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: MORPHOMETRIC RELATIONSHIPS AND SEASONAL VARIATION IN SIZE, WEIGHT, AND A CONDITION INDEX OF POST-SETTLEMENT STAGES OF THE CARIBBEAN SPINY LOBSTER
Review round: 1
Reviewer: 2

Output:
Basic reporting: This article included enough introduction although probably is so extended to arrive to explain the main goal of the study. Maybe exists to many supposition and idea linked to use the variable weight /Carapace length (index condition) to be used in order to understand a key factor to  explain the objective that the author would like to explain.
There are too many steps to understand which are the factor why Panulirus argus is an species that have a decouple the relationship between levels of settlement and abundance of subsequent benthic are phases are to explain if the nutritional condition is one of the causes that produce the decoupling.
The index of condition used by the authors is supported by different authors and it should be considered correct, although the author don’t use any direct parameter as ( percentage of fat, tax of ingested food, proteins,  or quality of food evaluated by isotopes). In the introduction the author should explain that the nutritional condition is only one of the factors to produce the die of the first juveniles, not the only direct evidence to decline the abundance of settled individuals.
All the steps to arrive at the direct results are well explained and justified by papers of the other authors published before.  Although, after a complex introduction the final goal proposed at the MS (lines 75-78), seem that is not the final aim of the study. I suggested that the introduction may be more clear and don’t suppose to much direct relation effect because finally the results showed, are not directly interpreted as the objective of the paper. The results of the paper are clear and correct developed but maybe it will be considered an important new information using a non invasive technique to evaluate the nutritional condition. In any case a direct relation that explain the lack relationship between the settlement and abundance recruits.
Experimental design: I propose to add a table to explain the samples used for each analysis with a information of the location and season that are captured. It offers clear information to the set of data that is used in any cases studied.

Line 207 must to say pigmented puerulus instead of benthic pueruli

The categories of sizes classes proposed in Line 207-208  must to be explained more clear the main reason , I understand that it is due to the color of each stage, but may be need to be according to the ecological role that it plays in the settlement.

The experimental design is so confused due to the aggregation of samples used by different purposes. Line 148 say that there are two locations. Line 150 said that the samples were obtained in 1 location , in the line 151 explain that exist an additional location to get samples. Avoid the line 150., only make confusion.

Line 161 The measures used in small size individuals and for using in a index may be getting more accuracy . (0.01 mm), the same for the total weight. In a present day to use a more precision instrumentation is to easy.

Statistical analysis proposed is correct to evaluate the objectives of any specific objective findings
Validity of the findings: The findings of the paper are well described an supported by statistical analysis, although a more detail analysis if the differences between the months were the differences are find may be to analyses statistically, in that sense the result and conclusion of the role that nutritional condition of the spiny lobster will be more robust.
The findings of the morphometric relationships propably are out of the main goal of the paper and don’t contribute any essential results to the general conclusions. It gives interesting information but low information to the main objective to the paper and is poorly debated.
Figure 5 plotB probably give more information if the blue dots out of the pool of data will be marked as a different color that explain individuals of a season that weight is anormal p.e. winter 2012.
Additional comments: The MS need to be revised heavily in order to put more clearly the information used and the identification of the main objectives of the MS.
Tables and plot are generally well proposed.


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: MORPHOMETRIC RELATIONSHIPS AND SEASONAL VARIATION IN SIZE, WEIGHT, AND A CONDITION INDEX OF POST-SETTLEMENT STAGES OF THE CARIBBEAN SPINY LOBSTER
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript has quite a few grammatical issues that need cleaned up, including problems with spelling, verb tense, and sentence structure which is not unexpected if one's first language is not English.  Still, the manuscript would benefit from having a native English-speaker with strong writing skills help them clean up the grammatical problems in the manuscript.

Introduction was choppy in terms of its treatment of different subjects; moved among topics and then reversed back to dwell again on an earlier topic.

Most literature seems appropriate but did not reference the Anderson et al 2013 paper on allometric growth in spiny lobsters that discusses morphometric and color changes in postlarvae, early benthic stage juveniles, and later-stage juvenile lobsters.

Conclusions were not conclusions, but instead were just a recapitulation of results.
Experimental design: Statistical analyses are severely flawed.  Could have used site and year as random factors in the analysis to remove those effects from the error term, and month within season as the source of replication for season.

In the description of the study where the authors talk about seasonal effects they also mention site effects, but from their description it looked like they only used data from one site.  What is going on?

lines 144-146:  samples taken once a month from collectors means that animals could have been on the collectors from 1- 30d.  That could affect some of these morphometric relationships, particularly the weight measure based on lipid catabolism of postlarvae and feeding by juveniles.  This is a big confounding factor.
Validity of the findings: Morphometrics not linked to nutritional condition in this paper. There remains a hypothetical link between the index and nutritional condition - if anything to make this more impressive the authors should have used a biochemical analyses in concert with this morphometric analysis.

Line 104 – States that biochemical analysis can be “expensive and time-consuming” (and I agree) but would not sampling larvae also be time consuming? Perhaps not to the same extent but this sounds misleading.

Line 261 – Seems obvious that the pueruli would be morphometrically different between stages.

Line 306 – Ascribes differences to greater availability of basal food but notes above that there were no differences among locations. Would not food resources be different for different locations?
Additional comments: This manuscript touches on an interesting, but fairly well-known hypothesis (particularly in fishes) that the link between levels of settlement and abundance of benthic phases may be decoupled if there is considerable variability in nutritional condition of settling stages that translates into lower post-settlement survival.  In this paper, they attempt to equate basic measures of morphology of postlarval and juvenile spiny lobsters with such a phenomenon.  But the manuscript only delves into the first steps of determining whether nutrition is a plausible link, because they never link morphology, to nutrition, to survival.  Thus, despite a hopeful introduction that outlines an interesting question, the study falls far short of delivering data that can be brought to bear on the question.  The data simply amount to a morphometric comparision among months of postlarvae, but whether such differences correlate with nutritional condition or have any impact on survival remains unknown. Moreover, the authors do not offer any predictions as to which morphometric parameters in particular should be associated with enhances or diminished lobster recruitment.


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: MORPHOMETRIC RELATIONSHIPS AND SEASONAL VARIATION IN SIZE, WEIGHT, AND A CONDITION INDEX OF POST-SETTLEMENT STAGES OF THE CARIBBEAN SPINY LOBSTER
Review round: 2
Reviewer: 1

Output:
Basic reporting: Basic reporting and structure have been improved. It is at an acceptable level for publication in a scientific journal. I have made minor edits to the text (MS-Word file, attached) to fix grammatical errors, or remove redundant text.
Experimental design: Good. See previous review
Validity of the findings: No comment
Additional comments: Reviewer comments on the first draft have been addressed in a satisfactory 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: LONGITUDINAL EVALUATION OF THE IMPACT OF TRADITIONAL RAINBOW TROUT FARMING ON RECEIVING WATER QUALITY IN IRELAND
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This study represents a 10-year longitudinal survey (2005-2015) of the impact of four consecutive FT trout farms in Ireland based on publically available and independently generated data. The main quality of this study is unique combination of very large time span with data sampled throughout the year, multiple fish farms and relatively complete set of relevant parameters for assessing the water quality. The manuscript is clearly written, data appropriately analyzed and all conclusions strengthen with relevant literature data. Therefore it is my opinion that the manuscript should be accepted for publication in PeerJ after the correction of some minor issues.

The minor corrections are as follows:

General comments:

1.When mentioning average values it should be done in the form  value ± SD or SE and if standard error is given than it should be accompanied with the number of samples (n=xx). Please correct that throughout the Results and discussion section.
2. It is customary to write p value as P. Please correct that throughout the Results and discussion section.

