Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: TEXT MINING FOR IDENTIFICATION OF BIOLOGICAL ENTITIES RELATED TO ANTIBIOTIC RESISTANT ORGANISMS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have addressed many of my comments from the previous review and I thank them for the improvements in the methodology and presentation. I have three aspects that could be easily addressed as a minor revision and complete the work as based on my previous review.

I can agree with the scope of the work as noted in the response to reviewer. I would still suggest this being clearer and directly stating in the Intro/R&D the scope of this work so it is properly contextualized by your audience.

It needs to be mentioned in the text that the resources were open to the public aka open source/open access articles so it’s clear to and correctly interpreted by the reader.

Limitations of this work should be clearly mentioned in the R&D/conclusions.
Experimental design: See above
Validity of the findings: See above
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: HOW TRAINING LOADS IN THE PREPARATION AND COMPETITIVE PERIOD AFFECT THE BIOCHEMICAL INDICATORS OF TRAINING STRESS IN YOUTH SOCCER PLAYERS?
Review round: 1
Reviewer: 1

Output:
Basic reporting: Overall I thought the manuscript/study design was interesting.  I believe this data will add some unique data that will spark a lot of conversations and future studies.  I so have some minor suggested edits. see below:

METHODS
Line 161-162 why was a 36 hour time period selected?
Lines 215-219 why was creatine kinase activity determined separately?
Line 252 Should “size of every variable…” be rephrased? The sample size of each variable was 18(n = 18)?
RESULTS
Lines 265-267 I think this was lost in translation
Lines 269-270 Same thing. Change “was get” to “was found”
Lines 272-273 Is this information that belongs in the methods?
Line 278 Change “was get” to “was found”
Line 280 Change “was get respectively” to “was found, respectively”
Line 291 Performed analyses? Change to “performed analyses”
Line 292  Change “doesn’t” to “does not”
Line 295  Change “was get” to “was found”
Line 306 Change “was get” to “was found”
Line 308 Change “was get” to “was found”
DISCUSSION
Mainly grammatical concerns
Line 410  change to “8 weeks of resistance”
Line 417 Change “analyzes” to “analyses”
Experimental design: no comment
Validity of the findings: no comment
Additional comments: no comment


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: HOW TRAINING LOADS IN THE PREPARATION AND COMPETITIVE PERIOD AFFECT THE BIOCHEMICAL INDICATORS OF TRAINING STRESS IN YOUTH SOCCER PLAYERS?
Review round: 1
Reviewer: 2

Output:
Basic reporting: The structure, figure and tables are sufficient.
Experimental design: Experimental design is well done
Validity of the findings: This research is valid.
Additional comments: General Comments

    This is an interesting study, assessing the changes in blood biochemical markers and rate of perceived exertion (RPE) in young male soccer players (n=18, mean age 18 years) following 6-month training period (January-June). Blood biochemical markers (cortisol, creatine kinase, serotonin, and brain-derived neurotrophic factor – BDNF) were measured four times: at the beginning of the preparation period, immediately after the preparation period, in the middle of the competitive period, and at the end of the competitive period. Blood samples were taken from players who had been out of training for about 36 hours (or 36 hours after training). The training loads were assessed using a session RPE, and the assessment time points were chosen so that fatigue after a soccer match would not be assessed.

The main findings of this study were that: (1) after the pre-season (most demanding training) period the values of all measured blood biochemical markers increased significantly; (2) the reduction of training loads in the competitive period resulted in a systematic decrease in the values of the measured blood biochemical markers; (3) the one exception was the BDNF concentration, which increased significantly. The latter could be related to mental and physical stress accrued over the course of the training time.
This text is well-written in general. However, before it is published, the design of this work should be improved.

1. I suggest not to use the term "indicators central fatigue (assessed by serotonin and BDNF) and peripheral fatigue (assessed by cortisol and creatine kinase)" in context of this study in Title and for explanation of the results of this study in Discussion and Conclusion. Fatigue during prolonged exercise has been defined as the inability to maintain the required or expected muscle force/power output that leads to a loss of performance in a given task (Edwards RH. 1981). This definition is generally accepted by exercise physiologist. In this study, the changes in force-generation capacity of skeletal muscles or in physical of performance (fatigue and recovery) were not studied. Neuromuscular (physical) fatigue is indicator of acute (short-time) adaptation to exercise. In this study, the long-term (chronic) adaptation to soccer training loads during 6-months period was assessed by 4 blood biochemical markers: cortisol – typical marker of chronic stress, creatine kinase – typical marker of muscle damage, serotonin – which is also marker of central fatigue, but only in complex with other central factors that might limit exercise performance (Meeusen R et al., Sports Med, 2006), and BDNF – participates in physiological processes such as glycogen homeostasis and lipid metabolism (Jimenez-Maldonado A et al. Front Neurosci, 2018). I suggest to use for explanation of the changes in blood biochemical markers in context of this study using terms "exercise-related stress", or "training stress". These terms more undestandable in context of long-term adaptation to training loads in young soccer playes.

2. Authors should better to explain the novelty of this study in Introduction because this is not the study of central and peripheral fatigue but study of physiological/biochemical adaptation to regular training loads in young soccer players.

 Specific Comments

TITLE: Please correct the Title according to General Comments

ABSTRACT: Please correct text avoiding term "central and peripheral fatigue" (see General Comments)

INTRODUCTION: Please explain better the novelty of this study in context of long-term physiological/biochemical adaptation to regular training loads in young soccer players (see General Comments)

DISCUSSION: Please correct text in context of long-term physiological/biochemical adaptation to regular training loads in young soccer players (see General Comments)

CONCLUSIONS: please correct text according to General Comments

TABLE 2: Please add Abbreviations T1, T2 and T3 behind this table.

TABLE 3: Please add Abbreviations T0, T1, T2 and T3 behind this table.

TABLE 4: Please add Abbreviations T0, T1, T2 and T3 behind this table.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: HOW TRAINING LOADS IN THE PREPARATION AND COMPETITIVE PERIOD AFFECT THE BIOCHEMICAL INDICATORS OF TRAINING STRESS IN YOUTH SOCCER PLAYERS?
Review round: 1
Reviewer: 3

Output:
Basic reporting: The reviewer’s comments on the paper are as follows:

I have reviewed the research article entitled “How youth soccer training affects the indicators of peripheral and central fatigue?”
It is interesting topic and totally, this manuscript is well organized and written. However, there are just a few points of clarification that need to be addresses. Therefore, I recommend that the manuscript must be revised before it can be reconsidered for publication. Here are my comments:

-	Page 6: The title doesn’t show in which training periods or mesocycles the fatigue markers were considered for investigation. So, please add these periods to the title (for example: preparatory and competitive period).
-	Page 7, line 74-78: Discussion at the end of the abstract doesn’t fully reflect the title mean. It is advised to the authors to rewrite this with priority of training effectiveness and then to mention the relations between the respective variables.
-	Page 7: Please add the word that represent an intervention including training in this study.
-	Page 7, Introduction: Considering the youth sample was selected in this research, please explain the reasons for choosing them rather than adults.
-	Page 8, Introduction: Serotonin and BDNF are acceptable as the central fatigue. However, it was better to measure or to add dopamine and calculating ratio of serotonin to dopamine as a more suitable indicator of CNS fatigue. Please clarify.
-	Page 9, Materials and methods, line 187-189: the authors wrote “, their nutrition and hydration habits were well controlled, following the recommendations by the soccer center nutritional staff. The players followed the same nutritional and hydration protocol during the soccer season”. I didn’t see any information about it. Please report the subjects’ nutritional information composed of macronutrients distribution and total calorie intake as an individual table. These could have remarkable influences on the dependent variables measured in this study such as sensitive marker of cortisol.
-	Page 25 & 27: Quality of figure 1 and 2 included in the PDF file is not appropriate and their size seems small. Please redraw them with more resolution and larger size.
-	Page 13, Discussion: the results are repeated at the first lines of this section (line 325-340) and specified in the numbers. It is advised to the authors to remove them and discuss each set of findings individually (To mention first result and continuing with required explanations).
-	Page 13-16, Discussion: All the p values throughout this section need to be removed. The authors reported them previously in the results.
-	Page 17, Limitation: Please add the lack of control group at this study as another limitation.
-	Page 17, Conclusions (line 481-486): the first 6 line are repetitive and redundant. Please rewrite briefly with emphasis on the principal points derived from the study.
-	Page 17-23, References: The number of references is very high (85 ref) for a research paper. Many of them are relatively old and it is suggested to the authors to remove less relevant references as possible. Also, the authors could include below reference related to this study in the references and apply its content:
-	Arazi H, Asadi A, Khalkhali F, Boullosa D, Hackney AC, Granacher U and Zouhal H (2020) Association Between the Acute to Chronic Workload Ratio and Injury Occurrence in Young Male Team Soccer Players: A Preliminary Study. Front. Physiol. 11:608. doi: 10.3389/fphys.2020.00608
Experimental design: Please refer to the basic reporting.
Validity of the findings: Please refer to the basic reporting.
Additional comments: Please refer to the basic reporting.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: HOW TRAINING LOADS IN THE PREPARATION AND COMPETITIVE PERIOD AFFECT THE BIOCHEMICAL INDICATORS OF TRAINING STRESS IN YOUTH SOCCER PLAYERS?
Review round: 1
Reviewer: 4

Output:
Basic reporting: Please check it in pdf file
Experimental design: Please check it in pdf file
Validity of the findings: Please check it in pdf file
Additional comments: Please check it in pdf file


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: HOW TRAINING LOADS IN THE PREPARATION AND COMPETITIVE PERIOD AFFECT THE BIOCHEMICAL INDICATORS OF TRAINING STRESS IN YOUTH SOCCER PLAYERS?
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: The design of this manuscript was improved in process of review.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: EARLY WARNING MODEL CONSTRUCTION AND VALIDATION FOR URINARY TRACT INFECTION IN PATIENTS WITH NEUROGENIC LOWER URINARY TRACT DYSFUNCTION (NLUTD): A RETROSPECTIVE STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: Thank you for the possibility to review this manuscript. I am especially pleased that the document comes from a nursing department, as nurses and nurse practitioners are usually more involved in patient care and the crucial link for a successful patient management. The authors construct and validate an early warning model for UTI susceptibility in patients with neurogenic lower urinary tract dysfunction. While such a model is highly warranted there are several concerns I have several concerns. One main risk factor (i.e. recurrent UTIs / previous history of UTIs) is not included in the model, the patients population is not very well described and while the study describes important risk factors the results would not allow any statements regarding targeted guidance or early intervention.

