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: OPTIMIZING THE TRAINABLE B-COSFIRE FILTER FOR RETINAL BLOOD VESSEL SEGMENTATION
Review round: 3
Reviewer: 1

Output:
Basic reporting: Again. I believe that the abstract does not reflect the true value of the research.
"The approach results are
better than the other state of the art methods used for vessel segmentation." not quit correct.
Experimental design: The manuscript is much better than before. It is in a good shape for publication.
Validity of the findings: no comments
Additional comments: no 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: OPTIMIZING THE TRAINABLE B-COSFIRE FILTER FOR RETINAL BLOOD VESSEL SEGMENTATION
Review round: 3
Reviewer: 2

Output:
Basic reporting: The paper presents a method of optimizing trainable B_COSFIRE filter for the retinal blood vessel segmentation. The manuscript get better results than the normal B-COSFIRE algorithm results, I suggest to publish this paper
Experimental design: no comment
Validity of the findings: no comment
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: THE RELATIONSHIP BETWEEN SOCIAL RANK AND SPATIAL LEARNING IN PHEASANTS, PHASIANUS COLCHICUS: CAUSE OR CONSEQUENCE?
Review round: 1
Reviewer: 1

Output:
Basic reporting: Throughout the manuscript the authors present some valid points; however they then fail to develop them. The initial points made in the introduction are not really discussed, nor is the significance of the task itself and its relation with social rank. More importantly, there is almost no mention of the rank-related characteristics that determine much of social animals’ behaviours. Since this is an experiment about social rank, this has to be extensively reviewed in the literature. The writing is sufficiently clear, however, some key sections in the manuscript need more flagging and rephrasing, as they are difficult to follow. Figures are relevant to the manuscript and raw data is accessible, although not really clear on what it refers to.

Below I refer to specific sections of the manuscript that need clarification or amending:

1. Lines 54-74: This whole section doesn’t really contribute much to your point that social rank determines cognitive performance. You only give examples (very good ones) of studies that have assessed this relation but you never discuss why so and so rank would be better at cognitive tasks. What are the life-history characteristics of subordinates or dominants that would make them more apt at a cognitive task? If you want to evaluate whether social rank is a cause of cognitive performance this has to be addressed. Additionally, you mention at the start of the paragraph (line 54) that the “social-state hypothesis” can happen through several mechanisms yet you only elaborate on “stress”. Is the unequal distribution of resources (line 74) also a mechanism? It seems to me that this point can also be linked to stress (i.e. nutritional stress). Again, you need to include some information about why ranks differ in their access to resources.

2. Line 59: In both papers (Bunnell & Perkins, 1980; Bunnell et al., 1980) authors refer to animals as crab-eating macaques. If this is not changed, then the Latin name should at least be added to clarify it’s the same species.

3. Line 65: Latin name is missing for the species mentioned here (i.e. crabs).

4. Line 68: What cognitive ability are you referring to here?  This has to be explicit.

5. Line 68: Latin name (or the type) is missing from the species mentioned here (i.e. mice).

6. Lines 80-82: Repetition with line 77. I think you mean task participation, rather than opportunities. Animals may have the opportunity to participate but choose not to do so due to a lack of motivation. This will obviously determine the likelihood of learning.

7. Lines 106-107: You have to elaborate a bit more on some of the life-history traits of pheasants. Are they seasonal hatchers? Why do they acquire their territories in October specifically? Does this apply to your study group?

8. Line 114: Wouldn’t having a bigger home range be a better indicator of spatial learning abilities? What about the satellite subordinates? Wouldn’t they need developed spatial abilities to avoid conflict with other males (i.e. avoid dominant’s home ranges)?

9. Lines 117-121: This paragraph should be moved to line 109.

10. Lines 123-124: The sentence is unclear. Please rephrase: “We investigated whether performance on a spatial discrimination task is suggestive of this ability causing male pheasants’ social rank, or whether it is more likely a consequence”

11. Line 125: How long is the breeding season normally?

12. Lines 142-144: The sentence is unclear. Please rephrase: “Third, we tested whether adult males’ cognitive performance assayed while males’ were housed in the perceived dominance condition, was related to their most recent recording of social rank”

13. Lines 265-267: “During most test sessions, we were required to use a temporary mesh partition that stopped the females from approaching the-” Incomplete sentence.

14. Lines 331-333: It is not necessary to explain how you made a figure. I would remove this from the main text and move it to the figure description.

15. Lines 344-347: How does this relate to cognition? You mention nothing of sexual behaviour associated with rank and/or cognitive behaviour. Is this a determinant of fitness based on differences in rank? Table 4 relates to sexual behaviour but it shows the rate of dominance behaviours. Are these behaviours also used in a sexual context? This needs further explanation or to be removed.

16. Lines 457-458: “…cognitive tasks designed to assay performances in the spatial domain may not correspond to interactions with conspecifics or their use of space on a landscape scale” This sentence is unclear. Please rephrase.

17. Line 496: “Stress provides an obvious candidate” Please reword.

STRUCTURE

1. References need to be formatted appropriately.

2. The “Results” section has a different format from what has been used in the first part of the manuscript.

SUPPLEMENTARY MATERIALS

1. Tables 1 & 2: How are these behaviours different from each other? Table 1 mentioned antagonistic outcomes based on winners and losers, but is this independent of rank (i.e. is the winner equally likely to be a subordinate or a dominant)? There’s even a reference to submissive behaviours in Table 1.

2. Tables 4 & 5: There needs to be a bit more description for what each table is showing. For example, what does OR refer to in Table 5?
Experimental design: This study poses some very interesting questions regarding the relation between social rank and cognition. They are well defined and clear from the start. The idea that cognitive abilities determine social rank has been presented before but so far has remained untested. Previous studies (Bunnell & Perkins, 1980), have recommended rank manipulation as a necessary step to answer such questions, which makes this a highly opportune study. Nevertheless, the methodology section needs a lot more detail, as some parts are really ambiguous.

Below I refer to specific sections of the manuscript that need clarification or amending:

1. Line 126: Why were individuals re-captured prior to the breeding season? It’s possible that their behaviour during this season is not normal as there are looking for mates. Wouldn’t this affect their performance?

2. Lines 131-133: “While males were in this perceived dominance condition and experiencing the same social rank, we assayed their performance on the same task that we had presented to the chicks” You mean the social rank was maintained during the social condition or was it the same social rank as before (i.e. previous to re-trapping)? How was rank determined after being re-captured?

3. Line 155: You mention you reared 194 pheasant chicks. Were all of these tested as well? This need to be addressed here or you need to provide a table that has all the information regarding the sample size used throughout the experiment.

4. Line 160: Ad libitum is the correct term as far as I know.

5. Line 166-167: You need to be explicit that from here on, you are referring to those groups as either “known” or “unknown”.

6. Lines 167-171: This needs more flagging. It reads as though there are 3 conditions: (1) Large group aviary with multiple females; (2) Small group aviary with four females; and (3) Small group aviary with two females.

7. Line 169: 60 males and 40 females in this aviary? This number doesn’t match the sample that was re-trapped.

8. Lines 185-187: “If individuals chose incorrectly, indicated by pecking at the crepe paper of the unrewarded well, the wells were removed and a new pair of wells was presented” Did individuals leave the other well untouched if they chose correctly? If not, then this needs to be addressed here or in the discussion.

9. Lines 201-202: At what time was each session carried out? Satiation affects motivation to participate (see Rowe & Healy, 2014). You need to specify here whether animals received any food before each session, as well as the time between sessions and between trials.

10. Lines 203-205: To what session (i.e. morning or afternoon) do these trials correspond to? Do they include trials of the afternoon session as well?

11. Lines 208-209: “Eleven unknown males and one known male that we captured as adults were assigned to the ‘Social Group (SG)’ condition (the large group aviary)” Why was only one know male included here and how was he chosen?

12. Lines 210-213: “Males were assigned to the social conditions in this way because we were initially only interested in known males and so wanted them to be included in the same hierarchy while in the SG condition” Unclear what this sentence means.

13. Lines 213-218: Were the “Cohort I & II” individuals assigned to the two-female or four-female groups of the PD condition randomly? This needs to be clarified.

14.  Lines 228-230: “We only included lateral struts which were directed towards females so this was consistent between social conditions (females are present in both social conditions, whereas multiple males were only present in the SG condition)” Why is this? Is male social rank also determined by male-female dyad encounters?

15. Lines 241-243: “Outside of cognitive testing we also collected behavioural observations on dominance behaviours (Table 2), for cohort I males” Again, you need to either elaborate more on the life-history characteristics of pheasants (i.e. differences between sexes). Are males always more dominant than females? This is not clear so it can be interpreted as though females can occupy higher ranks than males.

16. Line 246: “Observations begun at variable times of the day” Aggression levels may change throughout the day. Is aggression consistent despite the time of day? You need to elaborate why this was part of the experimental design.

17. Lines 254-255: “The apparatus was located between two opaque screens so that it could only be approached and viewed by a bird ‘front-on’” Was this the same setup as the one used when they were chicks? If not, then you need to address the differences in design.

18. Lines 256: Why wasn’t the auditory cue used again? This seems to be a completely different setup than the one you tested chicks with.