Specific comments in the text:

Line 157: there are two full stops, delete one.
Lines 164-173: I think that measured parameters should be listed in line; there is no need for such emphasis.
Lines 197-199: the sentence should be rewritten as follows:
The following range of assessments were considered when evaluating the impacts of the farms on the receiving river water – individual farm impact on river water quality, and cumulative impact of the 4 fish farms on river water quality.
Line 255: add space before the citation
Lines 434-450: please put a statement about statistical significance of changes in NO2-N
Legend for figure 4: change (2015-2015) with (2005-2015)


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: LONGITUDINAL EVALUATION OF THE IMPACT OF TRADITIONAL RAINBOW TROUT FARMING ON RECEIVING WATER QUALITY IN IRELAND
Review round: 1
Reviewer: 2

Output:
Basic reporting: After careful reading of the manuscript “Longitudinal evaluation of the impact of traditional
rainbow trout farming on receiving water quality in Ireland (#23597)” I have some considerations to make about it.

The study presented in the manuscript can be considered in a correct English. However, does not present deep knowledge about the proposed theme.

The text in general is very extensive and can be much more summarized. In some sections the information are repeated and can be presented and discussed together, due to they reach the same conclusions.

Figures and tables were not well labeled and need more information about them.

I thank you for providing the raw data, however your supplemental files need more information (legends and the values of the LOQ of each parameters) to be useful to future readers.
Experimental design: The research question was defined in the abstract, but not very well defined in the text.

I commend the authors for their extensive data set, compiled over many years. If there is a weakness, it is in the way that the data was analyzed e presented, which should be improved.

The methodology section should also be improved with more information about the farms (number of earthen ponds, volumes, inlet volumes, daily % of renewal, name of the river, among others relevant information).

The showed average inlet data (0.4 m³/s) is not relevant, due to the distinct activities of each farm. I think that this value of 0.4 m³/s is to high for the hatchery and juveniles production.

In the parameters monitored is missing the units of them, and some of them are named and others are in the chemical formulas.

The APHA 2005 is outdated.

The sampling section should be improved in many ways.

In the data treatment, the statistical test should have the description improved (e.g. box plot).

Finally, due to the high volumes of inlet and outlet, I suggest that your data should be analyzed as load instead of concentrations.
Validity of the findings: The presented tables (1-4) are not necessary and the content can be shown in the text.

The figure 1 is missing basic information: extension of the river stretch; inlet volumes of each farm; flow and river velocity; and distance between farms.

The figure 2 should analyze the inlet and outlet of each farm instead of global median.

Figure 3 OK.

Figure 4 should show data of the daily load that is more representative in that high volume,
instead of concentration (e.g. BOD 5: 2 mg O2/ L is the same of 69 kg/day).

I suggest that you analyze and discuss the load instead of concentration, because of the probable high renewal of the earthen ponds. This high renewal of the earthen ponds is diluting the pollutant loads and therefore they were low and not significant. The fish farms use an average of 36.4% (0.4 m³ / L) of the total river flow. When the effluents are released (outlet), they are still diluted in 63.6% (0.7 m³ / s) and they have at least 1km to be consumed by the ecosystem.

I think this is very good point to discuss, the high demand of water of those farms. This eliminates the possibility of future expansions in those fish farming due to the high commitment of water use.
Additional comments: The study presented in the manuscript can be considered relevance. Although, a revision in the way of how the data should be presented, analyzed and discussed is strongly suggested to be more relevant and to have more novelty. The text in general is very extensive and can be much more summarized.


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: PREVALENCE AND EXTENT OF CHRONIC PERIODONTITIS AND ITS RISK FACTORS IN A PORTUGUESE SUBPOPULATION: A RETROSPECTIVE CROSS-SECTIONAL STUDY AND ANALYSIS OF CLINICAL ATTACHMENT LOSS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Reviewers Comments:
Abstract: Very well written. All aspects of the study have been covered nicely.
Introduction: Relative and contemporary.
Experimental design: M & M: A convenient sample from a university clinical facility. Clinical parameters and health questionnaire, well explained. Inter-examiner correlation presented. Very appropriate use of statistical methods.
Validity of the findings: Results: Well explained.
Discussion: Compared with other studies and provided the rationale of the study design etc.
Conclusion: The prevalence and severity of the subpopulation used in this study gave upward results. Risk indicators are comparable with other studies from international populations.
Additional comments: Recommendation: In future, a true representative sampling technique should be used. The comparison of FMPE and partial recording of the same population, using CPITN should be used to find out over or underestimation of the periodontal disease. The findings of the current examined population cannot be generalized to general population of the city or country.
Final Recommendation:


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: PREVALENCE AND EXTENT OF CHRONIC PERIODONTITIS AND ITS RISK FACTORS IN A PORTUGUESE SUBPOPULATION: A RETROSPECTIVE CROSS-SECTIONAL STUDY AND ANALYSIS OF CLINICAL ATTACHMENT LOSS
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: A question regarding selection of the subpopulation:

From reading the materials and methods, my understanding is selecting patients who were specifically referred to the periodontology department to obtain a periodontal examination, after being screened in triage. Therefore, all cases that are referred are suspected to have periodontal disease.  As a result, the prevalence will accordingly be high.  Why not calculate the prevalence of the original population that was screened from your target period: September 2015 to March 2017, which was a total of 3648 patients.  This would give us a better idea on the prevalence in this subpopulation.
Validity of the findings: Regarding the following sentence in the discussion (lines 211-213):

“However, these results underline the fact that the majority of patients attended the periodontal consultation already in a state of advanced periodontal destruction and only a small percentage appeared in the early stages or healthy”

Can you define the threshold where triage sends the patients to the periodontal department? Their threshold could be high, and therefore maybe missing the mild periodontitis cases.
Maybe you can expand on this point in your manuscript.
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: PREVALENCE AND EXTENT OF CHRONIC PERIODONTITIS AND ITS RISK FACTORS IN A PORTUGUESE SUBPOPULATION: A RETROSPECTIVE CROSS-SECTIONAL STUDY AND ANALYSIS OF CLINICAL ATTACHMENT LOSS
Review round: 1
Reviewer: 3

Output:
Basic reporting: The Authors should clarify the fooling questions:
•	 The initials (name) of the calibrated periodontists;
•	Bibliography references formatting –“…. Four BMI categories were defined using WHO criteria (Kopelman 2000)…”
•	Bibliography reference to support this statement is missing: “This area has over 2.8 million inhabitants and is the largest Portuguese metropolitan area”
•	All tables need to have legend of the acronyms

Finally, it is advisable to have the text revised by a native English speaker since it would help the text understanding, there are some misspelling and grammatical issues.
For instance, “STrengthening the Reporting of OBservational studies in Epidemiology (STROBE)” or “27% of the patients indicated for periodontal treatment”
Experimental design: .	I felt a bit lost: is this a prospective or retrospective study? “Study was carried out between September 2015 and March 2017”, but when we analyze the documents, the ethic commission only gave the approval on 29th of November 2017, after the study was performed. In any part of the paper is mentioned that this was a retrospective cross-sectional study.

.	The informed consent doesn’t respect the Declaration of Helsinki revised in 2013 where: “…In medical research involving human subjects capable of giving informed consent, each potential subject must be adequately informed of the aims, methods, sources of funding, any possible conflicts of interest, institutional affiliations of the researcher, the anticipated benefits and potential risks of the study and the discomfort it may entail, post-study provisions and any other relevant aspects of the study. The potential subject must be informed of the right to refuse to participate in the study or to withdraw consent to participate at any time without reprisal. Special attention should be given to the specific information needs of individual potential subjects as well as to the methods used to deliver the information.” Analyzing the informed consent attached to the paper, even the study name is missing among with most of the others requirements of Helsinki.

.	How it was performed the first triage to select the patients to be treated into the periodontology department?
Validity of the findings: .	The purpose of this study was “to assess the prevalence, severity and extent of chronic periodontitis through the full-mouth examination of CAL, and its association with sociodemographic, behavioral and environmental risk factors, in a Portuguese adult subpopulation of a suburban area of the Lisbon Region forwarded to periodontal examination”. The authors report that the “Prevalence of chronic periodontitis was 83.5%”.