Major concerns:
(1)	Please delete all conclusions regarding targeted guidance or possibilities for early intervention. The provided manuscript does not allow any assumptions in this direction as it does not focus on intervention or on prophylactic measures but on risk factor assessment.
(2)	The most common risk factor for UTI is previous UTIs in the patient history. Why was this not included in the analyses. Could the model be corrected for this risk factor?
(3)	I strongly suggest to adhere to the to the terminology provided by the standardization committees from the International Continence Society (e.g. Abrams et al. 2002, NAU, The standardization of terminology of lower urinary tract function and Gajewski et al. 2018, NAU, An International Continence Society report on the terminology for adult neurogenic lower urinary tract dysfunction (ANLUTD)). Terms like neurogenic bladder, even if often used, are misleading as the functional problem is not limited to the bladder but to the bladder, the sphincter and the urethra (i.e. neurogenic bladder = neurogenic lower urinary tract dysfunction). Other not correctly used terms can be found in Table 1 / lines 89-90: While I would understand the term “Detrusor hyperreflexia” (what would should be “Detrusor overactivity”) I do not know what the following terms mean: “Detrusor non-reflex type and Hybrid”. There are several other terms that need to be corrected.
(4)	Line 81-84: The exclusion criteria should be refined: “(1) Patients with infections from other parts of the body, or UTI  followed by non-primary infectious lesions; (2) Patients with asymptomatic bacteriuria; (3) UTI caused by non-NGB; (4) Patients with severe heart disease dysfunction, liver and kidney dysfunction, blood system disease or malignant tumor disease, etc.”
•	(1) What does “UTI followed by non-primary infectious lesions” means in this contest?
•	(2) For a risk model at least two timepoint for each patient are needed, hence, it would not make sense to exclude patients if they showed asymptomatic bacteriuria at one but a UTI at another visit, please clarify
•	(3) UTIs are not caused by the bladder, please rephrase
•	(4) I would not understand why patients with heart disease would need to be excluded, please explain.
(5)	Lines 92-94: The authors make the statement: “The clinical diagnosis of UTI met the relevant standards in the "Guidelines on urological infections" formulated by the European Association of Urology (European Association, 2021)” However, up to date there is no definition for UTI in patients with neurogenic lower urinary tract dysfunction, while there are definitions for uncomplicated UTI, complicated UTI and specific sub-types such as catheter associated UTI. Please explain the exact UTI definition used for this manuscript (what symptoms were regarded UTI? What symptoms were not regarded UTI? Would it be possible to provide a table with the frequency of the different symptoms in the ?)?, how many patients had febrile UTI, how many urosepsis? etc.). In addition, please check the following link and use the format suggested for citing the EAU Guidelines https://uroweb.org/guidelines/how-to-cite-the-eau-guidelines/
(6)	At least two patient visits are needed for such risk models. Please explain how many timepoints per patient were used. Please show in the results the time differences between the visits for both groups (UTI and non-UTI) and explain how you corrected for different intervals in the model.
(7)	It would be interesting to get more information on patient characteristics. While some information can be drawn from table 1, it would further be important to have insights on following information: (1) Main underlying neurological diagnosis (2) in-patients vs out-patients (3) days/years after diagnosis of the neurogenic lower urinary tract dysfunction
(8)	Please explain bladder behavior training intervention in the methods in more details. In the discussion following information is given (lines 221-223): “bladder behavior training (scheduled urination, delayed urination, mental urination, and anal stretch techniques)” however, regarding table 1 all subjects in the study relayed on some type of catheterization to empty the bladder.
(9)	Lines 164-165: In the discussion the authors make following statement: “In the study, 70% of patients had NGB caused by lumbar disc disease, however in table 1 it seems that all patients included in the analyses relied on some type of catheterization for bladder emptying. Please describe in more detail why so many patients with “lumbar disc diseases” could not void spontaneously, I would not expect that “lumbar disc disease” would cause such a high number of neurogenic lower urinary tract dysfunction / need for catheterization, unless it is a cauda equina syndrome or a conus-cauda syndrome.
(10)	In the discussion the authors make following statement (line 177): “focused prevention of UTI in people with high-risk NGB”, in the introduction following statement is made (Lines 48-51): Studies have shown that the incidence of UTI in patients with NGB was up to 70% despite the use of individualized urinary catheterization or preventive use of antibacterial drugs (Amarenco et al., 2017). This seems to be contradictory, please clarify what preventive measures should be taken in what patients.
(11)	In patients performing intermittent self-catheterization there is evidence that bladder irrigations, the use of hydrophilic catheters and the frequency of intermittent self-catheterization can reduce the rist of UTI (Lapides et al., J Urol, 1972; Husmann Transl Adnrol Urol, 2016; Cox et al., Can Urol Assoc J, 2017; Li et al., Phys Med Rehabil, 2013). Please discuss.

Minor concerns
(1)	Lines 55-57: A recent study has shown that the incidence of chronic renal failure in patients with NGB complicated by UTI was about 24% (Na et al., 2014). Please rephrase or delete in this sentence, in the current version it could be seen misleading.
(2)	Line 58-62: please add history of UTI to the list.
(3)	Line 190: please rephrase the term: “decreased visceral function”
(4)	The ethical vote is written in the Chinese language. Please translate the relevant parts in English.
Experimental design: Please see "major concerns" in the basic reporting section:
(2); (4); (5); (6);
Validity of the findings: Please see "major concerns" in the basic reporting section:
(1); (10); (11)
Additional comments: Please see "major concerns" in the basic reporting section:
(3); (7); (8); (9) and all minor concerns.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: EARLY WARNING MODEL CONSTRUCTION AND VALIDATION FOR URINARY TRACT INFECTION IN PATIENTS WITH NEUROGENIC LOWER URINARY TRACT DYSFUNCTION (NLUTD): A RETROSPECTIVE STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1. Please cite the statistical software in line 101, standards in line 93,

2. In line 104, the logistic regression "model" instead of "equation"?

3. In line 132, please define Z.

4. There is no need to include Table 2 since it has redundant information with Table 3. The information in Table 2 can be easily incorporated into Table 3 by adding the levels to the 1st column.
Experimental design: 1. In Line 77, please provide more details on the number of participants screened, number of patients meeting inclusion criteria and etc. It would be great if a flow diagram of enrollment is provided.

2. In Table 1, why is age modeled as a binary variable instead of a continuous variable? Dichtomizing continuous variables tend to lose more information on the variable itself.
Validity of the findings: 1. In line 181-187, the authors commented that the prediction effect is medium and good since the ROC value of 0.832 was evaluated in the training dataset. However, we don't make comments on performance using the internal ROC due to the overfitting issue on training data.

2. In line 231, the authors mentioned that analysis's multicollinearity of hypoalbuminemia and age excluded hypoalbuminemia as a founding factor. Please properly evaluate the multicollinearity among these variables to back up this claim.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: EARLY WARNING MODEL CONSTRUCTION AND VALIDATION FOR URINARY TRACT INFECTION IN PATIENTS WITH NEUROGENIC LOWER URINARY TRACT DYSFUNCTION (NLUTD): A RETROSPECTIVE STUDY
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors have addressed all my comments.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: BREAKING THE MOLD: TELESCOPING DRIVES THE EVOLUTION OF MORE INTEGRATED AND HETEROGENEOUS SKULLS IN CETACEANS
Review round: 1
Reviewer: 1

Output:
Basic reporting: - The text is written in clear and professional English. I made some suggestions in the annotated pdf for minor changes (typos, style) that may slightly improve the reading. However, I am not a native English speaker, so authors should feel free to choose for alternate formulations.

- The scientific background is adequately presented, with a sufficient number of references. The authors clearly demonstrated an excellent knowledge of the general context and research questions.

- The text is properly organized. It is illustrated by very fine figures, all clear and useful. Figure captions provide enough details (I only made a few suggestions for the addition of some information. I am not familiar with the analyses performed here, but to my knowledge all the raw data has been made available with the ms at submission.
Experimental design: - Though originating from previous work on other tetrapod groups, this work focuses on a newly acquired dataset targeting a series of extinct and extant cetaceans, allowing for the discussion of new research questions with a cutting-edge technique.