19. Lines 261-262: “…the males proved difficult to test and appeared distracted by females during the breeding season” It seems to me that this was a possibility from the start. A subordinate’s access to females is male is normally restricted by dominants, so it seems likely that when housed alone with females and out of sight of other males, he will prioritise sexual encounters. Why test individuals at all during this period?

20. Lines 265-267: “The use of this mesh partition did not appear to be stressful as males readily engaged in cognitive testing shortly after the partition was implemented” But not all males participated right? This needs to be clarified, otherwise it contradicts what you just wrote in lines 261-262.

21. Lines 268-269: “Each session consisted of 20 trials. Individuals received one session per day, for five days, resulting in 100 trials in total” Why is this number of trials different from the one before? That’s 70 trials more than when they were tested as chicks. Can you justify this number?

22. Line 295: You need to specify whether the final trial (X) was evaluated in the chick phase, the adult phase or both.

23. Line 299: Same as above but in relation to Y = 80.

24. Lines 310-312: “We fit a generalized linear mixed model (GLMM) with a binomial error structure and a logit link function to assess whether adult learning performance (correct: 1 yes / 0 no) was predicted by group social rank” Were only animals in the SG group used here? This needs to be specified.

25. Lines 322-325: “We included choice on first trial (correct: 1 yes / 0 no) to control for random choice on this first trial; as this trial was prior to the opportunity for learning but may affect subsequent performance on the task and this left the trial variable with trial number 2 – 100 (after trial 1 was removed)” Needs to be moved after the sentence above (line 314).

26. Line 325: Not sure it is necessary to explain that the model failed to converge. Instead, you could write something along the lines of: “To facilitate convergence, we converted trial number, etc.”

27. Lines 333-334: “This model was conducted on eight adult males that each completed 100 trials” These males belonged only to the PD condition?

28. Lines 339-340: “Similarly, we did not include cohort in the model due to the small sample size” I thought the Cohorts were made to increase sample size? Surely the inner state (i.e. stress) of individuals who went from the SG to the PD is not the same as those ones who had the opposite treatment. This could have affected those individuals´ performance and should be controlled for here.

29. Lines 340-342: “Instead, we conducted a Wilcoxon Rank Sum test on the difference between cohort I (n = 3) and cohort II (n = 5) on their overall performance on the task (X=Final)” How did you control for the different groups in the PD condition (i.e. two-female, four-female)?

30. Lines 342-344: “Cohort accounted for the order in which males experienced the social conditions as well as their rearing history (i.e. whether they had experience this task as a chick)” This should be moved to the “Adult social conditions” section.

GENERAL COMMENTS:

There is a lot of inconsistency between the general description of the experiment and statistical analyses over the total sample size analysed at each stage and for each Cohort. A table that describes exactly the number of individuals used in each analysis in both stages is needed.
Validity of the findings: The overall manuscript has methodological issues that need clarification and further explanation. I have a big concern over the lack of consistency throughout the experiment, particularly over the difference in trial number between the chick and adult phases and how individuals were assigned to the cohorts. I believe the authors need to justify why animals were tested so extensively during the adult phase and provide more detail as to how differences in conditions were controlled statistically or in the experiment. I found the discussion rather ambiguous and not going into much detail. There seems to be a lot of ideas presented, but none of them are really developed, nor do they refer back to the literature or the main research questions. The results and methodology are quite interesting and there is sufficient literature for them to be well discussed.

Below I refer to specific sections of the manuscript that need clarification or amending:

1. Lines 382-383: “Of the ten males of cohort I, two males never crowed in either social condition…” What about on the two-female/ four-female conditions?

2. Lines 385-388: You repeat here what you’ve stated in the previous sentence. Is this a different result?

3. Lines 392-394: Same as in the previous comment.

4. Lines 422-424: “Our findings suggest that the effects of past, as well as current social interactions, are important in shaping inter-individual variation in performances on spatial cognitive tasks” Since this was not observed in either cohort, it must be the rank before trapping right? Also, you suggest above (line 418) that performance is predicted by the most recent recording of social group rank. Which record would this be? There needs to be a lot more flagging here and throughout your results section regarding the cohorts and past ranks. At the moment it is difficult to understand what you are referring to.

5. Line 426: “Cognitive performances have been suggested to determine social success“ Do you mean having a higher dominance rank? If so, then wouldn’t this suggest that cognitive performance is a determinant of social rank?

6. Lines 432-435: “This hypothesis originally focused on morphological attributes that were developed prior to the formation of the hierarchy, but were measured while the dominance hierarchy is established and active, with the inference that these traits assisted in the establishment of the dominance hierarchy” This should be moved to the start of the paragraph and the hypothesis mentioned here has to be specified.

7. Lines 436-438: “…measures must be collected prior to the formation of the hierarchy to avoid the confounding possibility that the expression of the attribute is simply a result of the hierarchy” This varies according to the species and in some cases, physiological differences (i.e. sex), so this suggestion is a bit unrealistic. If you want to argue this point then you must address species-specific differences here and what this means for cognitive abilities.

8. Lines 439-440: “…we expected that cognitive performance of chicks reared in controlled conditions, would predict their future social rank” You mean because animals were all released with a similar physical state (all of them received the same amount of food during this stage)? How can you then be sure that the hierarchy is not affected once other factors are introduced (i.e. food availability)? You would have to assume that chicks who were successful at spatial learning (based on the acquisition of territories) were equally successful at foraging challenges. This needs to be addressed when you propose this hypothesis.

9.  Line 445: “…small sample sizes and some extreme outliers may have confused the relationship” Not sure what you mean by “confused”.

10. Lines 445-447: “The number of trials it took for individuals to reach a learning criterion (Y=80) showed a strong positive relationship” How do you justify so many trials in the adult phase? Even for a captive study, 100 trials per individual seems excessive. Is it really indicative of spatial learning abilities? The inconsistency between both phases makes it look as though they are separate studies. Additionally, if you only analysed the first 20 trials in the chick phase, why didn’t you analyse the same trials in the adult phase as well? If adults learned the task past trial 20 (or even 30) you would naturally fail to get a relation between both phases. I would suggest running this analysis again with an equal number of trials in both phases.

11. Lines 447-451: This paragraph should be moved to the results section, although I would be more inclined to remove altogether as it offers nothing to your discussion.

12. Lines 459-460: “Perhaps performances on tasks assaying different cognitive domains, such as the ability to discriminate between social stimuli would better predict an individual’s future social rank” This is assuming social rank is not already established from an early age (i.e. when it is inherited). So far you have not mentioned why discrimination of social cues would be relevant for gregarious animals with hierarchies (i.e. avoid aggression, foraging)

13. Lines 465-467: “To truly examine whether cognitive performance predicts social rank, performance on a cognitive task needs to be assayed before any exposure to conspecifics” This is a bit unrealistic. Even in captivity gregarious animals are kept in social groups to avoid stress. You would have to test animals that have been in social isolation since birth. That’s also assuming you have species in which maternal-rank is not inherited.  Since you just suggested that discrimination of social cues would have been a better test this seems out of place.

14. Lines 470-471: “…spatial learning ability is flexible across an individual’s lifespan and indeed is influenced by social interactions” But your animals were tested in isolation no? You haven’t analysed whether the interactions they have before each test affected their performance.

15. Lines 496-497: “individuals suffering from nutritional stress or high parasite load not only have their cognitive performance affected…” But you provided food ad libitum here. Presumably, individuals were not nutritionally stressed when you tested them. Were they weighted when they were recaptured from the wild and also when they were moved from the SG to the PD condition to determine this?  Also, you don’t make any relation to social rank here. Are subordinates suffering from nutritional stress or have a higher parasite load? Stress resulting from aggressive interactions seems like a more appropriate reference here.

16. Lines 508-509: “…suggests that individuals may not remember this task from early life” This is a completely different explanation from what you have been arguing so far and you don’t elaborate any further than that.

17. Line 509: To what relationship are you referring to here? You mean the relation between performance and cohort?

18. Lines 525-527: “It is possible that male crows communicate dominance ability to conspecifics and males were able to assess their relative rank through neighbouring males’ crows…” It seems to me that auditory cues are a relevant part of establishing dominance. A discussion on how auditory cues may be used for spatial learning by dominants would be relevant here. You used an auditory cue during the chick phase testing but then you switched to a visual cue in the adult phase testing. Why was this, and could it have affected participation? On a different note, dominance is not an ability. A better word would be “status”.

19. Lines 534-537: “Perhaps the reduction in male-male social pressure takes longer to impact cognitive performances, compared with the effect that increased access to females has on cognitive performances, indicating that inter-sexual interactions are a stronger predictor of male cognitive performance than intra-sexual contests” You cite no references to support this observation. Why would an increase in the access to females impact cognitive performance? You never mention anything about the relation between cognitive abilities and reproductive success (i.e. Cauchard et al., 2013). You also never test the effect of inter-sexual interaction on cognitive performance so you cannot confirm this. If this is part of another study, I would remove it from here.
Additional comments: I think this study is relevant to the field of cognition and offers a novel perspective on the relation between rank and cognition. Testing animals under any condition is always challenge and in this case, you not only trained and tested individuals since early age, but later recaptured them and tested each one over an impressive 100 trials! That, to me, seems like a major success on its own. I do feel however that the manuscript lacks a lot of structure and detail. The methodology section in particular is difficult to follow and that sets the tone for the results and discussion section. While many of the comments I have are limited solely to clarity, I still suggest some major revisions to the manuscript are needed.