•	The authors only included in the study a pre-selected sample that was referred to the periodontology department. Due to that, is quite normal that the percentage of chronic periodontitis was very high. From my point of view, is absolutely necessary to explain that result tacking in consideration the sample selected, this result can’t be reported as absolute. [“From a total of 3648 subjects who sought a first consultation in the university dental clinic during that period, 1501 (41%) patients were referred to the periodontology department, based on their triage status. From these, 459 attended a periodontal consultation and were considered for this study.”]

•	For the same reason, most of the conclusion aren’t accord of the performed study eg. “Age and smoking were identified as risk indicators for chronic periodontitis” because this conclusion are based only in “patients that have been referred to the periodontology department based on their triage status”, so is normal most of them have periodontitis.
Additional comments: This cross-sectional study, as is stated in the conclusions, is a good base to “prepare future detailed epidemiological studies and appropriate public health programs”.
However, further clarifications are required to make this cross-sectional study suitable for 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: PREVALENCE AND EXTENT OF CHRONIC PERIODONTITIS AND ITS RISK FACTORS IN A PORTUGUESE SUBPOPULATION: A RETROSPECTIVE CROSS-SECTIONAL STUDY AND ANALYSIS OF CLINICAL ATTACHMENT LOSS
Review round: 2
Reviewer: 1

Output:
Basic reporting: the authors improved the paper and answered questions.
Experimental design: Not only in the line89 but all the paper including the title should be written that this is a retrospective cross-sectional.
The report at eg. line 177, 207, 240 are statements of a subpopulation not a population.
The autores need to review this statement along all the paper.
Validity of the findings: the authors improved the paper and answered questions.
Additional comments: Not only in the line89 but all the paper including the title should be written that this is a retrospective cross-sectional.
The report at eg. line 177, 207, 240 are statements of a subpopulation not a population.
The autores need to review this statement along all the paper.


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

Input:
Title: BEST IN THE COMPANY OF NEARBY MALES: FEMALE SUCCESS IN THE THREATENED CYCAD, ZAMIA PORTORICENSIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: - Clear and unambiguous, professional English used throughout.
- Literature references: very good, except regarding the Allee effect mentioned in the text. The points in the text regarding the Allee effect should be modified, explaining better what is the Allee effect (shortly) and how it is related to this study (more deep). Gascoigne et al. 2009 cited (be careful at line 472 you wrote GASCOIGEN) is about mate-finding Allee effects, and I strongly suggest you to add 10 lines in the Introduction section to introduce the concept of mate-finding Allee effects and how it is crucial for the comprehension of several aspects of the reproductive ecology (and success) of vascular plants.
- Professional article structure, figs, tables are OK. Raw data shared: YES
- Self-contained with relevant results to hypotheses: YES (but see below for aims)
Experimental design: - Original primary research within Aims and Scope of the journal: YES
- Research question well defined, relevant & meaningful: I have some doubt regarding aim #2: "is pollen availability associated with reproductive success?" Indeed you did not measure pollen production, vitality and availability in this study. As you state at line 159 "Pollen availability was assumed to increase with an increase in the male-to-female sex ratio". At line 181 you write: "reproductive success is assumed to be pollen limited". There are too much assumptions related to pollen production, that should be carefully discussed somewhere in the text, and discourage the use of "pollen availability" in the aims. So in the aims, you better use another term, not mentioning pollen availability: a reader would expect to find an analysis of pollen production and/or pollination efficiency.
- Rigorous investigation performed to a high technical & ethical standard: YES
- Methods described with sufficient detail & information to replicate: YES
Validity of the findings: - Impact and novelty of the work: YES
- Data is robust, statistically sound, & controlled: this is the weakest point of the manuscript: Authors declare to have studied two populations of Z. portoricensis (line 88) and to have established two 25x20 m plots at each site. Even if I understand that there could be many logistic difficulties to expand the range and number of surveyed populations, I think that somewhere in the text Authors should discuss briefly the weakness of studying "only" 4 plots (on a total studied area of "only" 1000 square meters). Furthermore, as they write at line 396, Authors worked at places characterized by high (or very high) densities for Cycads, whereas it is demonstrated that different ecological processes affect plant populations at their range limits, where they usually (but not always) show low densities (see, among others: Pironon et al. 2017. Biological Reviews 92: 1877–1909; Papuga et al. 2018. Ecography 40: 1-15). So, to my opinion, not only this study has the limit of a small spatial range and replicates, but its results and main conclusions can be valid only at sites with high cycads density, not where cycads have low densities. I recognize that it is probably not possible to expand the replicates and/or sites of the study in a short period (to improve the manuscript), but clarifications should be included in the manuscript, about the limits of the study and the applicability of the results here presented.
- Conclusion are well stated, linked to original research question & limited to supporting results: YES, but see comment above
Additional comments: Congratulations for this interesting, even if spatially limited, research.
I suggest you also to stress somewhere that you are dealing with probably the oldest seed plant group insect pollinated, this will increase the originality of your paper: as being the "first" Gymnosperms insect pollinated, Cycads were possibly the first seed plants experimenting also the ecological effects of pollen/pollination/pollinators limitation, constraints not experienced by other Gymnosperms like conifers.