- The research questions are clearly presented, they focus on topics that have been barely tackled in a quantitative way in the past, and results are adequately articulated with the introductory questions.

- As mentioned above, I am not familiar with the analytical tools implemented here. Methods are generally explained with sufficient detail, though in a few cases I suggested in the annotated pdf the addition of a few words (on data acquisition and some of the parameters of the recovered networks). This may help other researchers interested in this technique to apply it and to better apprehend the interpretations.
Validity of the findings: - The data supporting the interesting conclusions presented here are made available. Though one may expect an even broader taxonomic sampling for future work on this topic, the chosen taxa have been carefully selected and allow for the discussion of interesting evolutionary steps. It may be useful to add some details on why extinct taxa were selected, even if not all extant cetacean families have been sampled. I find this sample very fine for such a first analysis, but a few words could be added, especially considering that fossil skulls must be more difficult to investigate in some regions (palate, dorsal part of neurocranium) due to the lower visibility for suture lines.

- Most conclusions are adequately supported by the presented results. In some cases (see annotated pdf and comments below), the sample size may be slightly too small to allow for the unambiguous detection of evolutionary trends. I made a few comments about odontocetes, but it may be worth checking for other clades. In most cases my impression is that it is mostly a question of formulation, with more speculative interpretations to be more clearly identified.
Additional comments: - This is a great study, and I am glad to see this promising technique being applied to cetaceans. This really sounds like the perfect match considering trends previously detected among cetaceans. Obviously, the sample could be enlarged in future work, for example including at least one member of each modern family, but this dataset already provides the opportunity to discuss about a series of trends and adaptations. Most of my comments can be found in the annotated pdf, but a few others are listed below.

- I guess that the ontogenetic stage will have a rather strong impact on the results of such an analysis, with young individuals' rostral bones not reaching as far posteriorly in the facial region (at least for odontocetes). Could you add a few words about the ontogenetic stage of the selected specimens?

- I wonder how you dealt with ankylosed/fused bones. In some parts of the skull of aged individuals, it can be tricky to distinguish which bone(s) is(are) involved, for example in the dorsal part of the neurocranium, with contributions of the parietals/interparietal that are often difficult to assess. Could you add some words on this question? Also, it may be informative to add some words in the material and methods section about missing data in extinct species (I guess that you cannot reach the same resolution with a fossil skull compared to a modern one with all sutures visibles.

- Related to my previous comment, the position of Notocetus in the PCA (fig. 2) is very surprising. It seems way too far from Waipatia or Tursiops for example. Shouldn't the network data be checked for that taxon?

- For the more detailed PCA of cetaceans, considering the low number of odontocete taxa and the wide spacing of the different taxa in the graph I am not sure that this sample is large enough to draw firm conclusions. Indeed, you may probably expect additional taxa to further increase the surface of the morphospace occupied by odontocetes. This is just a comment, but in some places it may be worth slightly reformulating the interpretations (for example for the near absence of overlap between odontocetes and mysticetes, and for the description of several trends).

I am looking forwards to seeing this very interesting work published.
O Lambert


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: BREAKING THE MOLD: TELESCOPING DRIVES THE EVOLUTION OF MORE INTEGRATED AND HETEROGENEOUS SKULLS IN CETACEANS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Buono and Vlachos present a novel and interesting paper exploring the evolution of cranial telescoping using network analysis of cranial bones. They find distinct patterns consistent with the two modes of telescoping which dominate the two major groups of living whale, and that neocete whales in general occupy a distinct region of the tetrapod morphospace, highlighting the uniqueness of telescoping in whales.

Overall I found the paper (mostly) easy to follow with proper citations and a sensible structure, with conclusions that were well supported and explained. There are a few areas however that require improvement. Some of these are concerns over explanation of methods, which I will discuss in experimental design.

Relevant to Basic reporting, I found a fair bit of improper or odd phrasing and sentence structure, as well as incorrect use of words. These are mostly minor grammatical concerns, and when possible I do highlight cases of improvement. I would strongly recommend however additional passes through the manuscript to fix these.
Experimental design: The experimental design is appropriate and the research fits well within the aims and scopes of the journal, representing important advancements in our understanding of whale cranial evolution. I generally understood the paper, however I feel there are two significant aspects of the methods that need addressing.

First, I think more detail is needed in the methods. Anatomical Network Analysis is a fairly new method that is likely not going to be very familiar to many individuals interested in marine mammal evolution, and I feel the authors don't adequately explain the method in a way understandable for those who don't have a background in the technique. While I thought the different metrics were adequately explained, I wasn't sure how they were generated without reading up in more detail on the method. There should be a short section describing the method in more general terms, and how cranial configurations of bones are used to generate a matrix in which the listed metrics are generated.

On a related note, there needs to be an implicit statement that the different metrics are what is being used to create the PCA and PERMANOVA. My initial thoughts were that the authors were using the matrix produced in some manner to create the PCA.

I would also like to see the authors address cranial asymmetry. As the authors themselves mention, cranial asymmetry in odontocetes can significantly influence skull shape, especially in extremely asymmetrical taxa such as Physeter.  Did the authors treat right and left bone separately, or were both bones considered the same bone as far as the connections go. Were their differences in metrics for some odontocetes if the right and left were treated separately? If they were not treated differently, than at least a statement of WHY is needed: Is the asymmetry just not significant enough to affect the given cranial configurations? I don't necessarily expect a giant section on this topic...just a few sentences may be all that is required to address this concern.
Validity of the findings: The results make sense and are well supported. Most of the underlying data is provided. The one thing I didn't find was the raw matrix that was used to generate the different metrics, just a table of the metrics produced. This would be useful for supplemental information, as without that raw matrix other researchers  have to start from scratch to validate the results.

Now I should mention here that one of the supplemental files didn't download properly for me, and I am not sure if that is due to my computer or PeerJ. If this information was provided, feel free to ignore this comment, although perhaps double-check that the data can be exported in a meaningful manner.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: BREAKING THE MOLD: TELESCOPING DRIVES THE EVOLUTION OF MORE INTEGRATED AND HETEROGENEOUS SKULLS IN CETACEANS
Review round: 1
Reviewer: 3

Output:
Basic reporting: There are a few places where the phrasing or word choice was ambiguous, and there were also many typos. I’ve tried to point these places out as I went through the manuscript.

Overall, the structure and figures meet professional standards. I have made some minor suggestions to improve clarity and organization.

The Results and Discussion are self-contained and new insights about the evolution and anatomy of cetacean skulls. But, the introduction and definition of network parameters and how they relate to network descriptors and morphology is not self-contained. AnNA is still a relatively new method with which many morphologists may not be very familiar. While I myself have read numerous papers using AnNA, I still had to look up the mathematical definitions and interpretations presented in several papers by Esteve-Altava et al. I think the present paper would strongly benefit from clearer explanations of the network parameters and descriptors, and how they relate to morphology. The authors did this later in the Discussion (e.g. line 316, heterogeneity) but the reader needs to understand these metrics much earlier in order to understand the Results.
Experimental design: This work is original and provides important new insights about how cetacean skulls compare with other mammals and tetrapods, and falls within the aims and scope of the journal.

I think the research questions can be more clearly defined. The last paragraph of the Intro was particularly confusing and hard to follow. Perhaps the authors can add explicit details about how they hypothesize/predict telescoping will affect the network and then assess whether the data support these in the Discussion.

In the methods, I would like to see how the authors dealt with interspecific and intraspecific variation. For instance, balaenopterids have considerable morphological variation at the skull vertex (Tsai et al. 2014; Nakamura et al. 2016). How did the authors account for such variation, or does that morphological variation not affect the network? Additionally, were the authors only including adult specimens, and if so, how did they know they were adults? This is an important detail, because telescoping especially could change with age (which is still unclear).
Validity of the findings: The findings are valid, but I was curious why the authors did not include more odontocetes, especially some major groups, such as ziphiids and phocoenids. Odontocetes are more speciose than mysticetes, though their sampling does not reflect that. And, these additional odontocete taxa are morphologically distinct from the ones included in the study. While I think the results are meaningful even without including a broader sampling of odontocetes, I think these choices about species sampling should be more clearly explained in the Methods.

All data have been provided, with the exception of a mislabeled CSV file for Aetiocetus.

The conclusions are well-stated, but the original research questions could have been clearer. I think it would help if the authors clearly outlined hypotheses and predictions about how telescoping would affect the anatomical network, and then explain in the Discussion if their results support or reject these hypotheses/predictions.
Additional comments: 1.	Clearly define odontocetes as toothed whales or echolocating whales & mysticetes as baleen whales in the Intro. This will both make the article clearer to readers unfamiliar with cetaceans and can also help clarify toothed mysticetes vs odontocetes later in the article.
2.	The terminology around network descriptors and parameters seems to vary somewhat throughout the manuscript. These should be clearly defined in the Introduction and used consistently throughout the manuscript.
3.	I had a few questions in the methods section. How did the authors account for interspecific and intraspecific variation within a single genus? This question especially applies to the balaenopterids, where it has been previously shown that they can have a lot of variation in the morphology at the vertex of the skull (e.g., Tsai et al. 2014, https://doi.org/10.2517/2014PR009 ; Nakamura et al. 2016, https://doi.org/10.32211/lamer.54.1-2_1). Also, were all of the specimens adults, and how was this determined?
4.	Additional sub-section headers in the Discussion to break up the “Mysticete and odontocete skull network specializations” are needed. This section covers a lot of information and it would be helpful if the authors could more clearly point out when they are comparing mysticetes vs odontocetes or making comparisons among lineages within each group.
5.	In figure 2, it was surprising to see some of the cetaceans in the same region of morphospace as birds. Do the authors have ideas about why this might be the case? Also, I’m curious if the authors can provide more insights in the Discussion about how cetacean skulls compare with other aquatic tetrapods.
6.	Novel bone contacts (links) may not mean that there are novel sutures between those bones (i.e., no sutural ligament). In other words, the bones may be simply near each other, but not have a sutural joint between them. Can the authors provide insights about whether novel bone contacts have novel sutures, or whether the bones are only adjacent/neighboring? This question is especially relevant to lines 379-384, but also throughout the ms.