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 RELATIONSHIP BETWEEN SOCIAL RANK AND SPATIAL LEARNING IN PHEASANTS, PHASIANUS COLCHICUS: CAUSE OR CONSEQUENCE?
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is a nicely written study on the causal link between social rank and cognition in pheasants. I feel the authors nicely work towards their research question and propose a nice way of studying specifically the difference between cause and consequence in the relationship between social rank and cognition. I do, however, have some serious reservations about the study, especially regarding experimental design and the validity of the data (see below).

With regard to the introduction:
What I do not really understand is why they specifically choose a spatial learning task, as there is no real reason to assume a link between spatial memory/learning and social rank. Instead, I would have liked a task battery that gives us a more general idea of variation in cognition (which they did with the chicks), or if only one task a task that related more to social cognition (e.g. transitive inference). The authors seem aware of that themselves as they discuss this in l. 442, which raises the question why they nonetheless decide to do so. They mention that in a previous study (of themselves) they already did find a relationship between a spatial task and social rank, yet that in this study they could not differentiate cause from consequence. Given that though, I'm surprised that in this study they use a different experimental task (see l. 468).

The methods section lacks clarity: e.g. I think a picture/sketch of the apparatus/task would greatly benefit the readers' understanding of that task. Furthermore, the multitude of manipulations (2 or 4 females), conditions (SG vs. PD), backgrounds (tested as chick or not), and cohorts makes it very confusing, especially since the sample sizes across all this are not consistent. I suggest including a table in which, per individual everything is set out, with totals that then clearly show the sample sizes per performed tests.
Experimental design: The experimental design is very messy, which seems partly due to the fact that experimental designs of different studies are somehow intertwined. In fact, I would suggest publishing these two? studies as one.

For the current study, I, for example, don't see why animals are placed in differently sized groups in the PD condition, nor why they are placed in different cohorts. And if you choose to do the latter, the animals should have been placed in either cohort in a counterbalanced way with regard to whether they were tested as a chick or not. Consequently, ll. 203 - 206 make no sense to me.

ll. 217-223 are very confusing: What is the reason for taking these agonistic data towards females and not those towards males. Only later in the ms this becomes clear, but this needs to be explained already here, and a clear distinction should be made between data for calculating dominance rank and data for agonistic/self-aggrandizing behaviours.

Why were the animals from the different cohorts housed for different time periods in the PD condition before testing, and is this additional variable included in the analyses
Validity of the findings: I feel that the validity of the findings is harmed by the messy design, as it has created samples for some of the tests are really small. For example, the lack of consistency in spatial learning abilities between chick and adult is based on a spearman's correlation (where an Intra Class Correlation (ICC) would have been better) on only 6! individuals. Whereas the authors do mention this in their discussion, they nonetheless make strong conclusions based on this result (see conclusions and abstract), which they should tone down heavily.

Similarly, due to including the different group sizes in the PD condition, they increase the number of variables and thus decrease the power of their results, especially given the low sample size. The authors acknowledge this themselves and therefore do not include this variable in their GLMM's. Yet, subsequently they show that this manipulation has an effect on spatial learning and thus is a confound of the data used in the GLMM's. Consequently, the results of these GLMM's are not so easily interpreted; for example the interaction effect they find may be due to group size, if the higher ranking individuals have been randomly assigned to the larger group sizes. Again a table with all individuals, their rank, and the different manipulations may help us out here. Nevertheless, as it is a significant confound it should be included in the model.

Overall, given the debatable validity of their results the authors should tone down their conclusion and should especially be careful with generalizations; e.g. why doesn't the title mention that this is a study on pheasants, yet instead presents this as an overall study.
Additional comments: Some minor comments:

please provide latin names of species in intro.

l. 123-124. How well do the dominance ranks calculated form captivity represent what is happening / happened prior to that in the wild?

Methods section: it is ad libitum and not ad libertum

l. 255 .....approaching the APPARATUS while.....

l. 428 given that we don't know what these animals' social rank in the wild was, I would prefer it if you mention ESTIMATED rank here.


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 RELATIONSHIP BETWEEN SOCIAL RANK AND SPATIAL LEARNING IN PHEASANTS, PHASIANUS COLCHICUS: CAUSE OR CONSEQUENCE?
Review round: 1
Reviewer: 3

Output:
Basic reporting: The data files provided appear to be complete, although there is no description of variable names (ie. there is no READMe file) to assist in interpreting their data.

There is some awkwardness in the language, such as in lines 49-50 (“the stress experienced”), and line 184. The manuscript is generally very well written, although there are several mis-placed commas (eg. lines 22, 223, 384, 398).

Please provide the latin name for all species listed.

I found some sections to be quite confusing. For example, line 56 describes “several mechanisms", but it is not clear what those mechanisms are in the following sentences. In lines 80-82, an example of this statement would be helpful for the reader.

There is excellent justification in the Introduction for the Social state-dependent hypothesis (lines 54-82) but very limited justification for the prior attributes hypothesis. Please expand on this area (lines 84-94). I would also suggest expanding the first paragraph to better place the study in the field; the current opening paragraph is brief and provides limited context. Why would you expect spatial cognition, specifically, to be linked to dominance rank?

Please provide a citation at the end of line 118.

There are no citations in reference to the cognitive test. Is there any validity that this is actually a test for spatial cognition? Have others used an apparatus like the one used in this study? A figure of the apparatus would also be helpful. It is unclear why there are parentheses around “top” and “bottom” in lines 173 and 174.

The description of the adult social conditions (lines 201-210) is very confusing, when all that needs to be described is that adult males were placed in one of two cohorts, which experienced the social group treatments in reverse order.

The behaviours described in the ethogram in Table 1 actually describes two behaviours (eg. “threat/lunge” describes both “threat/lunge” and “flee/avoid”). However, threat or lunging behaviour can occur independently of fleeing or avoiding.
Experimental design: I am concerned as to why lateral struts exhibited in the PD condition were considered a dominance behaviour. Lateral struts can be used in multiple contexts to convey different signals. For example, when directed toward males, it may be a display indicating quality and thus strength (and potential to win in a fight), whereas it would display quality as a mate when directed toward females. Please address this concern with citations from the literature. Is this different from sexual behaviours mentioned in the methods (line 333)?

While many aspects of the statistical analyses are quite thoroughly described, it is unclear how the data specifically were incorporated into quantifying social rank. Were all behaviours described in Tables 1 and 2 included? Also, please elaborate on the equations described in lines 286 and 289. What do b0 and b1 represent?

Were observations in the PD condition randomized or was there any pattern to the observation periods (line 237)?

Please provide additional information on where/how the pheasant chicks were obtained (line 150). If they were hatched in the wild or in captivity could lead to different cognitive development and abilities.

How did you know the adults caught were 10 months of age, and not 22 months of age (line 160)?

Cohort 2 experienced the PD condition for twice as long as cohort 1. Given the effects of the PD condition, particularly on the results to the cognitive test, was there any effect of this difference? Please address.
Validity of the findings: no comment.
Additional comments: In this study, the authors assess the relationship between performance in a cognitive task in chicks and adults and their social rank in male pheasants. This study is well placed in the literature and appears to be the only study comparing two previously established hypotheses (the ‘Social state-dependent hypothesis’ and the ‘prior attributes hypothesis’). The authors do an excellent job of describing the hypotheses, how their research question and methods relate to each of the hypotheses and predicted outcomes, and where their results sit in the current literature. Although they had a limited sample size (n= 6, 8 and 8 for each of the research questions), they acknowledge this limitation and speculate appropriately in the discussion. As aggression is a highly plastic trait, the have provided new insight into how the social environment shapes cognitive performance.


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 RELATIONSHIP BETWEEN SOCIAL RANK AND SPATIAL LEARNING IN PHEASANTS, PHASIANUS COLCHICUS: CAUSE OR CONSEQUENCE?
Review round: 2
Reviewer: 1

Output:
Basic reporting: Literature references still need very minor formatting, as do two of the figures presented. Otherwise, I find the general structure and reporting of the manuscript well presented.

Below are the relevant comments for each corresponding section on the tracked manuscript:

Introduction:
1.L64-67: This is difficult to follow. In the first sentence (L64) you write that social rank is a consequence of cognitive abilities; while in the second one (L66) you say it is because of differences in dominance abilities. Can this be all incorporated into one idea? For instance, dominance abilities require certain cognitive abilities as you suggest below.
2.L147: “Motivation” is wrongly used here. In the example you cite, (Drea & Wallen, 1999) subordinate animals had a poor task performance when tested in a group because the presence of a dominant increased the chances of aggression, so they “played dumb” likely to avoid aggression not necessarily because they were unmotivated. Perhaps change motivation to something along the lines of social risk?
3.L215: Missing a word. It should read: “The ability to discriminate….”
4.L279: Typo in the word “conditions”.

References:
1. References still need a bit of formatting. Some of them provide the DOI; others have the phrase “Retrieved from”; and others have neither. In L891, the journal name is abbreviated. Is this correct?