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: BEST IN THE COMPANY OF NEARBY MALES: FEMALE SUCCESS IN THE THREATENED CYCAD, ZAMIA PORTORICENSIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Title; I suggest revising the title to be more descriptive and with no innuendo.
Abstract; Please use more conservative language when statements are not supported by data. For example, please change “…indicates that pollinator movement among plants is limited for this mutually…” to include “may be limited”, given that there are no data presented on pollinator movement.
Line 36-39; The first sentence is very busy and has a vague conclusion (“…influences the effects that different ecological factors have…”). I recommend splitting this sentence up and being more specific.
Line 42; The sentence starting with “For example..” does not exemplify the prior sentence’s subject ie genetic diversity. I suggest revising the paragraph to improve the logical flow.
Line 48-56; This paragraph seems like an appropriate place to mention dispersal mechanisms. The papers Burbidge & Whalen 1982, and Hall & Walter 2013 come to mind. Please mention dispersal mechanisms briefly as it relates strongly to your study.
Line 52-54; This sentence reads disrupted and could be more clear. I suggest revising to something like “Cycads may be particularly susceptible to Allee effects given that they are dioecious, and the majority of cycad species are threatened with extinction and have narrow distributions.” In my opinion, the goal here would be to connect reproductive strategy (dioecy) and population ecology (via invoking threatened status and implicitly from "narrow distributions").
Line 64-86; A few studies have shown that male and female reproductive cycles are often offset and that although there may be reproductive females each year, individual females often skip years. See work by Clark & Clark on Zamia sp. So here, I recommend citing such studies and comparing the observed reproductive trends of this species at these sites specifically.
Line 140; There has been some limited work in cycad species showing data to support the hypothesis that male and female cycads differ in their cost of reproduction but the only physiological study to date is Krieg et al 2017. This study included Z. portoricensis and showed that males and females differ in key aspects of physiology. This work should be cited here, and probably in the discussion as well.
Line 161; Typo – please add : between “variables” and “number of males”
Line 195; Please add a space between “reproductives,” and “to”
Line 260-267; Another place for Alverez-Yepiz et al 2014
Line 272; Citation needed after “…equal sex ratios”
Line 298; Consider adding Burbidge & Whalen 1982, and Hall & Walter 2013
Line 379; Please clarify what you mean by “flexibility”.
Experimental design: Line 96 & line 99; In regards to the percentages reported, please add a metric of variation, eg standard deviation.
Line 118-119; Given that at least three platforms were used for analyses (eg R, Statistica, JMP), I suggest being more specific about what which analysis was performed in each. This should be implemented throughout. Please specify which platform was used for each analysis.
Line 139; This may be true in other plant systems but there is much less data for cycads. Please add some rational and citation to support this expectation.
Line 141; Why did you choose the number of leaflets to rank whole plants into size classes? Please add some rationale and citations to support this decision.
Line 142-143; This expectation that female cone production will me dependent of plant size should either be well-supported with citations and the findings of other studies, or perhaps made a hypothesis.
Line 157-158; It seems like the absolute number of males is a far more direct approach to estimating the availability of pollen than the sex ratio. Imagine the scenario where two plots have a 50/50 sex ratio. One plot has one male and one female and the other plot has 10 males and 10 females. Given that pollen is made in ‘surplus’, the relationship between pollen limitation (in females) and number of males is not 1:1, but what I would expect to be a quickly saturating curve where a few males could theoretically supply an exponentially high number of females. Please also analyze your data with number of males or density of males.
Line 160; I do not think your assumption is valid. Please see above comment and re-run analyses with number or density of males.
Line 177-178; Was the threshold different across sites?
Line 180; This section isn't about multiple resources, it only addresses pollen. I suggest renaming the section to something like: Pollen Limitations, Assessing the role of pollen availability, etc
Line 213; Is it 4-5 meters or 3.8 to 5 meters as stated in line 210. Please clarify.
Line 220 & 222; My personal preference is to see the corresponding statistics in parentheses after stating the results.
Line 226-227; Is the standard deviation also in percent? Please make units consistent and clear.
Line 234; Please remove the word ”highly” due to the low predictive value (ie 18%).
Line 236; Please remove the word “positive” due to the statistical results indicating the slope is not significantly different from zero.
Validity of the findings: Line 252-253; I am having trouble seeing the connection between the assertion that “If pollen is not limiting seed production, then we would expect more seeds produced in larger cones”, and I do not think this assertion is logical. The second part of the assertion that larger individuals may produce more seeds is introduced earlier in the manuscript and without support or citations. Here, you have linked pollen limitation, again without support, and have not explained your logic for this connection. I strongly recommend revision of these assertions to include rationale and supporting literature.
Line 254-256; To my knowledge, this assertion about intra-specific competition leading to reduced reproduction is untested in cycads. The closest study I know is Alverez-Yepiz et al 2014, who showed that survival and grow rates both decreases in a Dioon sp with increasing intraspecific competition (ie density). Please situate your assertion within other studies including Alverez-Yepiz et al.
Line 266-267; A large proportion of seedling and juveniles relative to the number of adults does not suggest a thriving species; it may suggest the opposite. Please expand your discussion of seedling survival and why you think your sites offer favourable conditions.
Line 272-275; There have been many abiotic explanations proposed, some with data, to explain sex biased populations. Please cite and discuss.
Lines 280-291; This paragraph should include Krieg et al 2017 who showed that males of Z. portoricensis have higher photosynthetic rates than females, but that females of this species have greater water-use-efficiency – the opposite trend one could expected if females face greater costs in reproduction. Even so, females may show longer reproductive cycles because they play a more “conservative” game with reduced photosynthetic capacity and more conservative stomatal control. Please cite and discuss.
Line 301-303; Please add Alverez-Yepiz 2014 to support your reasoning and discuss alternative hypotheses from Burbidge & Whalen 1982, and Hall & Walter 2013
Line 303-306; The statement about interspecific competition is misleading here. Just because a species is dominant doesn’t not mean that interspecific competition is not occurring. Further, the sentence posits that interspecific competition is only “important” when the study species is the “loser”. Without data on interspecific competition, all you can say here is that “interspecific competition does not appear to be excluding Z. portoricensis from these sites since individuals of Z. port comprise a dominant understory element.
Line 363-366; You offer an interesting idea to explain the discrepancy between studies but stop short of an actual hypothesis, leaving this paragraph with something of a cliff-hanger. Please elaborate on your proposed connection between specialist vs generalist impacts on the relationship between RS and sex ratios/proximity to the opposite sex.
Line 373; I am not a horticulturalist but I understand asynchronous reproductive cycles between males and females to be common in many cycad species. Please use more conservative language and add revise to “…female cones is too asynchronous…”
Line 377; Please add questions around the popular phrase “living fossils” due to the oxymoronic nature of the name and the fact that it is technically inaccurate.
Line 378-379; Salas-Leiva et al., 2013 is not the foremost appropriate study to cite here. Nagalingum et al 2011 proposes that extant cycad species are as young as 12 myo, but this is the minimum age of some taxa and others are very clearly older. Moreover, subsequent phylogenetic studies from the same group have acknowledged some issued and violated assumptions with that 2011 study, eg Condamine et al 2015. Please add these studies and revise your statement to reflect the conclusions of these studies, ie that extant taxa are 20+ myo.
Additional comments: Overall, this is an interesting study and addresses fundamental questions of cycad biology that remain poorly understood. In particular, there have been few studies that examine cycad reproduction in natural populations. This study fills this gap and makes important connections to conservation efforts.
Generally, I recommend a stronger connection to the conservation implications throughout this manuscript. The conservation implications of this work are exciting and far better situated in the data presented than the attempts to make conclusions about pollinators. In some cases, the focus on pollinators manifested as unsupported conclusions and assertions for which no data are presented. I strongly recommend a thorough review of all language and statements relating your data to pollinator interactions to a more conservative stance on the implications.


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: BEST IN THE COMPANY OF NEARBY MALES: FEMALE SUCCESS IN THE THREATENED CYCAD, ZAMIA PORTORICENSIS
Review round: 1
Reviewer: 3

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: This is well-written, well-structured contribution that does an excellent job of hypothesis testing without over-stating its conclusions. It makes a useful contribution to the area of cycad reproductive biology. See some of my comments in the PDF.


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: HEPATIC AUTOTAXIN OVEREXPRESSION IN INFANTS WITH BILIARY ATRESIA
Review round: 1
Reviewer: 1

Output:
Basic reporting: I see a couple of minor issues in the basic reporting:

A. The statement "...infants who underwent liver biopsy for non-BA patients...," found in the abstract (page 2, line 31) needs to be modified. Perhaps the authors meant "...infants who underwent liver biopsy for reasons other than BA."

B. Line 119-121: As written, it sounds like 15 BA patients and 5 non-BA patients had only mRNA samples ("...and only available for ATX mRNA expression"); yet, Figure 3 clearly shows immunostaining results for all 7 non-BA patients. I suggest revising the sentence in the Methods section to make it more clear.
Experimental design: I see at least one major issue with the experimental design:

A. Most of the patients in the non-BA group had choledochal cysts (6 out of 7). Thus, an alternative explanation of the authors' data is that patients with that condition have lower expression of autotaxin in the liver. In fact, there is clearly one patient in the non-BA control group that had higher autotaxin than all of the others; is that patient the one who did NOT have a choledochal cyst? I am aware of the difficulty of obtaining liver biopsy samples from infants, but I strongly suggest that the authors expand their control group. This is especially necessary as the authors mention several other liver diseases that are associated with ATX expression and LPA in the Discussion.
Validity of the findings: Please see my comment for experimental design, as it also pertains to the validity of the findings.
Additional comments: This is a small, but potentially useful study that adds to our mechanistic knowledge of a poorly understood disease. Generally, I'd like to see larger sample sizes, but it is difficult to recruit BA patients prior to or at the time of operation. I would definitely like to see a larger and more diverse control group, though, and that should be doable.


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: HEPATIC AUTOTAXIN OVEREXPRESSION IN INFANTS WITH BILIARY ATRESIA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The following is a review of a paper from Udomsinprasert et al. on the presence of autotaxin in patients with bilary atresia. Given the uncommonness of BA, the authors collected a decent number of samples, as well as controls and tried to assess expression levels of autotaxin in BA infants given recent report’s of autotaxins role in fibrogenesis. The authors provide convincing data with solid IHC and well analyzed results. This is an appropriate paper for this journal.
Experimental design: Comments: The authors provide convincing data that ATX may serve a role as a biomarker of prognosis in BA; however, this does not mean that ATX has a role in the disease. Comments indicating ATX’s potential role should be eliminated. The paper should focus on the potential for ATX as a biomarker.