Specific Clarifications:
Abstract: When discussing integration and modularity in shape (Olsen & Miller, 1958), modularity and integration are often discussed as opposites. So, it’s confusing that cetacean skulls can be both more modular and more integrated. Could the authors clarify here how a skull can be both more modular and more integrated? Or, maybe point out in the Abstract that these terms have different meanings in AnNA, and then discuss this conceptually in the Intro?
106-107 This would be a helpful place to explain the network parameters/descriptors and how they relate to the concepts of integration, modularity, heterogeneity, and complexity.
107-110 This sentence and the following paragraph is confusing. It may be clearer to separate the results from Esteve-Altava et al. (2013a) and discuss them in the previous paragraph, and then to focus this paragraph only on explaining the current study. I also recommend that the authors outline clear hypotheses and predictions here or in a paragraph explaining the network parameters/descriptors. Given what they know about cetacean skull morphology, how do they predict it to affect the network?
137-141 This is another place where mathematical and morphological explanations of the network descriptors would be helpful. The authors did a good job providing this information for the centrality measures in lines 144-148, and I suggest they do something similar here.
140 Should all words be capitalized in Average Path Length? Also, is this the same as Mean Shortest Path Length, which is the term used by Esteve-Altava et al.? Or, is it a different metric?
201-202 In standard mathematical numbering, wouldn’t Physeter be in Quadrant II and Albertocetus is in Quadrant IV? Or, is there a different system being used here? The quadrants should be labeled in the figure to make this clearer.
271-273 It would be really helpful to have anatomical regions in some form described here, though I realize the modules don’t directly correlate with anatomical regions. For instance, is the posterolateral module in the general area around the ear or more in the area of the temporal fossa?
295 odontocetes are described elsewhere as having more complex skulls. So, this sentence seems to contradict other parts of the manuscript, saying cetaceans have evolved simpler skulls
316 It would be helpful to have this explanation of heterogeneity earlier in the manuscript (perhaps even the introduction).
324-326 “We hypothesize that telescoping...” This sentence is confusing to me. Do the authors mean that telescoping, in addition to bone loss of fusion, provides a mechanism to increase connectivity? Telescoping is an alternative to bone loss and fusion to increase connectivity?
379-384 “Due to sutures representing...” This sentence is also grammatically confusing. Also, does telescoping produce new sutures (meaning a new sutural ligament) or does it simply produce new contact between bones? In other words, does telescoping produce new contact without producing a new suture? Do the authors’ data or personal observations give insight to this?
406 I may have missed this, but what do the authors mean by “integration by proximity”? Are they juxtaposing this with integration by variation? This terminology should be clearly defined earlier in the manuscript.
458 What do the authors mean by important structural constraints? Also, could the authors expand upon and go into greater detail about what they mean by stronger functional and developmental codependence? This seems to be an interesting point they’re trying to make, but it needs to be fleshed out more.
467 What is meant by occipital-rostral bones here? Is this referring to the interdigitation between the maxilla and frontal, or something else?
520 Odontocete skulls were previously described as more complex, so this comment about slightly simpler skulls is confusing.

Tables/Figures
Table 1: Mark which network descriptors correspond with integration, complexity, etc. or provide this info in the caption
Figure 3: Label quadrants
Figure 4: The axis labels are illegible because they are too small; they need to be bigger. Also, it would be helpful if each plot had the same tick marks to facilitate comparison between plots. Archaeocetes appear to be missing from several plots, or aren’t clearly labeled.
Figure 5: A different style of arrow is needed in this figure. The arrows (> and <) too closely resemble less than or greater than symbols. This is particularly confusing, for example, when “less complex” is followed by the greater than symbol.
Supplemental Figures: Need a key for bone abbreviations.

Grammar/Typos
67 Word choice: the meaning of “experimented” is unclear here. Suggested replacements include “experienced” or “underwent” or “experimented with”
69 Remove “the” before telescoping
70 Typo: should be “extensive bone overlap”
67-70 Run-on sentence
73 horizontal sutures: Roston & Roth (2019) cite Gatesy et al. (2013) for this terminology, so Gatesy et al. should be cited here as well
87 Typo: “waipatiids”
93 Replace “Despite” with “while” or “although’ (e.g., “While telescoping was investigated in recent years...”)
99 Grammar: “studying” should be “study of”
102 “...has allowed its successful application...”
107 I was not sure what “This work” was referring to. At first, I thought the authors were referring to the present study, but the beginning of the next sentence suggests otherwise.
111 Typo: “archaeocete”
112 “In addition, we assessed if telescoping...”
122 Typo: archaeocetes
171 Typo: “...because they...”
193 “...toothed whales (Aetiocetus)...” This is a misleading way to write it, since Aetiocetus is a stem mysticete. Please rephrase
199 Typo: “...odontocete morphospace...”
224-225 Very confusing sentence.
279 Typo: “...remarkable cranial asymmetry...” Also, I recommend changing the word from development to evolution, as development is often interpreted as ontogeny.
292 typo: “especially”
306 typo: “overlap”
309 Typo. Remove “()”
328 missing period
330 “both reflecting” Should this say “also reflecting”? This sentence is a bit confusing.
356 typo: “dorsal exposure”
358-361 What kind of information and why would speed matter? The authors’ point is unclear here.
363 “...increment of modularity...”: Do the authors mean increased modularity?
370-372 “The amount of modules identified depends if the models of modularity identified a development correlation (in which case they identified 3 modules; del Castillo et al., 2017) or a functional correlation (between 5–10 modules; Churchill et al., 2018).” This sentence contains confusing grammar that obscures the authors’ intended meaning. The number of modules depends on whether the models are based on a developmental correlation or on a functional correlation?
387 Should not be plural: “Mysticete and odontocete skull network specializations”
393 Revise: “...the maxilla spreads over...”
399 revise: “...evolutionary framework, prograde telescoped skulls of mysticetes are...”
406 Revise: “...independent of...”
427 Might this also relate to the basicranial retroflexion of the odontocete skull?
430 Typo: “In addition to...”
437 Typo: “...compared with...”
443 Skulls should be plural here? Also, this sentence is missing a verb.
469 Typo: “...balaenopterid telescoping...”
477-479 The phrasing of this sentence is a bit confusing.
480-481 typo: “a stem odontocete”; Also, are they saying that Albertocetus has the smallest number of connections and least complex and least integrated skull?
477-487 Several typos: evidenced, exposure, platanistoid, network skull descriptors
492 I suggest a different word choice for patent, which can be confused with patent sutures (suture patency).
503-504 “The higher density...” This sentence appears to be missing a few words
523-526 Some confusing grammar & perhaps typos in these sentences.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: BREAKING THE MOLD: TELESCOPING DRIVES THE EVOLUTION OF MORE INTEGRATED AND HETEROGENEOUS SKULLS IN CETACEANS
Review round: 2
Reviewer: 1

Output:
Basic reporting: see below and previous review
Experimental design: see below and previous review
Validity of the findings: see below and previous review
Additional comments: Thank you for the detailed and convincing answers to many of the reviewers' concerns. The new version of the manuscript looks very fine. I only made a series of suggestions (in the marked .doc version of the main text) for generally very minor changes. In many cases, you should feel free to use alternate formulations.
I had to upload a pdf of the annotated text (with my changes and comments in red), but if it is easier I can also send the original .doc file by email.
I am looking forwards to seeing this very interesting work published (and maybe future analyses with a higher number of odontocete taxa sampled!).
O Lambert


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: MEASURING INTER-INDIVIDUAL DIFFERENCES IN BEHAVIOURAL TYPES OF GILTHEAD SEABREAMS IN THE LABORATORY USING DEEP LEARNING
Review round: 1
Reviewer: 1

Output:
Basic reporting: All basic reporting is good, except for clarity in some cases, which tend to be linked to methodological reporting. See Expt design section for more detailed comments and suggestions
Experimental design: I think the research questions and design is good. However the methods are not sufficiently described detail.

I mention specific issues in the general comment box below, but please focus on the behavioural assay procedure, the arena setup, the parameterisation of the software, and the analysis to compare the manual vs software scored videos. I also found some of the interpretation and claims seem to be overinflated or not adequately justified - and this may be linked to the lack of clarity in reporting of the methods.  One example which highlights both major issues is line 46, and lines 192-195. Line 46 suggests the writing suggests that this ms details a novel raspberry pi recording system, but the readers is given just 3 lines of information about the system in the methods (192-195), citing a separate paper (from different authors). I am left wondering how it is novel, and what it actually is, there is certainly not enough information to be reproducible. There are similar issues in other areas
.
I also found that the method section was a bit hard to follow and it will benefit from re-organisation. There are sections that deal with the fish subjects, the behavioural experiments, the software setup and the scoring, manual scoring, and the comparative analysis but they were not in a clear order and sometimes mixed together.