Figures:
1.Figure 1. This figure nicely illustrates how you conducted each experiment in each state. Two points: (1) The caption should include a reference for the opaque colouring of males in the PD conditions; (2) in the manuscript you mention that you were able to reliably test 6 known males (L400) of cohort II, but in the figure, you have only 5 males. Is this correct?
2.Figure 3. Shows only a blue line.
Experimental design: No comments
Validity of the findings: I believe the authors followed the comments and suggestions from both reviewers satisfactorily and now present a much more robust statistical analysis and results. There are some points that remain unclear, albeit, these are relatively minor comments that should not change the overall results. The new discussion is a lot more developed than before and is linked much more nicely to the original questions and the corresponding results.

Below are the comments for each corresponding section on the tracked manuscript:

Methods:
1.L327: Were differences in the testing time controlled for in the analysis? Participation may have been determined by satiation (i.e. they were hungrier in the morning tests compared to the afternoon ones).  If they were equally likely to participate regardless of the testing time then perhaps a couple of lines (or numeric data) mentioning this would be good.
2.L330: I think you have to be very explicit here that spatial learning was only assessed in the PD condition because, at this point, it is still unclear whether you test animals in both SG and PD. Perhaps a sentence after you present both conditions could incorporate this (e.g. L384-385).
3.L453-454: I understand the difficulties in testing the same animals repeatedly both, as chicks and adults, and believe you have successfully justified your sample size; however, I am concerned you technically have a sample size of 1 individual in cohort I for the analysis that compares X & Y with the adult mean Elo-rating. Can you be sure the differences in cohort did not affect the social rank acquisition?

Discussion & Conclusions
1. I wonder if there is much point in reporting the results associated with the number of females in the PD condition if they are part of another study. You repeatedly mention a significant relationship between the number of females in this condition and task performance, but what is then its relation to your initial questions regarding social rank?  At the moment it is not very clear to me where this fits in the general findings and discussion of the manuscript.
2.L485. Very minor comment. Since your conclusion is basically that chick performance does not determine social rank or adult task performance, I think you have to be clear that you are talking about a relatively recent past social environment.  Otherwise, readers might interpret this as a carryover effect from a young age, rather than differences experienced as adults.
Additional comments: I very much enjoyed reading this new manuscript. I think you incorporated all of the comments nicely and made the whole text a lot clearer and concise. Having those extra details really made the experiment and the initial ideas stand out.


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 RELATIONSHIP BETWEEN SOCIAL RANK AND SPATIAL LEARNING IN PHEASANTS, PHASIANUS COLCHICUS: CAUSE OR CONSEQUENCE?
Review round: 2
Reviewer: 2

Output:
Basic reporting: n.a.
Experimental design: n.a.
Validity of the findings: n.a.
Additional comments: I Think the authors have done a nice job revising their manuscript and dealing with my comments. I have only some minor comments left:

l. 128 & 1126. Please say long-tailed macaque

l. 182. I don’t see how this is relevant for this study; i.e. studying the causal link between rank and cognition. The subordinates clearly posses the ability, yet inhibit it when a dominant is present to avoid competition over the food to be gained from the task.

l. 450 ff. why did the author’s not counterbalance the place of reward over the birds? And did the authors control for olfactory cues?

l. 638. you just said only 8 adult individuals participated reliably, why then now suddenly an n of 9. Similarly, you mentioned before that only 7 of the known individual’s completed all trials as a chick and that looking at the first 20 trials only increased your sample with 1, leading again to a sample size of 8 and not 9. See also line 656

 l. 652. This does not correspond to fig 1. where it says that only 5 of the known individuals cognitive performance was essayed.

l. 868. This sentence needs to be reformulated making clear that the manipulation of social rank is a control for the set-up, as to avoid immediate effects of rank within a group.


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: TOXICITY OF MELALEUCA ALTERNIFOLIA ESSENTIAL OIL TO THE MITOCHONDRION AND NAD+/NADH DEHYDROGENASE IN TRIBOLIUM CONFUSUM
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript deals with the potential discovery of the essential oil (EO) modes of action in insects. However, the literature references do mirrow the work done by the authors and not necessarily the classical references with robust background to support the author´s ideas!

There are also several efforts to be applied in the figures in order to increase the readers comprehension. For instance, the panel A in figure 1 is overloaded with unneeded informations and panel B in this figure contains innapropiated (i.e., green and red) collors for reades that suffer of daltonism (or collor blindness). The same patters can also be detected in Figure 4 (information overload) and Figure 5 (collor blindness).
Experimental design: It seems like that these manuscript is a kind of follow up for the authors previous experiments. They only change the insect especies and conducted similar experiments done with other insects. They left it clearly in the first sentence in the abstract.
Validity of the findings: The findings described are indeed relevant and will be of great help for the PeerJ readers. However, the authors needs to reorganize the sifnificance level of their findings. For instance, the discussion sentence in their abstract is not not totally proved in their experiments. I mean, their results do not allow them to conclude that NAD+/NADH dehydrogenase may be the prime target site of ALL essential oils in insects. This conclusion would only be possible if they had conducted such experiments with much more insect species and with definitively many other essetial oil types.

For instance, the sentece in the lines 288-290 might not be completely true if someone use the concerns raised in Robetson et al. 2007 (Robertson JL, Savin NE, Russell RM, Preisler HK (2007) Bioassays with Arthropods, Second Edition -, Second edition. Taylor & Francis Group, Boca Raton, FL). To me, these insects' susceptibilities to this EO is the same! The authors need to show the Susceptibility Ratio (SR, described by Robertson et al. 2007) in order to write something like that!
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: TOXICITY OF MELALEUCA ALTERNIFOLIA ESSENTIAL OIL TO THE MITOCHONDRION AND NAD+/NADH DEHYDROGENASE IN TRIBOLIUM CONFUSUM
Review round: 1
Reviewer: 2

Output:
Basic reporting: The text will greatly benefit from language editing, The discussed  ideas and findings need to be clearly and concisely reported. Prior Literature needs to be appropritely referenced.
Experimental design: In order to be reproducible, details are still lacking in the method section
Validity of the findings: The findings and the data should be better analyzed and argumented to support the conclusions.
Additional comments: The ms is one of a serie of papers by the same group dealing with the essential oils and their major components ( especifically Melaleuca alternifolia and terpinen-4-ol) and their mode of action in insects.
The authors used a range of methods including toxicological bioassays, microscopy and omics to investigate the insecticidal effects of EOs.
Altough of actual importance, the ms suffers from many flaws and  needs a lot of improvements to be published. I have conserns about the methodology, the discussion and the interpretation of the findings.
Below are some comments to be considered by the authros:

Introduction

Lines 56-61:  from “EO” to “essential oil” , this section could be moved to the start of the paragraph in the line 43.
Line 74: delete  “Progeny of the maize weevil, Sitophilus zeamais, is affected by parental exposure to clove and cinnamon essential oils” and correct the reference it seems duplicated!!!
Lines 78-79: what do authors mean with “while focusing on the standardization of natural insecticides”?? In this ms no standardization was performed!!!!.. Rephrase…

Materials and Methods

Lines 98-99 : please provide more details on how insects of the same age were separated.
Lines 100-110: The toxicity bioassay is not well described… how many concentrations were used to determine the LC50? And how these concentrations were determined?  Did the authors use the same protocol to evaluate the toxicity of single components of the EO described in figure 1c?
Line 118: delete “ was”
RNA sequencing: what were the depth / coverage of the sequencing?
Line 133: delete [33] !!
Line 134: delete “.” before the reference.
Line 135: explain the FPKM at first citation!!!
Line 137: the DOI seems to be invalid.. Please check it out!!!
Line 141: correct to “differentially”

In the result section, there are results of the transmission electron microscopy but no corresponding protocol is described in the M&M section!!!

Line 180: the reference is not the best to use!!! … Please use the original reference describing the Probit analysis for LCs determination!!!

Results

Throughout the results section, the authors have been discussing various findings instead of only reporting them!!! See lines 187; 194; 200-204; 212-213; 276-281…

Lines 192- 193 delete from “For the same…
Line 198: invert the order of the α-terpinene and γ-terpinene to correspond to the LC50s!!!
Lines 226-230: From “ namely.. to database”, this part is only repeating what was described in the M&M section!!! Better delete..

Discussion

-	The ultra-structural alteration in the mitochondria should be taken carefully, firstly because the authors did not indicate the time after exposure of the sample used and secondly these alterations could be a result of the direct action of the EO on the respiratory process as well as subsequent result of the death process caused by the action of the EO on different metabolic targets. Furthermore, the authors do not discuss or argument over the changes in the NAD + and NADH found in the control along the 72 hrs of evaluation. In addition, the results of the RNAseq showed that beside the genes related to the mitochondrial respiratory chain, over 2000 genes have been found to be differentially expressed including various genes related to xenobiotic detoxification processes!!! Taking in consideration that the sequencing was done 72 hours after the exposure, it is quite difficult to conclude that the alterations found are directly linked with the action of the EO on the mitochondrial respiratory chain ( specifically and solely).  On the light of the above, the hypothesis that NAD+/NADH dehydrogenase is the prime target site of EOs in insects still needs stronger arguments and thorough discussion.

-	The authors did not discuss the fact that two main components: Terpinen-4-ol and α-terpineol were more toxic (smaller LC50s) than the essential oil itself.