The p value for the 10 year survival curve was .14 which is not significant by most standards. Why did the authors choose 10 year? Why not 5 year where there is a more stark difference. This should be included as additional data if possible.
Validity of the findings: Data are robust and sound. The authors did a good job at reporting their results. Conclusions are mostly well stated and the paper is referenced well. The authors attempt to extrapolate their data to the role of autotaxin which I find inadvisable. They have found a potentially interesting biomarker, and that is what I would focus on.
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: HEPATIC AUTOTAXIN OVEREXPRESSION IN INFANTS WITH BILIARY ATRESIA
Review round: 2
Reviewer: 1

Output:
Basic reporting: I have no additional comments.
Experimental design: I have no additional comments.
Validity of the findings: I have no additional comments.
Additional comments: I have 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: HIP MUSCULAR STRENGTH BALANCE IS ASSOCIATED WITH RUNNING ECONOMY IN RECREATIONALLY-TRAINED ENDURANCE RUNNERS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Some rework of the grammar is required.  Many ambiguous terms are used throughout the manuscript.
Experimental design: experimental design is relatively sound. As I have elaborated on in my comments however, the choice to express RE in terms of kcal/km is not justified in my opinion.
Validity of the findings: Difficult/impossible to comment on these given the expression of RE itself and some questions surrounding the specifics of how exactly the data were acquired.
Additional comments: General comments:
This study examined the relationships between hip muscular strength and the energy cost of running as well as various body composition parameters on the energy cost of running.  The study’s methodologies are reasonably sound; however, I am not convinced that the energy cost of running expressed as kcal/km (ie. in absolute body mass terms) is justified, particularly given the subjects ran at 1% and 3% treadmill gradient.  The justification for the expressing Ec in this way was not present in the introduction and so I’m not convinced similar results would be obtained had Ec been expressed in the more usual kcal/kg/km.  In and of itself, showing the relationship between Ec (expressed as kcal/km) and body mass is not new () so further justification for the use of Ec expressed in this way is required before the results can be interpreted correctly.  See a recent paper by Lundstrom (2017).  Further, there is little introductory statements regarding ‘conventional’ and ‘functional’ hip strength ratios or how these are defined.  I also have some contention with presenting ‘partial’ results for RE (eg. Only some male subjects could run below AT at 14 km/hr, so the other subjects are (rightfully) excluded).  However, this is now a ‘partial’ result of the whole subject cohort.  There are also frequent grammatical errors and/or vague statements that require correction and/or clarification.  I have elaborated on this and other issues I see throughout the manuscript in my specific comments below; however, given the confusion around how the results were acquired (ie. issues in the methodology) and how these results were interpreted (specifically why Ec is expressed as kcal/km), I cannot confidently comment on the discussion.

Specific comments:
L23 – why introduce the term “running economy (RE)” here when it is not used afterwards?  It is simply confusing when energy cost of running is defined and used later on throughout.
L26 – specifically what about ‘body composition’?
L29 – why is hip muscle strength (or strength in general) important for RE?
L35 – define conventional and functional hip isokinetic strength balance ratios
L38 – Level ground running is not 1% slope.  I realize this was done to simulate overground running according to Jones and Doust (1996), but they show that this ‘correction’ is only necessary at faster speeds (much faster than the speeds your subjects ran).
L47 – the suggestion that athletes should incorporate strength training into their training plans is not new.  See a recent review by Blagrove (Blagrove, Brown, Howatson, & Hayes, 2017; Blagrove, Howatson, & Hayes, 2017).
L72 – ‘the maximal oxygen uptake (VO2max)”…
L75 – VO2max determines the maximal RATE of o2 uptake, not exactly the utmost limit of the aerobic system.
L77 – Bassett & Howley
L79 – the positive relationship between RE and VO2max arises from the inappropriate measurement of RE.  This is explained by Fletcher et al. (2009).
L89 – when citing previous literature on any associations with RE, it is important to consider and make obvious to the reader, which studies used RE as the VO2 measured at a common speed vs. those studies which used the more appropriate cost of transport (eg. Kcal/kg/km or J/kg/m etc.).
L91-93 – Fletcher and MacIntosh (2017) offer a much more detailed explanation on the relationship between body mass and energetics of running.
L94-97 – not relevant.  Consider removing.
L97 – why is a lower FFM considered to be associated with a good RE?  Again, this is already well-explained (at least theoretically) by Fletcher and MacIntosh (2017).
L99 – “neuromuscular components” is quite vague.
L100 – Westerblad et al (1996) SHOWED a negative relationship…
L101-102 – why is hamstring strength, quad eccentric endurance associated with beter running performance?
L103 – I think the evidence is substantial enough to suggest that resistance training is able to improve RE (see review by Blagrove et al. (2017)).  However, this is not a result of improvements in any ‘muscular elastic components’ (this statement itself is not physiologically relevant) as shown by strength training interventions to increase tendon stiffness (Fletcher, Esau, & MacIntosh, 2010; Kubo et al., 2010; Kubo, Kanehisa, & Fukunaga, 2002) as well as the minimal energy return of elastic energy from tendons ((Fletcher & MacIntosh, 2015).
L110 – why is the strength ratio important to consider?
L114 – this statement re: speed increases, as in sprinting, is not relevant to the paper, since the measurement of RE is only relevant and measureable below the anaerobic threshold.
L120 – some additional background regarding the relevance to ultra-trail running?  RE is more relevant than other distance running events because the intensity of trail running is below the anaerobic threshold.  However, Millet (2013) showed ultra-trail runners in fact sacrifice RE, presumably to reduce muscle damage.
L127-128 – vague sentence.
L130 – what defines ‘adequate’?
L131 – cause and effect RELATIONSHIP
L133 - …and therefore LEAD to IMPROVED performance.
L134 – energy cost of running (Ec) is just now being introduced without any definition or how it may differ from RE.
L144-146 – ‘the body composition’… this statement belongs in the intro and needs further elaboration.
L149 – why those specific speeds tested?
L151 – how was ‘well-trained’ defined?
L162 – as the comment above (L151), what is meant by ‘reaching a race pace of….”?  That the subjects could sustain that pace for the entire race?  If so, then simply state ‘could complete a 10km race in ______ mins”.
L171 – reliability and validity of DEXA to asses fat and fat-free mass?
L183 – replace ‘shortness of breath’ with ‘dyspnea’?
L185 – avoiding substantial dehydration is not the reason graded exercise tests are usually 8-12 minutes.
L190 – superscript ‘1’ in 150 ml min-1
191 – ‘AT was assessed using established criteria’…there are many established criteria for the definition of the anaerobic threshold and how to determine it.  A clear definition of how it was determined and whether it was the first or second ventilatory/lactate turnpoint is required.  How was the speed at Anaerobic threshold determined specifically?
L203 – as above, the authors need to justify the use of a 1% treadmill gradient, especially when considering the effect of body mass on RE.
L204 – the TESTED speeds WERE lower than the AT… how was this confirmed?
L209 – how many runners were able to run below AT at 14 km/hr?
L210 – how long were the RE tests?  How was steady state confirmed in the RE tests specifically?
L213 – to determine the Ec USING RER as proposed by Shaw et al. 2013.  Really, it was Fletcher et al. (2009) who proposed this (and who is referenced by Shaw).
L217 – were the left and right legs tested?
L223 – gravity correction of what?
L225 – 90 deg relative to what?
L226 – what is meant by ‘neutral extension’?
L228 – there is no mention of a table with the Biodex.  Perhaps a figure would be best to show the specific subject test set up?
L231 – 0 deg. Relative to what?
L232 – replace ‘evaluation’ with ‘strength’
L240-242 – Unless I missed it, what is CR and FR and what does it mean pragmatically?
L247 – replace ‘gender’ with ‘sex’.
L260-265 – again, the authors need to justify why expressing Ec as kcal/km is most appropriate.  When expressed relative to body mass, in fact the male subjects are more economical (eg. 1.15 kcal/kg/km for males and 1.21 kcal/kg/km for females when taking mean values for BM).