Other Important issues
Provision of additional information on the occasions where there were large errors, or mismatch between video and human scoring, would be hugely useful. I would recommend providing some additional data if possible, for example, the number of such errors of certain magnitude (especially for presence/absence scores).  Maybe also provide some information on what caused these errors and what steps could be taken to address them.

Discuss the very basic shapes/ structures used in your assay, e.g. the shelter used in this study is a simple box shape. How might this system be impacted other commonly used forms of shelter? I think this is a limitation of the study given the arguments used in the introduction framed the research question around addressing the issues surrounding the importance of this tool in aiding tracking and scoring in semi-natural settings (rather than plain white arenas).

Non-essential general suggestions  - that may be useful in [providing a large benefit to readers and usefulness with relatively little extra work (you have already done so much of the hard work).
1.	Add a glossary of terms used in the DL and tracking section, with some details as to why they are important.
2.	Discuss some of the practical issues encountered in running and using the software and solutions you found/ helpful resources.
Validity of the findings: As mentioned above the research question is useful, and the data seem robust. Some of the conclusions are overstated and I would recommend revising these, or highlighting the justification for the claims (see specific comments below).
Additional comments: I think this is a good manuscript that provides a useful case study and examination into the behavioural tracking of fish using automatic image processing software. Behavioural scoring technologies are going to become more relevant as they mature and become increasingly widely used and this study has potential to be very useful for many researchers that wish to use such systems in the future. Currently I would however recommend significant revisions, with the major issue being that there is insufficient methodological detail at several levels.

Specific issues and comments:

Line 46 and elsewhere if you are arguing the raspberry pi setup you used for recording is novel, then share far more details of that, how it was setup, the code you used etc, the costs. And/ or point to an open-source location or paper detailing the technical details of your system. It is not really the focus of this manuscript.
Line 66: Not clear what you are referring to here please expand/ add details to clarify ‘interpersonal differences’ here.
Line 148 ‘menaged’ ? clarify if this is technical term or use different word.
Line 178 (and other places) ‘relevant’ instead of saying relevant. explain why it is relevant e.g., commercially important/ commonly studied etc.
Line 181- 187: There are many methodological details missing here and this needs to be addressed to ensure replicability/reproducibility and for the interpretation of the results of behavioural assays. Specific examples are: what temperature was the water, what was the grain size, colour, depth of the sand provided, what were the dimensions of the shelter provided, and why was that particular object used as shelter (e.g. have previous studies shown fish use this form of shelter). Please see a recent guide for reporting these enrichment details Jones et al. (2021) [Note I am an author on this paper - please do not feel obliged to cite it - but please read it to address the reporting issues]
Line 184-185- careful of subjective anthropomorphisms ‘to feel safe’ - I would delete this part, do they feel safe there? How do we know? What does ‘feel’ mean for these fish?
Line 188 – why was three days used for acclimation?
Line 190 – when were the tests conducted, what was the actual measures scored, e.g. amount of time spent swimming at x speed, or x body length per y time, or movement vs no movement. When did trial start i.e. under what conditions? Did the fish need to be outside or inside the shelter, before or after feeding before a trial was started? If it was ad hoc trial start, how did you account for the initial position of a fish?
Line 192 – I assume tests were repeated daily 4 days per fish, but clearly state this.
Line 193 – how was exploration scored? How many trials were run, when? What was the toy. Lots of detail missing here.
Line 204 – why did you use fish from two populations. Just add a bit of explanation here even if it is something like ‘as per the design of the overarching project we collected fish from 2 locations.’
Line 219 – extra ‘I’
Line 231: what is a proposal here (see glossary suggestion)
Line 236 – how/ why where these 60 vids selected, you mention in the next sentence to cover the full range of video conditions – but add a bit more detail please. E.g. how many of each ‘condition’ and why did you chose that many.
Line 244-255. It is very important but expand a bit here on why it is important and connect to the number used in your study.
Line 255 - provide, drop the ‘s’.
Line 281 – why randomly select videos? Or rather why only randomly select videos, you recognise the potential impact that different video conditions (e.g. lighting etc) can have on image processing and detection etc. I would like to see a direct comparison of some selected videos with specific conditions (as per your selection on line 236)
Line 358 – word mixup, reword to something like : ‘significantly reduced the effort (time to score the videos)’
Line 359 - You cannot state this as you did not actually test whether ‘the accuracy and the precision of the analysis, is free from human errors.
Line 360 – 361 – I find this problematic:  “we therefore have developed a novel algorithm that can  help analysing the behaviour of a relevant species for aquaculture. Our Faster R-CNN”. From my reading, this is not your algorithm, and not novel. As you state just a few lines above, you adapted the Faster R-CNN.
Line 374 – Again, I would argue with the argument that this is a ‘new’ tool. It is more of an adaptation (for a very specific setup and species).
Line 385-373 – I really like this section of text that discussed to some of the interesting practical details and places your study in the context of similar work in this field.
Figure 2 ‘dorada’ maybe add for non-Spanish readers an additional clarifying description (sea bream or fish) to make it obvious to the casual reader what dorada means and connect it to the study species.
Figure 3: Add explanation of ‘DL’ and (especially) ‘supervised’ to the legend to make it stand on its own.
Figure 6: is hard to understand at first look. Consider adding some additional clarification to the legend e.g. something like ‘longer lines represent greater positioning error’.

Ref mentioned
Jones, N. A. R., Webster, M. M., & Salvanes, A. G. V. (2021). Physical enrichment research for captive fish: Time to focus on the DETAILS. Journal of Fish Biology, 99( 3), 704– 725. https://doi.org/10.1111/jfb.14773


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: MEASURING INTER-INDIVIDUAL DIFFERENCES IN BEHAVIOURAL TYPES OF GILTHEAD SEABREAMS IN THE LABORATORY USING DEEP LEARNING
Review round: 1
Reviewer: 2

Output:
Basic reporting: The work entitled "Measuring laboratory fine-scale behavior in the gilthead seabream using deep learning" is very interesting. Despite the title, the work actually presents from a purely technical point of view the application of a deep learning algorithm to the recognition of a sea bream within an arena of behavior. It is understandable that the authors have chosen a simple behavior for this type of application, but the work is completely focused on the technical question of the algorithm. So in reality the work is not focused on the behavior of the sea bream, but simply on the algorithm performance. The Discussion is a very clear example that the behavior problematic in the sea bream is completely omitted. If the authors want to keep a title like this they should delve into these aspects and clearly highlight what the findings are regarding the behavior of the sea bream. Or perhaps the paper should be directed to a section of the journal specific to deep learning issues. This is a general comment for the rest below some minor comments.
85 the authors have to explain what mean semi-natural arena
88 the sentence is unclear
87-97 The hypothesis of the authors is that the light is the main problem for this type of study.
127-141 The aim of the study is unclear and vague
195-197 the procedure is not clearly explained
281 About the 14 videos sampled: are they regarding the activity, the exploration or both?
288-290 The sentence is unclear
301 presence or absence of the fish mean outside or inside the shelter?
Experimental design: no comment
Validity of the findings: no comment
Additional comments: no comment


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: MEASURING INTER-INDIVIDUAL DIFFERENCES IN BEHAVIOURAL TYPES OF GILTHEAD SEABREAMS IN THE LABORATORY USING DEEP LEARNING
Review round: 1
Reviewer: 3

Output:
Basic reporting: - Although in general the article reads well, there are still quite a lot of textual mistakes in the text, including simple spelling mistakes (e.g. "pounds" instead of "ponds" , line 36), wrong grammar (e.g. " ..being usually its analysis time consuming and always subject to errors...", lines 65-66), bad English (e.g. "more information about what it is a fish than about what it is not a fish", line 387; "The time in seconds is on the x-axis and the probability of the detection of the fish is on the y one.", figure 3 caption), non-professional English (e.g. "the majority of them get only a little bit better", line 335) etc. The whole MS should be carefully reread and corrected by (someone with a similar level as) a native English speaker.
- The introduction and background provide relevant context
- The structure seems to be mostly conform PeerJ standards. I however found the other of the methods a bit unusual, starting with a description of the CNN, then discussing details about the animals and experiments, and then again how the CNN was used.
- The Figures are mostly relevant but: the captions for figure 4 and 6 should start with the x-axis not the y-axis and it should be clarified what the different videos are or why they are included; Figure 6 has much smaller axes so should be changed; figure 7 it is not clear enough in the axes the plot region is the tank borders, it is not clear where in the tank the refuge is, and it is not stated how much time each trajectory represents. It would also be very helpful to include some figure that shows the different augmentations or potentially difficult situations for the CNN.
- Raw data is supplied but I cannot find an easy explanation how the data is organised and what the data and filenames represent.
Experimental design: - I believe the research is within the scope of Peerj, although I question a bit if it can be labelled as "primary research" as it is mostly methodological
- It is clear what the authors intend to do with this article, their objective is meaningful, and it is clear what gap it fills in the literature, but I wouldn't call this a knowledge gap.
- The research seems to be performed using proper standards
- The methods are described in sufficient detail to replicate the experiments, but some more step-by-step (supplementary) descriptions would be needed to be able to also replicate the computational work performed that is central to the paper.
Validity of the findings: - The findings overall seem valid but actually no statistics have been done and only means and standard deviations (? this is actually not specified) provided and compared. I am not sure if a more quantitative and statistical approach is more appropriate here. The conclusions are based on the provided metrics and link back to the original research aims.
Additional comments: I agree that deep learning has much potential to help further automate behavioural observations under difficult and varying environmental conditions. But I think that the conditions used in the study, empty experimental tanks with a single refuge under standard lab conditions, are not the best to properly test the DL approach. As a matter of fact, I think the present videos generated with the used setup and conditions can be more quickly and easily analysed using tracking scripts/software compared to the used and proposed DL approach. Using computer vision it has become very easy to keep track of animals, especially individually, and even with shadows and changing backgrounds. I unfortunately do not see a clear way how the authors can address this point without collecting new data under much less standardized and uncontrolled conditions. To help clarify this point, the authors could revise their manuscript to better discuss the benefits of animal tracking versus using deep learning approaches and when each may be better and faster, including by providing details about the time it takes to analyse say 1h of video data using their deep-learning approach. The manuscript is also lacking a proper description and showdcase of the disturbances or potential difficulties for tracking using their setup. An actual comparison with simple tracking software that uses static or dynamic background substraction would be very valuable. Note also that the manuscript discusses the arenas as "semi-natural behavioural arenas" (line 35; 133) while criticising automated tracking studies to use "plain, white, homogeneous behavioural arenas" (line 83), while the tank used in the present study is actually also a rather blank tank with an artificial refugre (as is clear from Figure 1), so this wording needs to be changed.