Line 289: correct to 24 h

References

-	All the scientific names have to be in italic
-	Some references are duplicated: see Li et al., 2013 and Liao et al.,2016.
-	Lines 45- 47: references needed to support your
-	Line 47-49:  the following references may be included
Silva et al., 2017 : “Progeny of the maize weevil, Sitophilus zeamais, is affected by parental exposure to clove and cinnamon essential oils”
 Haddi et al., 2015 :  “Sublethal exposure to clove and cinnamon essential oils induces hormetic-like responses and disturbs behavioral and respiratory responses in Sitophilus zeamais”


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: TOXICITY OF MELALEUCA ALTERNIFOLIA ESSENTIAL OIL TO THE MITOCHONDRION AND NAD+/NADH DEHYDROGENASE IN TRIBOLIUM CONFUSUM
Review round: 2
Reviewer: 1

Output:
Basic reporting: That manuscript increase the scientific quality with the efforts done by the authors!
Experimental design: thais OK now!
Validity of the findings: it is fine and better adjusted now!
Additional comments: I would only strongly recommend some more efforts on the figures. Please, organize the figures 1, 3 and 5 in away that they can increase the font size of the "X" and "Y" axis. Maybe the authors may try to organize these multipanel figures in the vertical stile (suggestion: try to create the figures in a way that they will not exceed the 8.9 cm wide)


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: TOXICITY OF MELALEUCA ALTERNIFOLIA ESSENTIAL OIL TO THE MITOCHONDRION AND NAD+/NADH DEHYDROGENASE IN TRIBOLIUM CONFUSUM
Review round: 2
Reviewer: 2

Output:
Basic reporting: the structure of the ms improved and is meeting the standard of PeerJ .
Experimental design: The experimental design is suitable and allow to collect valid results.
Validity of the findings: Findings are sounds and support the conclusions made.
Additional comments: The authors took in consideration all the comments from the previous round of reviewing and the quality of their manuscript dramatically improved.
I do beleive that the findings here presented will be of great interest of the PeerJ readers. Hence I recomend the publication of this manuscript in its actual from.


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: CMTCN: A WEB TOOL FOR INVESTIGATING CANCER-SPECIFIC MICRORNA AND TRANSCRIPTION FACTOR CO-REGULATORY NETWORKS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The resources gathered by the authors is highly valuable. The authors should make available to download in a human and/or computer readable format (delimited text file such as csv, tsv or SIF and perhaps, though less important, an XML based format such as SBML):
1. the currently analyzed network
2. the set of resources used
Experimental design: Overall, methods are insufficiently described.

It is unclear how the network associated with a specific disease is built. In particular, the refinement step is not described. One can suppose it is done by removing any mir->gene or tf->gene edge that has a Pearson correlation of 20% or less or a correlation p-value above 5%, but this needs to be clearly stated.

Are positive correlation between miRNA and genes or TFs simply discarded?

For usability purposes, the authors limit by default the number of visible co-regulatory pairs. How are these ordered to only show 100 by default?

Identifying genes associated with drug-response is not a trivial task. The tool proposes an input list containing such genes. How were these gene sets defined? To what drug are they associated?
Validity of the findings: How are TF dealt with when these are among the input gene list? Are they considered only as TF? Could it be possible to add co-regulatory pairs and FFL with TFs as target genes?

Gene enrichment and network motifs are valuable resources. However, listing hundreds of motifs can make the analysis difficult. It would be interesting to prioritize TF and miRNAs based on the number of co-regulatory pairs it appears in, as well as to order the mirna TF pairs by the number of motifs in which they both appear in. One of the values of CMTCN is the possibility to see how TF-miRNA co-regulatory interactions are disrupted in a particular disease. Therefore, it would greatly help to be able to analyze the most relevant pairs first. As for now, scrolling through a table with hundreds to thousands of entries is too tedious for this type of analysis.

The knowledgebases column in the co-regulatory interactions table should be split in two, one for TF and one for miRNA DB.

It is important to differentiate positive and negative regulation of TF. For instance, TF-FFL with a positive or negative regulation of a miRNA has broadly different biological implications.
Additional comments: The authors propose a novel aggregated resources for TF and miRNA gene regulation as well as an efficient online application to analyze cancer-specific networks. The app is well designed, easy to use and fairly reactive. The analysis of the co-regulation between TF and miRNA is an interesting approach and the proposed app greatly facilitates its analysis in a context-specific manner.


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: CMTCN: A WEB TOOL FOR INVESTIGATING CANCER-SPECIFIC MICRORNA AND TRANSCRIPTION FACTOR CO-REGULATORY NETWORKS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is well written and uses clear unambiguous language. There are a few cases were it seems that a wrong word was used, e.g.

Line 26: “the disorder of gene expression regulation systems has concerned closely with disease” should probably be something like “the disorder of gene expression regulation systems is closely associated with diseases.”

Line 146: “prevailing web browsers” - probably means “prevalent web browsers”.
Experimental design: It should be made clear which version of each database is currently used. I suggest adding a separate tab where the sources are listed with source URL and date of download.

Similarly, it is not clear from where the TCGA data was obtained (source, date of download). It should also be made clear how these data were processed. This information should be added to both the web application as well as the manuscript.

In the methods section (line 120) it is not explained how TCGA data is actually used to refine co-regulatory interactions. Only when using the application does it become clear that correlation thresholds (and corresponding p-values) are used.

CMTCN considers only pairwise correlation between TFs, miRNAs and genes. However, in triplets partial correlation could be used to isolate the contribution of a specific regulator. This should be briefly discussed.

In the methods section, it should be explained how exactly survival-relevant, drug response related and top mutated genes have been identified.
Validity of the findings: No comment
Additional comments: With CMTCN, Li et al present a shiny-based web application that allows its users to study TF-miRNA co-regulatory pairs and feed-forward-loops for 33 cancer types. The web application is well designed and intuitive. It is well documented and provides all functionality I would expect from such an application. During my testing I did not find any issues or bugs. The web application is certainly a useful feature for cancer researchers.

The only issue I have is that the web application does not clearly indicate when it is processing data in the background. Such background data processing could be indicated to the user with an overlay, for instance, also to avoid that the users just continues clicking on other things.

I strongly recommend the authors make the code for their web application available via github or a similar code repository.


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: CMTCN: A WEB TOOL FOR INVESTIGATING CANCER-SPECIFIC MICRORNA AND TRANSCRIPTION FACTOR CO-REGULATORY NETWORKS
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors answered to all the comments that were raised.


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: CMTCN: A WEB TOOL FOR INVESTIGATING CANCER-SPECIFIC MICRORNA AND TRANSCRIPTION FACTOR CO-REGULATORY NETWORKS
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors have addressed all of my previous 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: A DIVERGENCE BETWEEN UNDERLYING AND FINAL CAUSES OF DEATH IN SELECTED CONDITIONS: AN ANALYSIS OF DEATH REGISTRIES IN PERU
Review round: 1
Reviewer: 1

Output:
Basic reporting: Some English language editing necessary throughout. For example in abstract:  “the 53.9% was men.” is not grammatical.  Likewise in line 90: “Two were the variables of interest”, and line 172 “evidence lacks in Peru”, etc.

Line 208: Should be "sensitivity" analysis.
Experimental design: The study is observational, so there is no experimental design.  Nonetheless, representativeness and data quality are issues that deserve some discussion.

There is no mention of coverage of the death certificates for the population of Peru.  77,000 deaths in a country of 30 million people would be a death rate of a quarter of a percent in a year.  The correct death rate is approximately 6 per 1000 per year, making the data in this study equal to about half of expected deaths.   Where are the 50% of the deaths?
Also no mention of the quality of the death certificates, number of certificates with incomplete or impossible fields, etc.
Validity of the findings: The authors excluded many deaths if the final cause of death was the same as the underlying cause of death, which is worrisome.  For example, breast cancer could not be both an underlying and acute cause of death.  This is not justified by the authors, nor explained in any way.  They promise a flowchart showing the number of these exclusions in a supplementary figure, but I could not find this figure.

Line 95:  Final causes of death were defined as “communicable, cardiovascular (CVDs) and neoplasms”.  I don’t understand what happens to external causes of death (e.g. accident, homicide, suicide, overdose, etc).
Additional comments: The authors note the importance of mortality statistics in international comparisons, as a broad indicator of health, social policy and medical systems.  They study the underlying-final cause of death pattern in one LMIC (Peru).

The abstract states “The underlying-final cause of death pattern has not been explored at the country level” but this statement is not true in general, only true of Peru.  In rich countries this is not an unusual analysis. Even globally, while it seems that no paper has specifically targeted Peru, many papers using the WHO mortality database do include Peru data (e.g. PMID 29717336), and many papers focus on other LMICs in the region (e.g. PMID 22124693) or in specific cities in the region (e.g. PMID 21986787).

Background:  The authors discuss underlying versus acute causes of death as registered on death certificates, but they do not cite a large literature on this topic, for example, discussing the methods by which underlying causes are inferred (PMID 27127419, 29060620, 27994280) or the historical evolution of these conventions and their intended interpretations (e.g. Jentzen JM Death Investigation in America. Harvard, 2009).

Discussion:  The authors conclude that there is a divergent profile between underlying and final causes of death.  It is implied that this is somehow unusual, but the is little justification provided to suggest that this is a novel or informative observation.  Is the same pattern common in rich countries, or in other LMICs in which it has been examined?   The authors do mention a few specific examples, such as a study of diabetes in Mexico, COPD in Spain, and kidney disease in Canada, but no general principles regarding the relations between underlying and acute causes.