Refernces:
Blagrove, R. C., Brown, N., Howatson, G., & Hayes, P. R. (2017). Strength and Conditioning Habits of Competitive Distance Runners. Journal of Strength and Conditioning Research, 1. http://doi.org/10.1519/JSC.0000000000002261
Blagrove, R. C., Howatson, G., & Hayes, P. R. (2017). Effects of Strength Training on the Physiological Determinants of Middle- and Long-Distance Running Performance: A Systematic Review. Sports Medicine, 1–33. http://doi.org/10.1007/s40279-017-0835-7
Fletcher, J. R., Esau, S. P., & Macintosh, B. R. (2009). Economy of running: beyond the measurement of oxygen uptake. Journal of Applied Physiology (Bethesda, Md. : 1985), 107(6), 1918–1922.
Fletcher, J. R., Esau, S. P., & MacIntosh, B. R. (2010). Changes in tendon stiffness and running economy in highly trained distance runners. European Journal of Applied Physiology, 110(5), 1037–1046.
Fletcher, J. R., & MacIntosh, B. R. (2015). Achilles tendon strain energy in distance running: consider the muscle energy cost. Journal of Applied Physiology (Bethesda, Md. : 1985), 118(2), 193–9. http://doi.org/10.1152/japplphysiol.00732.2014
Fletcher, J. R., & MacIntosh, B. R. (2017). Running Economy from a Muscle Energetics Perspective. Frontiers in Physiology, 8(June), 1–15. http://doi.org/10.3389/fphys.2017.00433
Jones, A. M., & Doust, J. H. (1996). A 1% treadmill grade most accurately reflects the energetic cost of outdoor running. Journal of Sports Sciences, 14(4), 321–327.
Kubo, K., Kanehisa, H., & Fukunaga, T. (2002). Effects of resistance and stretching training programmes on the viscoelastic properties of human tendon structures in vivo. The Journal of Physiology, 538(Pt 1), 219–226.
Kubo, K., Tabata, T., Ikebukuro, T., Igarashi, K., Yata, H., & Tsunoda, N. (2010). Effects of mechanical properties of muscle and tendon on performance in long distance runners. European Journal of Applied Physiology, 110(3), 507–514. http://doi.org/10.1007/s00421-010-1528-1
Lundstrom, C. J., Biltz, G. R., Snyder, E. M., & Ingraham, S. J. (2017). Allometric scaling of body mass in running economy data: An important consideration in modeling marathon performance. Journal of Human Sport and Exercise, 12(2). http://doi.org/10.14198/jhse.2017.122.03
Millet, G. Y., Hoffman, M. D., Morin, J. B., Millet, G. Y., Hoffman, M. D., & Morin, J. B. (2013). Sacrificing economy to improve running performance −− a reality in the ultramarathon ? Sacrificing economy to improve running performance — a reality in the, (April 2012), 507–509. http://doi.org/10.1152/japplphysiol.00016.2012


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: HIP MUSCULAR STRENGTH BALANCE IS ASSOCIATED WITH RUNNING ECONOMY IN RECREATIONALLY-TRAINED ENDURANCE RUNNERS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The English language is clear.
The introduction was able to present the study problematic.
The paper structure is conforms to journal guidelines.
There is not a supplement file.
Experimental design: Original research within journal scope.
The research question is well defined and relevant.
The Methods section is well described with sufficient detail to replicate the study.
Validity of the findings: Conclusion is well stated, however the conclusions did not support the study results (see general comments).
Many speculations were supplied. The authors highlight these speculations.
Additional comments: The manuscript entitled “Hip muscular strength balance and body composition evaluated by the DXA are associated with running economy in well-trained runners” tests the relationship between running economy and hip flexor and extensor peak torque, strength balance ratio (CR and FR), and body composition. Although the topic is interesting, some concerns should be considered. The following issues need to be addressed.

Title
Suggestion: Hip muscular strength balance and body composition are associated with running economy in recreationally trained runners.

Abstract
Lines 46-47: The authors stated that strengthening programs should improve neural factors instead muscular hypertrophy. How the results of the present study support this statement? (In the conclusion section the reviewer will discuss again this aspect).

Introduction
In general, the introduction is well writing, congratulations.
Lines 100-102: Are there more current references?
Lines 113-116: This statement is more related with sprinters than endurance runners? How hip muscles that are involved in the power generation can influence running during submaximal intensities (i.e., running economy)?

Material and Methods
Line 151: Please change “…recreational, well-trained endurance runners..” to “ recreationally trained endurance runners…”.
Lines 182-183: Please, provide the initial speed of CPET.
Lines 197-210:
Why the authors choose 3% slope for uphill running?
The reviewer main concern is related to running economy velocities. In this study, the inclusion criteria was pace below 4min:30s (i.e., ~13 km/h) for male and 5min:00s (i.e., ~12 km/h). However, considering that trained endurance runners can run 10 km race at least 100% of AT, the reviewer believe that 12 (uphill) and 14 (level ground) km/h are very high speed to running economy, for all runners analyzed. Although nine runners had AT above 14 km/h, these velocities (12 and 14 km/h) are in the heavy domain, which has VO2 slow component. Additionally, for 10 (3% slope) and 11 (1% slope) km/h is possible that some runners also reach the heavy domain, which preclude the running economy analysis.
Line 246: Considering the sample size, the normality test of Shapiro-Wilk is correct.
Why the authors did not use multiple regression analysis?

Results
Lines 260-263: This result was expected. Since female runners has lower VO2MAX than male runners. Thus, the reviewer suggests add this result after “…higher values for VO2MAX…” (Line 258), as a consequence of lower VO2MAX for female runners.
Lines 265- 266: The authors stated “this represents a moderate running intensity (below AT)”, actually below of AT the running intensity can be moderate or heavy. The intensity is moderate when exercise is performed without blood lactate change, that is, the speeds used in the study indicate that running intensity is heavy for most runners.
Suggestion: The authors can show the joint stability classification, that is, how many runners have good or bad joint stability assessed by CR and FR.

Discussion
Lines 316-318: The authors stated “ … the better ratios the runner has, the lower the VO2 should be during running…”. What is better ratios? For example, FR above 1 is good, but if FR value was 1.70, is this good too? The authors need show the PT, CR and FR values (mean and standard deviation).

Lines 324-326: CR and FR showed no relationship with Ec. Perhaps CR and FR values present a large range. Again, is necessary demonstrate CR and FR values.
Line 353: Please, provide the number of participants of cited study.
Lines 382-383: The authors stated “In this regard, strengthening programs, aiming to improve muscular strength as a consequence of neural factors instead of muscular hypertrophy, should be better for Ec”. The current study cannot support this statement.

Conclusion
Regarding neural factors, the authors need be careful with statements. Since just hip muscle strength was assessed. Thus, you cannot stated that resistance training for runners should avoid hypertrophy and focus on neural factors. Perhaps, eccentric contractions and stretching shortening cycle should be the target for endurance runners.


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: HIP MUSCULAR STRENGTH BALANCE IS ASSOCIATED WITH RUNNING ECONOMY IN RECREATIONALLY-TRAINED ENDURANCE RUNNERS
Review round: 1
Reviewer: 3

Output:
Basic reporting: As mentioned in the general comments, the manuscript should be shortened to make it more concise. Also, a thorough review of English language (especially the structure of some sentences) should be made.
Experimental design: See general comments below. Research objectives may need precisions based on between-sex analyses. Overall very well done.
Validity of the findings: Please provide more details on p-values. Also, make sure conclusions are based on findings from this study.
Additional comments: This manuscript describes a study which aimed at cross-sectionally investigating the association between hip muscles and body composition and running economy. This is an interesting topic, but I feel this manuscript needs major revisions before it can be considered for publication. First, I think the authors can justify their study better. Also, the manuscript could be significantly shortened and more focused.

General comments:
I found the introduction of the paper to be lengthy, and sometimes confusing as there are a lot of speculations (the purpose of an introduction is simply to show the state of literature in a concise manner so that it justifies the current study). Better structure and more ‘to-the-point’ arguments would improve readability. Then, the authors interchangeably use the terms ‘recreationally trained’ and ‘well-trained’ – which is it? Overall, the results section is really heavy to read and should be shortened. The impressive number of abbreviations and numbers (a lot of them are repeated in Tables) does not make it easy to read. Finally, the authors talk about ‘stability’ during running; however, ‘stability’ is a very vague term and is not the topic of this study or isn’t a construct that can actually be assessed.