The study is very focused on the deep learning method but actually does not provide much to the interested reader to help them on their way to also start using this approach. In my opinion the article could be much improved if some more background was provided about the different deep learning approaches and how researchers may go about using them, as well as considerations and potential simple-to-understand steps to employ a CNN. This is more of a suggestion as it is not about the potential readership of the paper, but also about its suitability to be published as it should be clear what time investments are really needed to set up, trial, test, augment, and validate neural networks.

The authors highlighted throughout the manuscript that they used "a novel Raspberry Pi high throughput recording system", but then actually do not provide much detail or any further attention to this point, such as why and how these computers were used. It therefore remains a bit unclear why this information is highlighted. Then in the last paragraph of the discussion the authors state they are working on incorporating deep learning on the Raspberry Pi to perform similar work. With this in mind, the manuscript could be improved by explaining the computational requirements of DL approaches and discussing the (future) potential for (real-time) analysis, like on single-board computers as the Raspberry Pi. Actually including some data on this in the paper, which the author seem to have (lines 455-458), and revising it accordingly (i.e. that this is possible using low-cost computers), would be valuable.

The authors set as their final aim "to serve as a tool for evaluating individual differences in fish behavioural types, also known as temperament or personalities, and to search for behavioural syndromes" (lines 128-130), but this is more the aim of their own research with this tool, not the aim with the present paper as no data is provided at all on this point. The authors should therefore revise their aims statement. I do however feel the article is rather methodology heavy and some more attention should be placed on to the actual behavioural data acquired and what types of (temporal) analyses that this enables.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: MEASURING INTER-INDIVIDUAL DIFFERENCES IN BEHAVIOURAL TYPES OF GILTHEAD SEABREAMS IN THE LABORATORY USING DEEP LEARNING
Review round: 2
Reviewer: 1

Output:
Basic reporting: I believe all basic reporting criteria are met. However, I have some final remarks concerning the ambiguity of the text.

I see all previous reviewers had some issue with the aims/ main message of the manuscript. It is tricky for the authors as this ms straddles two areas, and they have made a good attempt at re-focusing the manuscript, however there is still room for improvement. For example, the aims outlined on lines 123- 124. I think this important sentence could be far more precise. Currently the line says “..to automatically track a marine fish…” However, more specifically it was used to train and validate the ability to track several behavioural measures commonly used in for assays of individual differences (behavioural types /personality) e.g.: …including, 1) level of activity, 2) Shelter use and 3) Exploration of novel objects (neophobia).. . etc. I think this could be re-worked. Similarly, there are other places in the ms where the aims are mentioned, e.g. in the abstract, the methods and the first paragraph of the discussion each time with slightly different wording and each could be more focused on what the study actually aimed to and or achieved.

Relatedly, I think the title could be changed to be more reflective of the study. ‘Fine-scale measures’ is a bit too ambiguous. I might suggest linking it specifically to measures of inter-individual differences in behaviour. The abstract might also be amended to be more specific about the behavioural measures validated.

Also, please may the authors be more more consistent with their use of terminology. For example, behavioural types/ individual differences/personality/ behavioural variation and other terms were all used to refer to the same thing. I am not a fan of ‘personality’ and I like the authors use of behavioural types, but they should select one (or max two terms) and use them consistently in the ms. Otherwise it gets a bit harder for the reader to follow.
Experimental design: See above about clarity of the aims. I would like to say the authors made some significant changes to the methods and they are much clearer and more reproducable.
Validity of the findings: Good, however, again the conclusions would be more impactful if they are linked directly to more precisely described aims of the study.
Additional comments: Line 94 - Authors refer to fish here but until this point the ms has been forced more generally at animals - maybe change to animals here too. Or re-focus the intro to fish studies more explicitly earlier.

Line 97-99 add some minor details to the examples mentioned e.g. What species were involved?

Line 108-109. I don’t believe it is difficult to foresee at least some of the advancements this sort of technology can lead to. In fact, the authors clearly mention some of the benefits and changes we might expect and are already seeing at other places in the ms.…

Line 172 – Don’t forget to add in the actual sizes of the tanks ( the XXXXL)


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: MEASURING INTER-INDIVIDUAL DIFFERENCES IN BEHAVIOURAL TYPES OF GILTHEAD SEABREAMS IN THE LABORATORY USING DEEP LEARNING
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors revised the manuscript, following all comments of the reviewers. Thus the manuscript is now ready to be published
Experimental design: Now the experimental design is clear
Validity of the findings: The manuscript in this version face much more aspects linked with the sea bream behavior  not purely from a technical point of view.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: MEASURING INTER-INDIVIDUAL DIFFERENCES IN BEHAVIOURAL TYPES OF GILTHEAD SEABREAMS IN THE LABORATORY USING DEEP LEARNING
Review round: 2
Reviewer: 3

Output:
Basic reporting: As this is a review of a revision, see below.
Experimental design: As this is a review of a revision, see below.
Validity of the findings: As this is a review of a revision, see below.
Additional comments: The authors have improved their manuscript throughout and properly addressed many of the points raised by me and the other reviewers, but I still remain with my main concern that the manuscript does not make a clear enough case how the CMM approach is beneficial over more conventional approaches such as using CV. You have included a paragraph in the discussion stating your difficulties to use CV and in the introduction highlight some limitations, but this is not enough. Your statement that "computer vision tracking algorithms require plain and homogenous experimental conditions" (lines 174-175) is not correct as it is also possible to track objects in very heterogeneous environments and also in environments that change over time, such as by using a dynamic filter. It is also not too difficult to update the tracker when the environment has changed, such as when a novel object has been provided. Furthermore, given that the environment you used was also very static and controlled and homogenous I cannot see why the CMM would be much more beneficial. You do now state in your discussion you tried CV but failed to use it properly, but I would think that with a bit more effort CV could actually work.
	You actually start your discussion by stating "Our neural network reduced significantly our time effort and increased the accuracy and the precision of the analysis, reducing human error" (lines 1358-1360). My key criticism about this is that you (still) do not provide any quantitative measures comparing the approach to an alternative approach such as using CV. So you can actually not make this statement. I asked in my original review already to provide more information about the time investment that is needed to set up, train, validate, and run the deep learning approach and highlighted its benefits to future readers but this was not properly addressed either as you still don't provide thorough details nor describe the costs and benefits of each approach. Currently the paper only shows the DL approach works relatively well but does not provide much consideration about why one would not use CV approaches. Related to this, I also commented to provide more background information for researchers to use and employ CNNs, including about the time investments needed, to which you replied that there are tons of detailed explanations and tutorials on the internet. This is not reallh satisfactory. I didn't mean that you should state in detail the exact steps how to use DL but to provide more context why to use it, what considerations to take into account, and what costs and benefits there are, for which I really recommend to better discuss some specific cases where conventional tracking or DL might be most benficicial. Let me clarify that I do see a lot of value in a DL approach and I think publishing a paper like this about it is valuable, I just think it is very limiting to only say it works without providing proper discussion of its costs and benefits.

Besides this major point, I just had a couple further comments:

You removed "semi-natural" and now use "enriched". This wording is not really appropriate either as you still used relatively blank tanks with just a shelter. That is not enrichment, as you state it on line 299.

For the Raspberry Pi you cite Gay, 2014. This is not the proper reference. You should cite the Raspberry Pi Foundation instead (e.g. Raspberry Pi Foundation, 2020, Raspberry Pi foundation annual review) or a relevant review that highlights its relevance and use.

You don't state from where the cameras filmed the fish. From in front or above?

Why did you for validation randomly sampled 11 from the activity and only 3 from the exploration trials?

You say that for validation you manually recorded the presence or absence of the fish at every second. Since the videos were one-hour each, do you mean you manually went through all 3600 frames per video?