For example, that people with chronic illnesses often die of pneumonia, sepsis, hospital acquired infections or other communicable cause is hardly surprising.  It does not seem to relate to the epidemiologic transition, as suggested by the authors.  Rather it seems to be a natural consequence of reduced immunity, exposure to hospitals, bedsores, injections, etc.

Public health and clinical relevance:  The authors note a divergence between the underlying and final cause of death as the primary insight, but at least some of this was iatrogenic, since they purposefully deleted many observations if these fields matched.

The authors seem to find that the significance of this analysis is to reinforce the concept that a non-communicable disease is not the only possible complication over an underlying non-communicable condition.  I can’t imagine that any clinician ever thought otherwise.  For example, about a quarter of all Alzheimer’s patients die acutely of a respiratory infection (PMID: 27192207).  This pattern is therefore of no particular surprise.


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: A DIVERGENCE BETWEEN UNDERLYING AND FINAL CAUSES OF DEATH IN SELECTED CONDITIONS: AN ANALYSIS OF DEATH REGISTRIES IN PERU
Review round: 1
Reviewer: 2

Output:
Basic reporting: Basic Reporting
1.	The main argument for the importance of this study is the differentiation of final vs underlying causes of death. The authors make three points in the introduction, related to the public health, clinical and epidemiological transition relevance of this differentiation. While the clinical and epidemiological transition ones are well explained, I fail to understand the public health argument: “For example, whether a patient with type 2 diabetes is likely to finally perish of a coronary event or sepsis, could guide what information should be provided to these patients. Information could thus target prevention of non-communicable diseases, communicable disease, or both”. How is this a public health argument, when it relates to patients and information? If this is a clinical argument, then this paragraph should be reworded to avoid this confusion.
2.	Moreover, and related to comment #1 above, the authors need to define how “final” and “underlying” causes of death are defined in death certificates and what are the instructions for professionals filling them.
3.	The English language should be improved to ensure that an international audience can clearly understand the text. A few examples from the abstract: the second sentence is missing a word (or ultimately should be replaced with other word); the second sentence of results is odd (“the 53.9% was men”); the last sentence of the results section gives the impression that COPD, CKD, cancer and diabetes are all communicable diseases.
4.	The sensitivity analysis lacks detail. How are the GBD categorizations different? It is hard to interpret the meaning of this analysis without knowing the difference between the author’s and GBD’s categorization.
5.	The Sankey diagram of Figure 1 is quite hard to read and interpret. “All deaths” is smaller than any of its subcomponents, which are then similar in size to the third level. The authors detail that they have used proportions, but the figure is deceptive by not using a height that is proportional to the number of deaths across columns. It is also unclear (just from looking at the figure) that the middle ones are final causes of death and the right ones are underlying causes, so an horizontal axis would help (although this is included in the footnote).
6.	Table 1: what is the meaning of the N=<number> rows? Are these the number of unique final causes of death? In that case, this should be made explicit. Moreover, table 1 could contain more information to be more useful. For example, by looking at table 1 it’s hard to see the contribution of each final cause of death to the OVERALL amount of deaths in each underlying cause. See for example Cancer (final?) and diabetes (underlying?). There are 3 unique final causes of death, but it’s hard to see in the table whether cancer makes up a sizable amount of the deaths with diabetes as an underlying cause. It’d be more informative if the N=<number of unique causes?> was replaced with the proportion of deaths in each large group of final causes. Even better, it’d be good if the authors showed raw numbers and overall proportions, so that the proportion of “Malignant neoplasm of gallbladder” is actually the % of deaths with diabetes as underlying with that cancer as the final cause of death.
7.	The first reference (Fitzmaurice 2018) refers only to cancer burden. I suggest the authors reference the general GBD papers instead of the cancer specific ones.
Experimental design: Experimental Design
8.	The authors mention underreporting briefly, but according to the Peruvian ministry of health (http://bvs.minsa.gob.pe/local/minsa/2722.pdf), PAHO (http://iris.paho.org/xmlui/bitstream/handle/123456789/34329/CoreIndicators2017_eng.pdf?sequence=1&isAllowed=y), and others (https://www.ssc.wisc.edu/cdha/latinmortality/) this happens in around 40-43% of the deaths, with some Departamentos (such as Loreto) having around 80% of under-reported deaths. The authors need to devote some time to explaining how this underreporting may affect their results. For example, if this underreporting is differential by age or sex, then some final causes of death may be more underreported than others. Or, if areas with more underreporting have a higher degree of communicable diseases, then results may be biased.
9.	The authors do not justify their selection of deaths in people aged 18 or above. My guess is that this is because they have chosen deaths uncommon in children, but this should be made explicit.
10.	The authors exclude cardiac arrest deaths (coded as a final cause), which are coded as garbage codes by GBD. The authors do not also detail what was done with other garbage codes as defined by GBD (such as R codes). Are these just excluded? Some of them have been included (like “unspecified sepsis” or “unspecified heart failure”), but it is unclear what criteria was used for this.
11.	It is unclear why authors exclude deaths with missing location of death (see Supplementary Figure 1). Moreover, does this refer to the district (geographical location) or type of institution (like hospital vs home)?.
Validity of the findings: Validity of Findings
12.	My main concern with the validity of the findings is that the authors stress that this shows that Peru is in a different stage of the epidemiologic transition, but offer no evidence to compare Peru with other countries in this part of the manuscript. How is this “divergence” different in other countries? Are the distributions of final causes of death different by underlying cause in other countries?  In fact, the authors compare the specific results of diabetes to Mexico and show that their results are similar, and some of the results in USA/Canada/Spain are similar too. I think the authors need to do a more systematic comparison here
13.	My second comment on validity is related to the first: isn’t this divergence between final and underlying causes of death occurring by design? Since the authors do not devote much time to the conceptual difference between them it’s hard to see if this is an expected outcome.
14.	My third comment on validity is related to comment (2) in basic reporting above: are instructions to fill final/underlying causes of death the same in Peru as compared to other countries? If instructions are different, then these results may be the result of measurement differences and not differneces in underlying public health. An internal comparison in Peru over time may be more interesting in this case.
Additional comments: PeerJ-30352
Title: A divergence between underlying and final causes of death in selected conditions: An analysis of death registries in Peru

This study leverages the reporting of final and underlying causes of death in mortality registries in Peru, in order to understand what final causes of death were most common among 9 selected underlying causes of death. The study seems interesting for people interested in understanding the burden of disease using death records. However, I believe the authors need to improve the reporting of the study and work on changing unsubstantiated claims that are not related to the study findings. Comments are structured in basic reporting, experimental design, and validity of findings.


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: A DIVERGENCE BETWEEN UNDERLYING AND FINAL CAUSES OF DEATH IN SELECTED CONDITIONS: AN ANALYSIS OF DEATH REGISTRIES IN PERU
Review round: 2
Reviewer: 1

Output:
Basic reporting: The English language in the revised submission is adequate.  Basic reporting issues seem sound.
Experimental design: no experimental design (not applicable)
Validity of the findings: I still question the utility of the findings given the underreporting of deaths, and there is no quantitative attempt in the paper to confront the potential bias if these are differentially unreported, as seems likely (by region, by cause, by social factors, etc).  But the authors have at least been transparent about this concern.
Additional comments: Building capacity for demographic surveillance in Peru is an important goal.  Building reporting systems will probably be necessary before real improvements in data quality can be realized, but this at least is a first step.


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: EVALUATION OF 17 MICROSATELLITE MARKERS FOR PARENTAGE TESTING AND INDIVIDUAL IDENTIFICATION OF DOMESTIC YAK (BOS GRUNNIENS)
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: I recommended minor revisions for the manuscript because the abstract is too long, I suggest that the authors reduce the description at lines 31- 38. Indeed, by the excellent quality I consider that the manuscript could be accepted in the current form.

Manuscript Peerj 22873 “Validation of 17 microsatellite markers for parentage testing and individual identification in domestic yak (Bos grunniens)”
The manuscript is clearly written in professional, unambiguous language. The supplemental files are clear and will be useful to future readers.
The most important issue is a set of 17 microsatellite markers with a high variability that could potentially be used in individual genotyping, parentage verification, and individual identification in domestic yak (Bos grunniens).
The abstract is too long, I suggest that you reduce the description at lines 31- 38 and to provide essential item for your study.
I commend the authors for this important research that could be useful for future biodiversity studies in domestic yak (Bos grunniens).