Abstract:
-	Please limit the use of abbreviations as it becomes somewhat confusing. For example, peak torque is usually maintained in its complete form and does not need to be changed to PT.
-	Conclusions from the abstract are not related to findings of this study. How do you know if strengthening hip flexors will result in better running economy?
-	The last sentence needs to be restructured as it doesn’t make any sense.

Introduction
-	L90: Restructure sentence
-	L129: why would a strength ratio improve RE, since contractions are submaximal during running?
-	Better balance between arguments relating to hip muscles, body composition and uphill running as they relate to running economy should be put forward, and more focused.

Methods
-	L144-146: This sentence sounds like it should be in the introduction instead.
-	L161: could you describe ‘long distance running’? How many km per week to be included?
-	L224-231: Please provide a figure to facilitate comprehension. This paragraph could be reduced in length at the same time.
-	L239: see previous comment about PT
-	Were strength data normalized to body mass?
-	L247: use sex instead of gender. Also, I don’t recall seeing a comparison of men and women in the study objectives. If it is an objective, you should clearly state that.

Results
-	L255-258: Data is repeated in text and Tables. I suggest taking that out of the text to improve readability and refer to tables only.
-	L284: This should be described in Methods.

Discussion
-	L303-308: This paragraph looks like a Methods paragraph and does not belong to a Discussion.

Conclusion
-	Revise first sentence. Also, your conclusion is too succinct and does not reflect findings from this study very well.

Tables 2-3: Please provide detailed P-values for correlations. I’m not sure to understand why FFM (g) and FFM (%) are opposite. Unless I’m wrong, the higher the FFM mass, the higher the FFM % should be.


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: HIP MUSCULAR STRENGTH BALANCE IS ASSOCIATED WITH RUNNING ECONOMY IN RECREATIONALLY-TRAINED ENDURANCE RUNNERS
Review round: 2
Reviewer: 1

Output:
Basic reporting: the revised manuscript has improved substantially since its original submission.
Experimental design: the experimental design fills a small, but interesting, knowledge gap.  Methodology has improved substantially since first submission.
Validity of the findings: The authors should temper their discussion to reflect that many results are correlated and correlation does not necessarily imply causation.
Additional comments: The authors should be commended for a thorough revision of the submitted manuscript.  I think the manuscript is improved substantially from its previous version.

With regards to my specific comments, I have but a few clarifications that should be addressed.  I have highlighted my responses to the author responses in bold below.

L26 – specifically what about ‘body composition’?
Answer: Thank you for your comment. Total body mass seems to be a crucial factor for RE.
Thank you for clarifying.  I suggest then to replace ‘body composition’ with total body mass throughout the manuscript (eg. line 32 of revised manuscript).  Further, remove ‘body composition’ from line 50 (“no significant relationships were found between Ec, today body mass or body composition).  Or simply clarify that ‘body composition’ refers to fat mass, and replace body composition with fat mass.

L47 – the suggestion that athletes should incorporate strength training into their training plans is not new. See a recent review by Blagrove (Blagrove, Brown, Howatson, & Hayes, 2017; Blagrove, Howatson, & Hayes, 2017).
Answer: There is evidence that strength training is beneficial to RE (Blagrove et al. 2017; Denadai et al. 2017); however, the results are still contradictory (Blagrove et al. 2017). Several general strengthening programs have been evaluated, including isometric resistance training (Johnston et al. 1997), explosive resistance training (Berryman et al. 2010), plyometric training (Saunders et al. 2006), and a combination of different strengthening programs (Giovanelli et al. 2017). However, the present study does not suggest that athletes should incorporate general strength training into their training plans. The present study aimed to verify if the hip flexor and extensor isokinetic peak torque (PT) and isokinetic strength balance ratio were associated with running Ec. The main finding was that the hip functional strength balance (flexor eccentric-to-extensor concentric) was more strongly associated with Ec than absolute muscular strength. In light of these results, a specific eccentric strengthening program directed to the hip flexor muscles may improve the functional balance ratio and Ec. This sentence has been rewritten for clarity.
Denadai BS, de Aguiar RA, de Lima LC, et al. Explosive training and heavy weight training are effective for improving running economy in endurance athletes: a systematic review and meta-analysis. Sports Med. 2017;47(3):545–54.
Johnston RE, Quinn TJ, Kertzer R, Vroman NB. Strength training in female distance runners: impact on running economy. J Strength Cond Res. 1997;11(4):224–9.
Berryman N, Maurel DB, Bosquet L. Effect of plyometric vs. dynamic weight training on the energy cost of running. J Strength Cond Res. 2010;24(7):1818–25.
Saunders PU, Telford RD, Pyne DB, et al. Short-term plyometric training improves running economy in highly trained middle and long distance runners. J Strength Cond Res. 2006;20(4):947–54.
Giovanelli N, Taboga P, Rejc E, Lazzer S. Effects of strength, explosive and plyometric training on energy cost of running in ultra-endurance athletes. Eur J Sport Sci. 2017;17(7):805–13.
Thank you for a thoughtful and insightful response.  The reference to Fletcher et al. 2009 likely refers to Fletcher et al. 2010.  Please revise.

L47 – the suggestion that athletes should incorporate strength training into their training plans is not new. See a recent review by Blagrove (Blagrove, Brown, Howatson, & Hayes, 2017; Blagrove, Howatson, & Hayes, 2017).
Answer: There is evidence that strength training is beneficial to RE (Blagrove et al. 2017; Denadai et al. 2017); however, the results are still contradictory (Blagrove et al. 2017). Several general strengthening programs have been evaluated, including isometric resistance training (Johnston et al. 1997), explosive resistance training (Berryman et al. 2010), plyometric training (Saunders et al. 2006), and a combination of different strengthening programs (Giovanelli et al. 2017). However, the present study does not suggest that athletes should incorporate general strength training into their training plans. The present study aimed to verify if the hip flexor and extensor isokinetic peak torque (PT) and isokinetic strength balance ratio were associated with running Ec. The main finding was that the hip functional strength balance (flexor eccentric-to-extensor concentric) was more strongly associated with Ec than absolute muscular strength. In light of these results, a specific eccentric strengthening program directed to the hip flexor muscles may improve the functional balance ratio and Ec. This sentence has been rewritten for clarity.
Denadai BS, de Aguiar RA, de Lima LC, et al. Explosive training and heavy weight training are effective for improving running economy in endurance athletes: a systematic review and meta-analysis. Sports Med. 2017;47(3):545–54.
Johnston RE, Quinn TJ, Kertzer R, Vroman NB. Strength training in female distance runners: impact on running economy. J Strength Cond Res. 1997;11(4):224–9.
Berryman N, Maurel DB, Bosquet L. Effect of plyometric vs. dynamic weight training on the energy cost of running. J Strength Cond Res. 2010;24(7):1818–25.
Saunders PU, Telford RD, Pyne DB, et al. Short-term plyometric training improves running economy in highly trained middle and long distance runners. J Strength Cond Res. 2006;20(4):947–54.
Giovanelli N, Taboga P, Rejc E, Lazzer S. Effects of strength, explosive and plyometric training on energy cost of running in ultra-endurance athletes. Eur J Sport Sci. 2017;17(7):805–13.
Thank you for a thoughtful and insightful response.  The reference to Fletcher et al. 2009 likely refers to Fletcher et al. 2010.  Please revise.

L149 – why those specific speeds tested?
Answer: The force–velocity relationship was hyperbolic, and a slow test speed (60º/s) was chosen to evaluate the maximum strength values. On the other hand, functional movements occur at faster angular speeds, therefore a faster test speed (180º/s) was also chosen. Volunteers cannot develop torque at higher angular speeds, therefore the speed of 180º/s was the maximum speed used. These tests speeds were previously used by Julia et al. (2010) and Zapparoli and Riberto (2017).
Thank you for elaborating.  The information above should be in the revised manuscript to clarify why 60 and 180º/s were specifically chosen.