Could you clarify how the trained dataset could be used in the future? Would you be able to run new tests using the same set up and species and then get an accuracy similar like the 92.79% you found? I think some more discussion of this (related to my main point) would help improve your paper.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: UNBALANCED RELATIONSHIPS: INSIGHTS INTO THE INTERACTION BETWEEN GUT MICROBIOTA, GEOHELMINTHS, AND SCHISTOSOMIASIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article presents an important review on the interaction of macrobiota (helminths) and microbiota (bacteria). The paper structure is very clear and easy to read.
Experimental design: Did the authors not use a temporary limit of consulted articles? If the authors used a specific literature review period, add in the section Survey methodology.
Validity of the findings: no comment
Additional comments: Just a few suggestions:
Add italics to species names (taxonomy rules) and in other cases, lines: 21, 137, 191, 226 (in vivo), 332 (Trichuris), 364-365
Line 290: It is a topic discussed by different research groups, based on the agreement or disagreement of the Hygiene theory. I suggest a small adjustment in the sentence: ...allergy and are actually protected..., change to: ...and may be protected against...
Some typos, lines: 247, 266, 288, 303 (worms), 311, 317, 426
Line 333: Trichuria colonization, change to whipworm colonization.
Lines 337, 370 : microflora, change to microbiota
Lines 356, 357 and 358: T. trichiuria, change to T. trichiura
Line 365: infestation, change to infection.
Line 366: review the number 450.68 million.
Line 469: disbiose, change to dysbiosis.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: UNBALANCED RELATIONSHIPS: INSIGHTS INTO THE INTERACTION BETWEEN GUT MICROBIOTA, GEOHELMINTHS, AND SCHISTOSOMIASIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment'
Validity of the findings: no comment'
Additional comments: This manuscript is scientifically sound  the results are important in the field and relevant this work contains important obserations about the regulatory capaity of parasites in the intestinal ecosystem. I suggest to publish it


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: UNBALANCED RELATIONSHIPS: INSIGHTS INTO THE INTERACTION BETWEEN GUT MICROBIOTA, GEOHELMINTHS, AND SCHISTOSOMIASIS
Review round: 1
Reviewer: 3

Output:
Basic reporting: This review is a timely and an important topic in regards to tropical medicine.
Major improvements in grammar and language are needed throughout, and in parts the text is very difficult to follow.
Line 35, the term depleted infers the whole (entire) resource has been used, reduced of diminished may be better.
Line 87-88, the authors are referring to Schistosoma but Ducarmon references is related to Necator. I would recommend the referencing here and in other parts of the paper with the recent work of Cantacessi for S. mansoni and Gordon for S. japonicum.
Other publications that should be considered include, PMCID: PMC7580221; PMC8660641 & PMC5851687 (Trichuris)
Table 1 is very useful.
Lines 252-3 the statement on PZQ is misleading since the drug has varying efficacy between developing and adult stages within the mammalian host.
Please be consistent with the use of abbreviations ie line 255 praziquantel should be PZQ.
Some sections contain material that is a little ad hoc ie lines 257 261 following on from PZQ and under the section title that doesn’t fit, then comes back to PZQ. Ideas sometimes do not flow particularly well, with some topics not connecting within paragraphs. Statement in lines 269-273 not supported by the text and seems not very feasible, considering novel antibiotics are very difficult to develop and their use to treat helminths would not be very appropriate.
Line 277, some reports present little to know change with helminth infections. Lines 277-281 is confusing.
Line 281 change deceive to modulate.
Line 284 suppress what?
Line 305, less concern or less information? This contradicts the statement in lines 323-324.
The breaking of sections into diseases, works particularly well.
Line 415 change form to stage.
Line 426 yet another referencing formatting error. Species names should be italicised in the reference list.
Line 445-6 “In another study…”, which one? No reference provided?
Lines 452-455 is that a clinical or animal study.
Lines 455-472, much of this is confusing. Line 474 “….were also studied.” Add reference here.
The conclusion section does not say too much and should instead state more specific approaches that should be taken and why.
trichiura is misspelt throughout
Experimental design: see above
Validity of the findings: see above
Additional comments: see above


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: THE RESPONSE OF GEOPHYTES TO CONTINUOUS HUMAN FORAGING ON THE CAPE SOUTH COAST, SOUTH AFRICA AND ITS IMPLICATIONS FOR EARLY HUNTER-GATHERER MOBILITY PATTERNS
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is an excellent paper that makes important contributions to our understanding of the exploitation potential of USOs (underground storage organs) in sub-Saharan Africa. With some revision as suggested below, all relatively minor, I strongly recommend that the paper be published. Most of the suggestions which follow are requests for some additional information; a few are more substantive; all should be relatively easy to complete. I present most of them in the order in which I encountered an issue or question, not in terms of any order of priority. A few of my comments early on are more general issues that came to mind after reading the entire manuscript. To help the authors find the precise place in the manuscript to which I am referring, I extract a direct quote from their text, flagged in quotation marks, followed by my comment in brackets.

[O'Connell is misspelled throughout the paper.]

"The Cape south coast falls within the Greater Cape Floristic Region (GCFR) (Manning & Goldblatt 2012; Snijman 2013), an area supporting 11,423 plant species (80% endemic), making t the richest concentration globally of extratropical plant diversity and endemism (Snijman 2013). Within the Cape Floristic Region (CFR; a sub-region of the GCFR that excludes the Succulent Karoo component and incorporates the Cape south coast) 1,552 species (17% of total) are geophytes—species with underground storage organs (USOs) (Procheş et al. 2005)."

[Given the unusual nature of the area’s flora compared to other areas of Africa, it might be worth commenting briefly on why this study might still provide relevant comparative insights for other areas where early hominins evolved and used USOs, such as East Africa.]

[It would be helpful to the reader to add a brief discussion of two additional topics: (1) the presumed nature of the natural fire regime (e.g., frequency of lightning-ignited fires in comparison to other arid or semi-arid regions of Africa such as in East Africa. In other words, is the natural fire regime in any way typical or unusual? (2) Perhaps more important to the overall argument is the history of the intensity of grazing by domestic livestock especially since European conquest and colonization. In short, what is the nature and degree of grazing or over-grazing by domestic livestock and how, if at all, might that impact the nature and results of your study? (3) You also need to say something about government policies concerning fire suppression. In the USA the government systematically suppressed natural fires, and others, for decades, with catastrophic consequences. If that has been the case in South Africa to any significant extent, such a policy may conceivably have altered geophyte densities and distributions.]

"We established 19 permanent plots and harvested all edible biomass from the plots for three consecutive years; foraging was conducted by local people from nearby settlements who still have knowledge about indigenous edible plant species (De Vynck et al. 2016c)."

[This quote begins at line 97 in the manuscript. As I read it, I was left with many unanswered questions such as: What do you mean by “established”? Permanent? How big are they? Did you plant geophytes or did you simply fence off an existing natural stand? What sort of enclosure? Why 19? What do you mean by “edible biomass.” Was that edible in your judgment or in the judgment of the villagers who did the harvesting? Just USOs, or seeds, leaves, stems, and other edible biomass as well? How did you determine that you harvested “all”? Did the enclosures keep out grazing ungulates or other animals that might target above-ground or below-ground parts of geophytes? Reading through the rest of the manuscript, not surprisingly, you do address all or at least most, of these questions. So what is needed in the section that begins on line 97 is a statement telling the reader to be patient as the details in answer to these unexplained statements will be provided below....]

"To our surprise, edible biomass was only significantly reduced after three consecutive years of harvesting—yet nonetheless there remained an unexpectedly high yield in some plots."

[What constitutes “significant”? Again, if this is addressed later in the paper, tell the reader that further explanation is coming below.]

"Blombos and Pinnacle Point caves are of global significance as they have provided some of the earliest evidence of human cognitive complexity (Brown et al. 2009; Brown et al. 2012; Henshilwood et al. 2002; Henshilwood et al. 2011; Marean et al. 2007)."

[I know statements like this are popular in some circles, but I am bothered by the phrase “earliest evidence of human cognitive complexity.” Cognitive complexity is obviously a relative concept and is only meaningful in comparison to something else. Hence, one could easily argue that Australopithecines show the earliest evidence of cognitive complexity if your comparison is with fleas. And I suspect fleas show greater cognitive complexity than earthworms, and so forth. In any case, I would rephrase this. I would have only minor qualms if one states that they had "increased" cognitive capacity, but drop the word "earliest." The earliest came when the living organism for the first time was smarter than the average rock and that was probably some time very early in the Precambrian!]

"The study area occurs within the non-seasonal rainfall regime, where rain can fall in any month but with peaks in late winter to spring (Aug-Oct) and in autumn (Mar-Apr)(Engelbrecht et al. 2014)."

[The lack of seasonality makes this region different from East Africa where most studies that talk about USOs have been conducted (e.g., among the Hadza of Tanzania). You need to say something about why and how this difference does or does not matter when drawing general implications for early human use of geophytes.]

"Kedrostis nana is a deciduous vine with a large tuber, and a good surrogate species for Fockea edulis and Dioscorea elephantipes, two well-known edible USOs that have a similar growth form."

[Why is it a good surrogate? Explain.]

"The main reason the USO resource was not depleted across species and plots after the initial harvest was the emergence of new species and new individuals in year two and three that buffered the decline of harvestable USOs."

