing coefficients), which is what we want to know, as the goal is to estimate the proportional contribution of each organic matter source to the food webs. After reading sections 2 and 3 multiple times, I still find it unclear how these values are calculated. Could you provide a more detailed explanation of how these unknowns are handled in the model?
In the code below (supplementary material):
plot_basepost_sim(posts, posts.long, Data.sources, Data.zoops, base.sim, Tracers, Variables, LDA.full)
This code generates a plot with organic matter sources (sampled), food web base (estimated by the model), and zooplankton samples (simulated). However, it is unclear why the food web base has both a “posterior mean” and a “true value”. Since these values are estimated by the model, could you clarify what is meant by “true value”?
Additionally, are the posterior values for ẟ15N in each amino acid considered to be the probable values based on a combination of the proportional contributions from each source (mixing coefficients)? This part of the model needs further clarification.
Text readability and flow: while I acknowledge the complexity of the work and commend the authors for the organization throughout the text and supplementary material, sections 2 and 3 require some reorganization to improve readability and flow. The text contains a lot of back-and-forth between concepts, which can make it difficult to follow. For example:
• Equations for estimating FWL and MTS are presented in Section 2.1 with ẟ15NALA and ẟ15NGlx, respectively, as the tracers selected to use in each equation, but the rationale for selecting these amino acids is only explained later in Section 3.4. I believe it would improve readability to introduce the rationale for tracer selection in the same Section.
• Sections 3.1.2 and 3.3, which introduce how the trophic discrimination factors to be used in the models were determined, could be combined into a single section. This would allow for a smoother explanation of how TDF data from published research were compiled and analysed (currently 3.1.2) and determined (currently shown only later in section 3.3) to be implemented in the model.
• After Section 3.1.4 (Procedures for model assessment using simulated zooplankton data), where all the steps of the model are described, the text is back at “determining organic sources for the model”, which could have been presented earlier. The sequence of sections would be clearer if the topics about determining model variables (TDFs, organic matter sources, tracers) were presented first, followed by a description of the model’s execution with simulated zooplankton data. This way, we go through each of the steps of model implementation from determining variables to running the model, and after that it makes sense to go to section 4 where finally the model Results are presented.
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Minor/specific clarifications and corrections:
Line 97: a) could you specify what is meant by “trophic relationships”? Does this refer to the number of trophic steps (FWL, PTS and MTS) introduced later in the manuscript?
Line 100: please remove the extra “c)”
Line 130 and Line150: Could you provide further explanation on why the model requires prior information about organic matter source tracer values (even if these could be vague probability distributions)? This is not clear, since these tracer values are a requirement for model run (as defined in Part 2).
Line 180: Please remove “some” in this sentence: “(…) mixing coefficient, fi, k, represents the fractional contribution of organic matter source i to the base of the food web…”
Equation 1: Here is where it is difficult to understand, mixing models use the isotope values of potential sources (e.g., prey items) to estimate their contribution to a mixture (e.g., consumer). To do that, they require the isotope values for each potential source as well as the mixture. The only unknown is the fractional contribution of each source. Could you provide more explanation on how Equation 1 is solved, given that it contains two unknowns: the mixing coefficients (fractional contribution of each organic matter source) and the tracer isotope value at the base of the food web (μ_(j,k,base))(misture)?
Line 346: Please clarify: in the equation TDFGlx/Ala is presented, not TDFAA (which is what is described), or is it supposed to describe ∆15NAA (as the TDFAA)?
Line 620: Please review this sentence: “and underscoring and value of...”
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