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: EVALUATION OF 17 MICROSATELLITE MARKERS FOR PARENTAGE TESTING AND INDIVIDUAL IDENTIFICATION OF DOMESTIC YAK (BOS GRUNNIENS)
Review round: 1
Reviewer: 2

Output:
Basic reporting: The study by Pei et al. proposes a state-of-the-art genotyping methodology for the problem of parentage confirmation and individual identification in yak. The study has novelty and relevance in the field of animal breeding and conservation.
Although this study has scientific merit, the manuscript suffers from poor scientific writing, and general presentation and organization. I recommend that the report is thoroughly rewritten and revised by a proficient English speaker who is also an experienced author in the field of population and forensic genetics.
A lot of attention to detail needs to be invested in this report. I am afraid that all has to be revised, from the keywords to the tables’ and figures’ legends. I am under the impression that the authors have insufficient experience in presenting scientific reports and must seek assistance to upgrade this manuscript. The vast amount of improvement that it demands at this point is beyond the scope of my responsibilities as a reviewer. However, I believe that a fresh rewrite, focus and organization can bring the study up to the standards of a scientific report for publication in an international journal such as PeerJ.
In its present form, I cannot recommend it for acceptance without major revision.
Experimental design: No comment. See above.
Validity of the findings: No comment. See above.
Additional comments: No comment. 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: EVALUATION OF 17 MICROSATELLITE MARKERS FOR PARENTAGE TESTING AND INDIVIDUAL IDENTIFICATION OF DOMESTIC YAK (BOS GRUNNIENS)
Review round: 1
Reviewer: 3

Output:
Basic reporting: This MS characterizes a set of 17 microsatellite loci previously used in cattle. The paper reads well and the cited literature suffices. All the most important information is supplied in the main body of the paper and as supplementary material.
Experimental design: Several families - father, mother, ofspring - as well as half-sibs should have been included in the sample panel. At least a small justification on this omission should be given.
Validity of the findings: The large sample size assures a higher accuracy of the obtained summary statistics. None of the final set showed significant frequency of null-alleles, deviations from HWE expectations or was in linkage disequilibrium.
Additional comments: This work reports a complete and almost flawless characterization of a set of microsatellites for parental testing in the yak. The minor weakness of this paper is the lack of known families and half-sibs in the sample panel. The inclusion of these samples would permit not only to verify the allele segregation as well as experimentally test the robustness of the estimated probabilities of parental exclusions.

Nonetheless, this is a clean and straightforward note that is worthy of publication.


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: EVALUATION OF 17 MICROSATELLITE MARKERS FOR PARENTAGE TESTING AND INDIVIDUAL IDENTIFICATION OF DOMESTIC YAK (BOS GRUNNIENS)
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript is written in professional, unambiguous language. The article includes sufficient introduction and background, and literature is appropriately referenced. The structure of the article is conformed to an acceptable format.
Experimental design: The investigation was conducted rigorously and to a high technical standard. Methods are described with sufficient information to be reproducible by another investigator.
Validity of the findings: The data are robust, and conclusions are appropriately stated
Additional comments: This important research providing a resource for the genetic improvement of domestic yak and could be useful for future studies of yak population structure, history, and biodiversity. I consider that the manuscript Peerj 22873 could be accepted in the current form.


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: EVALUATION OF 17 MICROSATELLITE MARKERS FOR PARENTAGE TESTING AND INDIVIDUAL IDENTIFICATION OF DOMESTIC YAK (BOS GRUNNIENS)
Review round: 2
Reviewer: 2

Output:
Basic reporting: This new version of the study has greatly improved, and the authors invested in corrections according to the reviews. I am particularly impressed by the editor's generosity in guiding the authors in this task.
However, the presentation of this work is still substandard, and further improvement is necessary to warrant acceptance for publication in PeerJ.
Again, I strongly suggest that the manuscript should be reviewed by an English-speaking geneticist.

(see comments to authors)
Experimental design: Acceptable.
Validity of the findings: Needs improvement (see comments to authors).
Additional comments: ABSTRACT

Methods
“A standardized set of microsatellite loci was assessed and applied in the parentage testing and individual identification of yak.”
This introductory phrase for the methods section of the abstract is redundant. The authors then proceed to describe the method they used, and finally say that 17 STRs were employed. Is the “standardized set of microsatellite loci” the 17 STR panel? The authors may also want to check what a standardized set of microsatellite loci means in the context of ID and parentage analyses (see e.g. van Asch et al. A new autosomal STR nineplex for canine identification and parentage testing. Electrophoresis 30(2):417-23. doi: 10.1002/elps.200800307).

Results
“These results indicated that this combination of 17 microsatellite markers could improve the efficiency, reliability, and utility of parentage testing and individual identification in yak.” Is this relative to another method that was already in use?

“Nevertheless, these loci [cattle] cannot be directly applied to yak identification because the two breeds have different genome sequences and
organization.” Cattle and yak belong to different bovid species and not breeds. Cattle are Bos Taurus and yak are Bos grunniens.

“Thus, this set of microsatellite loci are suitable for parentage/relatedness analysis in yak breeds.” This set of STRs worked for the population under study (polled yak), its use for other yak “breeds” must still be assessed.

Keywords Excessive number of keywords?

INTRODUCTION

Excessive number of references for facts that are not relevant for this particular study. Example: “The ability of yak to survive in such rugged natural environments is the result of numerous behavioral, physiological, and genetic adaptations (Barsila et al. 2014; Ding et al. 2015; Hu et al. 2012; Huang et al. 2012; Qiu et al. 2012; Wang et al. 2017b).”

“Although there are 18 yak breeds in China, only one (Datong) has been bred (Wu 2016). This phrase makes no sense to me, please clarify. Also, do the yak under study belong to the Datong breed?

“When yak graze, however, mating is very difficult to control. Semen samples could be erroneously mislabeled during preparation, and mating records might be confused because of clerical errors made during artificial insemination.” These two phrases are in contradiction. Do yak mate randomly, or is artificial insemination used?

“A highly informative set of DNA markers whose alleles can be easily scored is critical for effective paternity testing and individual identification.” This phrase is redundant.

“The present study aimed to develop and evaluate multiplex microsatellite systems that are specifically designed for polled yak parentage control and kinship analyses but that include microsatellite loci commonly used to characterize cattle genetic parameters.” Revise this phrase. According to the M&M, the authors tested mostly cattle STRs (and a few yak STRs) on polled yak, and selected an informative panel.

“The following 14 loci did not need adjustment” It’s not clear to me what adjustment means.

“Genomic DNA was extracted from white blood cells digested with proteinase K.” Did you isolate white blood cells from total blood? If not, you extracted DNA from the total blood.

“to identify repeat markers”. It’s not clear to me what this means. Do you mean that the PCR products were sequenced by Invitrogen?
“fluorescently labeled PCR products were identified by capillary electrophoresis”. Capillary electrophoresis does not identify PCR products, it separates them according to size.

“Using combinations of microsatellite markers can produce amplification fragments with high specificity, allowing a relatively cost-effective genotyping.” Unnecessary statement, everyone in the field is aware of the advantages of multiplexing.

“distinctive”: not an appropriate term in STR genotyping.

“within this subset of 17 loci.” Redundant information, it is mentioned in the previous phrase that this paragraph refers to the 17 STRs.

DISCUSSION

“On the other hand, clerical and insemination errors and stain disappearance may also influence pedigree error rates.” It is still not clear to me whether this polled yak is inseminated artificially or allowed to mate randomly. Also, it’s not clear to me what “stain disappearance”.

“the performance characteristics of a yak identification panel have not yet been distinguished”. Not clear what the authors mean by “distinguished”.

“This system uses the advancements made in DNA fragment analysis technology.” I disagree: multiplex PCR amplification with labelled primers and automatic detection of fragment size with capillary electrophoresis are standard genotyping methodology.

In my opinion, the discussion does not focus on the essential but diverges to compare STR vs SNP genotyping, the repeat structure of microsatellites (etc…), and fails to address the fundamental aspects of this work. The authors should compare their results with previous works performed on yak, and discuss the limitations of their approach (e.g. only polled yak were analysed, future developments…).

Table 1. The motif of the repeat for each loci is given (RM). How was this confirmed? The authors do not report sequencing of the alleles they have found in their sample population. If this is cattle data, it should be clarified. The authors used the yak genomic sequence to map the cattle loci, they should give the correspondent location in the yak, at least with regards to the chromosome.


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: EVALUATION OF 17 MICROSATELLITE MARKERS FOR PARENTAGE TESTING AND INDIVIDUAL IDENTIFICATION OF DOMESTIC YAK (BOS GRUNNIENS)
Review round: 3
Reviewer: 1

Output:
Basic reporting: Same comment to the previous review.
The manuscript is written in professional, unambiguous language. The article includes sufficient introduction and background, and literature is appropriately referenced. The structure of the article is conformed to an acceptable format.
Experimental design: Same comment to the previous review.
The investigation was conducted rigorously and to a high technical standard. Methods are described with sufficient information to be reproducible by another investigator.
Validity of the findings: Same comment to the previous review.
The data are robust, and conclusions are appropriately stated.
Additional comments: Same comment to the previous review.
This important research providing a resource for the genetic improvement of domestic yak and could be useful for future studies of yak population structure, history, and biodiversity. I consider that the manuscript Peerj 22873 could be accepted in the current form.