[Your explanation of this seems to conflate two different issues. Staggered emergence would seem to be most relevant to members of the same species. Reduced competition might be a factor involved in the emergence of new or different species, although staggered emergence could also be involved.... As I continued reading that entire section, I kept saying to myself "but what about....?" The flow of the arguments would be clarified if right at the beginning of this entire discussion you had something like: There are x number of reasons that have been offered to account for such staggered emergence: (1) climatic vicissitudes; (2) herbivory; (3) etc.... That would tell the reader at the outset where you are going with the discussion that follows.]

"Resource resilience is an important driver in determining early hunter-gatherer mobility patterns. De Vynck et al. (2020) work on determining the resilience of the intertidal shellfish resource of this region, showed that the resource, largely comprising Turbo samarticus (92%), is exceptionally resilient, nutritious and productive (De Vynck et al. 2016a)."

[Here I will reflect my own biases and leave it up to the authors' judgement as to whether and how they might want to handle (rephrase?) this section. Personally I don't think food, either what one eats or how one gets it, has anything whatsoever to do with the emergence of "cognitive complexity." But taking this a step further, I instantly reacted with skepticism to the use of the word "nutritious" when applied to shellfish. It's a very slippery term in general and I got curious about what was supposedly so nutritious about Turbo. So I took a bit of a "deep dive" into the literature to see what that might mean. The results are interesting. As shown by Mclachlan, Anton, and H. W. Lombard, 1980. Seasonal Variations in Energy and Biochemical Components of an Edible Gastropod, Turbo sarmaticus (Turbinidae). Aquaculture 19(2):117-125, the dry weight percentage of protein in these gastropods is over 70%. That's a whopping amount (which nutritionally is a negative, not a positive, Kim Hill notwithstanding). If, as has been argued in numerous studies and venues, humans are limited to a daily intake of protein of less than about 35% of total calories (actually an absolute daily limit in grams of protein per kg body weight), that means that the value of the gastropod as a food is limited no matter how abundant, available, and resilient they are, or how many calories they produce when burned in a food analytics lab. In other words, resilience matters, but only up to a point. This means that well over half of the daily diet of these coastal foragers (i.e., more than roughly 65% of their calories) cannot come from those lovely little gastropods or they would likely suffer from what explorers in the arctic called "rabbit starvation." The high protein content of the gastropods actually increases the likely importance of starchy and oily plant foods and hence the likely value of your geophytes. Interestingly, one of the earliest statements about this issue came from South Africa and was written in part concerning shellfish use: Noli, Hans Dieter, and Graham Avery, 1988. Protein Poisoning and Coastal Subsistence. Journal of Archaeological Science 15(4):395-401. Those authors in their abstract made the following comment: "Current hypotheses concerning coastal palaeodiets are based on excessive protein intake and do not deal adequately with this problem." That was 1988. The situation seems largely unchanged today! Nutrition and calories obviously aren’t the same thing. You need all three macronutrients, protein, fat, and carbs, plus a handful of micronutrients (vitamins, minerals, etc.). Marine mollusks are generally high in protein (Turbo seems typical in that regard), and most are pretty poor in fat and low to modest in carbs. So you may get a fair number of calories from them but might still die if they form the mainstay of your diet. The geophytes therefore could have been absolutely critical to coastal foragers even if their total calorie yield was not as high as you might like or expect. You simply can’t live on just protein. The enzymes in your liver can’t cope with all the nitrogen that is produced by deaminizing the protein. You have to have a diet with some 70-75% of calories from sources OTHER THAN protein. And that’s a lot! I’m sorry but both for these nutritional reasons and just on the logic of the arguments, I simply don’t believe that gastropods had anything to do with making humans cognitively modern. Excessive dependence on them would probably have made humans under-nourished or maybe even starving or dead, but not cognitively superior. They make a great supplement to an overall healthy diet, but they are just that, a supplement, they don’t make a whole diet, not even close. If you could somehow boil them, skim off the fat and carbs, and throw away the bulk of the protein, you’d have a more valuable food, but that would require a huge labor input, untold masses of gastropods, and it probably isn’t technically feasible in the first place. And if you are one who thinks that big game hunting is driven more by costly signaling and prosocial motives, as do Hawkes, O'Connell, and Bliege Bird, then little marine gastropods won't get you very far as a "public good." I think Marean and colleagues are barking up the wrong tree if they try to link shellfish to modernity. Early modernity may have emerged in Southern Africa but I seriously doubt that shellfish, any more than baobab fruits or seeds in Tanzania, or catching bunnies in Europe, had any causal role in it..... So what am I asking the authors to do????..... I think the geophytes offer an important, perhaps critical, source of carbs to augment a diet which may have faced problems posed by resources such as shellfish which contained very high levels of protein and limited amounts of non-protein calories. In my opinion, that critical supplemental roles can and should be emphasized. As written, the paper bemoans the fact that the geophytes aren't as resilient as the gastropods. In my opinion they are as valuable if not more so than those snails. A life based overly heavily on snails would have led to quick extinction, not cognitive complexity..... For discussion of upper protein limits, see for example Cordain et al., 2000. Plant-Animal Subsistence Ratios and Macronutrient Energy Estimations in Worldwide Hunter-Gatherer Diets. American Journal of Clinical Nutrition 71(3):682-692; or Speth, JD, 2010. The Paleoanthropology and Archaeology of Big-Game Hunting: Protein, Fat or Politics? Springer, New York.]

"Secondly, once the resource has been depleted (over a period of two to three years), it would take much longer than that of Turbo samarticus to recover a plant species’ population to its former densities. We observed very little/no recruitment and saw no evidence that geophytes profit from human digging by being dispersed, such as what mole-rats may do when they store USOs in underground caches for later use. However, indirectly, persistence of geophyte species after human foraging was noted. Natural harvesting behaviour is not constrained to a demarcated plot (Botha et al. 2020; Eder 1978; O'Connel & Hawkes 1984) and foraging efforts were intensified in a small space because the task set out was to harvest a fixed area of all edible foods to determine depletion rates. Even in a small space with intense foraging, a combination of forager error and discernment appeared to buffer complete USO extinction. For example, foragers would leave a few individuals behind that they failed to see (forager constraint), or the plants were left behind because they were too small to yield any worthwhile return (plant constraint)."

[I think the above gets the authors in unnecessary difficulties. No foragers in their right mind operated in 10 x 10 m squares. The authors are well aware of that and yet this statement seems to ignore that fact and emphasizes the fact that the 10 m squares got depleted, and the geophytes didn't disperse, and life looks bad for the geophyte forager. I think it should be pretty obvious that the whole region wasn't depleted in three years, just those 10 m2 plots. Later you cite Bliege Bird's study of fire-stick farming in Australia. Why not weave those sorts of models into this discussion right from the get-go? What your study shows is that the 10 m plots get depleted so to use the resource effectively over the long-term one has to use the overall landscape and presumably burn it in a staggered and mosaic pattern much like what Bliege Bird observed in Australia. Under that sort of exploitation regime, it might provide a quite stable and predictable resource and hence an important source of carbs to complement the protein sources typical of shellfish from the coast.]

"Alyawara gatherers in Australia, whose traditional ways of foraging for food are still partially intact, corroborate this prediction—they ignore low-ranked foods where returns fall below energetic efficiency (O'Connel & Hawkes 1981; O'Connel & Hawkes 1984)."

[True, but you are citing rather outdated studies. These same authors have gone on to write many articles on costly signaling and prosocial behavior, arguing that men hunt for big game largely for political or prosocial reasons (prestige, displays of reliability and dependability, generosity, skill, knowledge, fostering cooperation), often deliberately bypassing smaller game. As a result they often come home empty-handy when in fact they could have come home with food. For a fairly recent example, see Hawkes, Kristen, James F. O’Connell, and Nicholas G. Blurton Jones, 2014. More Lessons from the Hadza About Men’s Work. Human Nature 25(4):596-619. Bliege Bird has also written lots on the same topic. See for example Bliege Bird, Rebecca L., and Eleanor A. Power, 2015. Prosocial Signaling and Cooperation Among Martu Hunters. Evolution and Human Behavior 36(5):389-397. In other words, these authors have gone on to emphasize that male hunting is first and foremost about social and political goals, not calories or family provisioning. The hunters commonly bypass small game, not because it has fewer calories, but because it has less value as a “public good” when shared with other males, often other unrelated males.]

"We found significant, but not necessarily the expected substantial, declines in harvested resources, suggesting humans could re-visit the same location a few times. The cues, whether environmental or physiological, that trigger a proportion of USO individuals to emerge in any given year is not understood and thus emergence patterns are not predictable."

[This conclusion as phrased is once again misleading and undermines the importance of this study. I don’t think any forager in their right mind would return year after year to the same 10 x 10 m plot. The authors are well aware of this. So why write it this way? Instead, thought of as a region, esp. if the foragers burned it in some sort of mosaic fashion à la Bliege Bird in Australia, the geophyte resource could likely have been repeatedly harvested year after year. In fact, your study builds a great case that they would have to use it in that staggered mosaic fashion. One archaeological goal will be to figure out when landscape burning that is not natural but cultural gets underway in the region (e.g., via fly ash in pollen cores). That would be an interesting key. Perhaps such data already exist? Another interesting question is how long it would take for an individual 10 m2 depleted plot to recover? Are we talking about a few years? Decades? Longer? Can you at least speculate on that?]
Experimental design: Excellent
Validity of the findings: Excellent
Additional comments: Nothing additional. See basic comments above.