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: EVALUATION OF 17 MICROSATELLITE MARKERS FOR PARENTAGE TESTING AND INDIVIDUAL IDENTIFICATION OF DOMESTIC YAK (BOS GRUNNIENS)
Review round: 3
Reviewer: 2

Output:
Basic reporting: I appreciate the effort of the authors to produce a manuscript up to the standards of PeerJ. Although the manuscript is now more readable, this is not the case, and there is plenty of room for improvement. The authors have followed my suggestions, but I was disappointed to verify that they have failed to provide a deeply and self-critically revised, mature manuscript. As I stated in the comments of the previous version of this manuscript, ensuring adequate language editing and scientific writing style is beyond my responsibilities as a reviewer.
While strongly recommending that the authors use these suggestions to scan their manuscript for other opportunities for improvement, I’ll make a few comments (by no means comprehensive) as examples:

Line 41 – “The 17 loci obtained”. Loci were not obtained, they were selected from the literature and tested.
Line 42 – “Easy genotyping”. Do you mean unambiguous genotyping? “Easy” is not a scientific term.
Line 43 – “Parentage/relatedness analysis”. I have to disagree, you tested for individual identification and parentage (PE, PEI and PESI). Relatedness has a very different scope, and involves other types of kinship that you did not test for.
Line 88 – Phrase is redundant.
Line 101 – “Considered”: do you mean tested? You refer “Many studies” but you only cite two. “Relatedness identification”: please be precise on the kinship relationships that were tested in the works that you cite, if it was parentage testing and individual identification, it must be referred as so, not as relatedness.
For example, the phrase “Although many studies have considered the application of microsatellites in relatedness identification, including primary paternity testing in yak, most microsatellite loci and their primers were directly employed from a cattle reference (Li et al. 2013; Nguyen et al. 2005).” could be written as:
“Previous studies have reported microsatellite genotyping for individual identification and parentage testing in yak; however, these loci and their primers were originally developed for cattle, and used directly in yak (REFs).”
Line 99 – Eliminate “breeds”, you are improving on the transfer of cattle markers to yak, i.e. from one species to another species.
Line 101 – This paragraph needs total revision as it fails to provide a clear summary of the aim of your study. The last phrase belongs to the conclusions.
Line 113 – Replace “references” by the appropriated actual cattle references, as you did for (Li 2004).
Line 116 – What do you mean by low scores and high scores? Please be precise. There also seems to be a contraction because you say that most loci were not adapted to yak because of “low scores”, but you also say that the primers used to amplify BM1824 etc presented “high scores” and, therefore, were nor adjusted to yak. Does “adjusted” mean that you redesigned the primers based on the yak sequence?
Line 134 – It is common practice not to separate white blood cell from total blood before extraction of total DNA. Was there a reason for this separation? If yes, please explain.

Line 155 – It is not clear why you sequenced those loci, please explain. Loci were sequenced, therefore, sequences of these loci should be provided in Supplementary Material. Unidirectional sequencing may not be sufficient to survey the number of repeats and the flanking sequences correctly, due to slippage of DNAPol during the replication steps of PCR and sequencing reactions. Please discuss.

References
As I commented before, this manuscript presents a list of 49 references, which I consider excessive given the scope of this study and the depth of the discussion. Example in line 63: four references are presented supporting the significant contributions of yak to human life. I suggest that the authors decrease the number of references for introductory facts that add little to the focus of their work.

Table S1 – A column informing on the original literature refs should be included for the loci mined from previous works.
Experimental design: Please see comments on basic reporting.
Validity of the findings: Please see comments on basic reporting.
Additional comments: I appreciate the effort of the authors to produce a manuscript up to the standards of PeerJ. Although the manuscript is now more readable, this is not the case, and there is plenty of room for improvement. The authors have followed my suggestions, but I was disappointed to verify that they have failed to provide a deeply and self-critically revised, mature manuscript. As I stated in the comments of the previous version of this manuscript, ensuring adequate language editing and scientific writing style is beyond my responsibilities as a reviewer.
While strongly recommending that the authors use these suggestions to scan their manuscript for other opportunities for improvement, I’ll make a few comments (by no means comprehensive) as examples:

Line 41 – “The 17 loci obtained”. Loci were not obtained, they were selected from the literature and tested.
Line 42 – “Easy genotyping”. Do you mean unambiguous genotyping? “Easy” is not a scientific term.
Line 43 – “Parentage/relatedness analysis”. I have to disagree, you tested for individual identification and parentage (PE, PEI and PESI). Relatedness has a very different scope, and involves other types of kinship that you did not test for.
Line 88 – Phrase is redundant.
Line 101 – “Considered”: do you mean tested? You refer “Many studies” but you only cite two. “Relatedness identification”: please be precise on the kinship relationships that were tested in the works that you cite, if it was parentage testing and individual identification, it must be referred as so, not as relatedness.
For example, the phrase “Although many studies have considered the application of microsatellites in relatedness identification, including primary paternity testing in yak, most microsatellite loci and their primers were directly employed from a cattle reference (Li et al. 2013; Nguyen et al. 2005).” could be written as:
“Previous studies have reported microsatellite genotyping for individual identification and parentage testing in yak; however, these loci and their primers were originally developed for cattle, and used directly in yak (REFs).”
Line 99 – Eliminate “breeds”, you are improving on the transfer of cattle markers to yak, i.e. from one species to another species.
Line 101 – This paragraph needs total revision as it fails to provide a clear summary of the aim of your study. The last phrase belongs to the conclusions.
Line 113 – Replace “references” by the appropriated actual cattle references, as you did for (Li 2004).
Line 116 – What do you mean by low scores and high scores? Please be precise. There also seems to be a contraction because you say that most loci were not adapted to yak because of “low scores”, but you also say that the primers used to amplify BM1824 etc presented “high scores” and, therefore, were nor adjusted to yak. Does “adjusted” mean that you redesigned the primers based on the yak sequence?
Line 134 – It is common practice not to separate white blood cell from total blood before extraction of total DNA. Was there a reason for this separation? If yes, please explain.

Line 155 – It is not clear why you sequenced those loci, please explain. Loci were sequenced, therefore, sequences of these loci should be provided in Supplementary Material. Unidirectional sequencing may not be sufficient to survey the number of repeats and the flanking sequences correctly, due to slippage of DNAPol during the replication steps of PCR and sequencing reactions. Please discuss.

References
As I commented before, this manuscript presents a list of 49 references, which I consider excessive given the scope of this study and the depth of the discussion. Example in line 63: four references are presented supporting the significant contributions of yak to human life. I suggest that the authors decrease the number of references for introductory facts that add little to the focus of their work.

Table S1 – A column informing on the original literature refs should be included for the loci mined from previous works.


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: EVALUATION OF 17 MICROSATELLITE MARKERS FOR PARENTAGE TESTING AND INDIVIDUAL IDENTIFICATION OF DOMESTIC YAK (BOS GRUNNIENS)
Review round: 4
Reviewer: 1

Output:
Basic reporting: I appreciate the effort and tenacity of the authors in the revision and improvement of their manuscript. I hope that this long process has been a fruitful learning experience that will have impact on their future manuscripts, for the sake of the authors and for the sake of the reviewers. I wish the authors all the best for their future endeavors.
Most of my concerns have been addressed to my satisfaction. However, please consider the following comments.
References
In my previous review, I comment that: “As I commented before, this manuscript presents a list of 49 references, which I consider excessive given the scope of this study and the depth of the discussion. Example in line 63: four references are presented supporting the significant contributions of yak to human life. I suggest that the authors decrease the number of references for introductory facts that add little to the focus of their work.”
The authors replied: “The number of references has been reduced to three, and the number of references for introductory facts has been reduced according to the suggestion of the Reviewer.”
Despite my suggestions, the authors did not significantly decrease the number of references they use for introductory facts that do not represent important information within the scope of this work. The authors merely excluded a single reference pertaining to the specific example that I gave, and failed to revise the remaining of the manuscript.

The revision did not correct all the language mistakes. Examples:
“Of these, 17 microsatellite loci had polymorphic information content (PIC) of >0.5, and they were included in Hardy-Weinberg equilibrium without linkage disequilibrium.” Please revise.
“The 17 loci selected were deemed suitable for yak parentage testing based on their efficient amplification, unambiguous genotyping, and high PIC. Thus, this set of microsatellite loci is suitable for parentage analysis in polled yak populations.” Please revise. This second sentence is totally redundant.
“So, the study planned […]” Please revise. Studies do not “plan”, studies have aims and objectives.
“which have been commonly reported by studies on kinship relationships in cattle and yak” Please make sure that you are using “kinship” in the correct sense, and revise the manuscript with regards to this, not just the example that I am highlighting here. Parentage and kinship are different, non-interchangeable concepts. I commented on the use of the work “kinship” in previous reviews of this manuscript.
“The primers for most of the loci used in the previous studies were not adapted to the yak genome due to low scores.” Consider replacing “not adapted” with “not suitable”.
“presented relatively high scores, and therefore, were not adjusted for yak” Consider replacing “not adjusted” with “not redesigned”.
“There were no disequilibrium found in the interlocus between each locus within the same chromosome (Table S6)” Please revise this phrase, it makes no sense.
“Previous studies have indicated that 4.3% of the annual losses in genetic progress”. This phrase makes no sense, please revise. What is “genetic progress”?
I am afraid that the manuscript need to be revised again by a native English speaker with expertise in the field. I strongly suggest that JPeer editorial staff provide further assistance to the authors in the final editing.
“Genotypic disequilibrium within the polled yak resulted in 136 comparisons. There were no disequilibrium found in the interlocus between each locus within the same chromosome (Table S6).” I would rather use the most common expression “linkage desiquilibrium” instead of “genotypic disequilibrium”. The second phrase is non-sensical and must be revised.
“Therefore, the identity and parentage PEs based on the 17 core loci were highly different.” Phrase makes no sense. Do the authors mean that the PE values indicated the discriminatory power of the 17 loci was high?
These are some examples that I picked up from the revised manuscript. I suggest that the authors along with the editorial staff invest in polishing the remaining issues.
Experimental design: No comments.
Validity of the findings: No comments.
Additional comments: Please see Basic reporting.