L204 – the TESTED speeds WERE lower than the AT… how was this confirmed?
Answer: The grammatical errors have been corrected.
The CPET test was performed to individually check the velocity corresponding to the VT. After verifying the speed corresponding to the VT in each volunteer, we chose a speed below the minimum VT (11 km.h-1) to evaluate the RE. The RE at 14 km.h-1 was only evaluated in a small subgroup of athletes (n = 9) who presented VT at 15 km.h-1. Therefore we can confirm that all volunteers ran at a moderate domain during the RE test using a 1% gradient.
When the RE test was performed using a 3% gradient, the treadmill speed was decreased by 1 or 2 km/h (from 11 to 10 km.h-1 and from 14 to 12 km.h-1). Toownshend, Worringham & Stewart (2010) demonstrated that the speed decreased by 0.1–0.3 km/h for each 1% gradient increase during uphill running. Considering that the treadmill grade increased by 2% (from 1% to 3%) in the RE test, the speed need to be reduced by at least 0.6 km.h-1. As the treadmill speed was reduced by 1 or 2 km.h-1, we conclude that the test was also performed in moderate phase.
Townshend AD, Worringham CJ, Stewart IB. 2010. Spontaneous pacing during overground hill running. Medicine and Science in Sports and Exercise 42:160–169

The revised methodology is substantially improved; however, specifically, the revisions do not address how ‘VO2 stabilization’ was defined (eg. change of <100 ml/min over the final 2 mins).

L210 – how long were the RE tests? How was steady state confirmed in the RE tests specifically?
Answer: RE tests lasted for 4 minutes. The steady state was confirmed by VO2 stabilization during the last 2 minutes of the test. This information has been included in the text for clarification.
The revised methodology is substantially improved; however, specifically, the revisions do not address how ‘VO2 stabilization’ was defined (eg. change of <100 ml/min over the final 2 mins).


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: HIP MUSCULAR STRENGTH BALANCE IS ASSOCIATED WITH RUNNING ECONOMY IN RECREATIONALLY-TRAINED ENDURANCE RUNNERS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The English language was improved.
The introduction was able to present the study problematic.
The paper structure is conforms to journal guidelines.
There is not a supplement file.
Experimental design: Original research within journal scope.
The research question is well defined and relevant.
The Methods section is well described with sufficient detail to replicate the study.
Validity of the findings: Conclusion was improved.
Many speculations were supplied. The authors highlight these speculations.
Additional comments: My comments have been addressed. Thank you.


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: MULTIPLE TRANSGRESSIONS AND SLOW EVOLUTION SHAPE THE PHYLOGEOGRAPHIC PATTERN OF THE BLIND CAVE-DWELLING SHRIMP TYPHLOCARIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper reports molecular data of three of the four species of the genus Typhlocaris, which allows to discriminate between two alternative scenarios for their origin.  These are rare species with high conservation interest, but also very interesting from an evolutionary and biogeographic perspective. I think the data and the general conclusions re. the origin of the species are valid, but there are some methodological aspects, and some considerations on the evolutionary rates, that should be revised.

Some detailed comments follow:

Abstract (also similar expresions in the text) “T. salentina (Italy) and T. ayyaloni (Israel) are more closely related than T. galilea (Israel).” The text is confusing, possible alternatives are: "more closely related to each other than either of them is to T. galilea", or better, "they are sister species, and both sister to T. galilea."

line 62: “is the large blind prawn of the genus Typhlocaris.” Should be plural.
line 135: give commercial brand and city.
lines 150-151: the two “transisthmian” pairs are used only for comparison in the Discussion, there is no need to specify this in the Methods.
lines 195-196: there is no need to mention the results of a NJ tree. This is not a phylogenetic method.

In Table 1, the informative positions as with or without outgroups? Also, the BIC and AICs of the best models on their own are meaningless: they should be compared with the values obtained under different models. Unless all the values obtained with the different models tested are given, so that they can be compared, there is no point in giving those of the best models.
Experimental design: lines 148-149: more details are needed re. the choice of outgroups. There are only two species, it is said that both belong to the infraorder Caridae, but no family or superfamily is given. According to current taxonomy, it seems that one of them belongs to the same superfamily as Typhlocaris (Palaemon), but the other to a different superfamily (Ephyrina). If so, the trees should be rooted in Ephyrina, not in the split between Typhlocaris and (Palaemon+ Ephyrina) (see e.g. a recent molecular phylogeny of Palaemonoidea in Kou et al., 2013, Inv. Syst.), as this renders Palaemonoidea paraphyletic. This has no implication for the topology of the genus Typhlocaris, but could have some implications for the dating.

In reference to this question, did the author build a calibrated, ultrametric tree? From their explanations is not clear if they did, but they certainly should, either with MrBayes, BEAST or other similar method. They should also figure it – and make sure that the outgroups are rooted properly.

Line 170++: The tree is calibrated with the split between T. galilea and its putative sister. This node is thus fixed a priori, and should not be considered a result, or given the impression that is a finding of the work. In some cases this is not clear, e.g. in lines 212-216. It should be more clear that the dating of this node is not a result of the study. This means that the evolutionary rates are fixed by this a-priori dating, and should be considered with caution.
Validity of the findings: Lines 265++ The whole discussion on the reasons for the low evolutionary rates is just far too speculative, especially considering that, as noted above, they are the result of an a-priori calibration of a node. The easiest solution to the problem is to change the age of the node: perhaps the separation between T. galilea and its sisters was not 7Ma, but in a more recent time. Then the problem of the very slow rates would be solved without the need to invoke obscure reasons (see below).

Lines 265-267: I cannot follow this argument. The authors say that as evolutionary rates differ between genera within the same order, differences should be mainly due to ecological differences between them. There are many other potential sources for these differences: effective population size, generation time, body size, metabolic rate, presence of selective pressures….. They could be related to ecological differences, but they may not.

Lines 280-283, 288-289,311-314: same as above. The authors do not give any convincing reason for which the subterranean environment, or the lack of competition, should slow down the evolutionary rate. In fact, there are many subterranean groups, even among crustaceans, that do not show any slow down in evolutionary rate, despite having a similar ecology and way of life that then species of Typhlocaris (see e.g. Jurado-Rivera et al., 2017 Sci. Rep., or Bauza-Ribot et al., 2012 Curr. Biol., not to mention many other papers in other arthropod lineages).
Additional comments: A nice work, which conclusions I think are well founded, but that should be presented more convincingly and without needless speculation.


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: MULTIPLE TRANSGRESSIONS AND SLOW EVOLUTION SHAPE THE PHYLOGEOGRAPHIC PATTERN OF THE BLIND CAVE-DWELLING SHRIMP TYPHLOCARIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is written in English and easy to follow, literature well referenced and relevant, figures of high quality and raw data are available. The reporting, however, should be more focused. In the Introduction authors formulate two biogeographic questions. The two questions are not explicitly linked with the methods, and major part of the Discussion does not discuss the two question. Authors should try to make the manuscript more coherent, the Discussion could be shortened for at least for  50%.
Experimental design: The research is within the scope of the journal, the methods are appropriate for addressing the question and sufficiently well described. However, I have serious problems with experimental design. The objectives of the MS are to 1) reveal phylogenetic relationship of the Typhlocaris species and 2) to infer geological processes that have shaped their divergence pattern. The text that follows is only partly following the objectives.

The authors studied the relationship of three out of four species of this genus. This part is mostly clear. An exception is the long-branch among Italian populations, which may indicate an error, and authors should discuss this result. Furthermore, the authors studied only three species. I understand it is not possible to get the fourth species, but make this impediment clear and clarify it in the Introduction / where you postulate the hypotheses. Please note that it may impact the second aim!

The second aim is less clear to follow. Authors are not explicit, what test they used for testing hypotheses. On the one hand, Figure 2 implies that phylogenetic hierarchy itself is a test for either of hypotheses. I am fine with this, once the putative problem with the missing fourth species is accommodated. On the other hand, authors devoted much debate to timing and give an impression that they searched for temporal congruence in geological and splitting events. In theory, this approach would strengthen the test, but not in the way the authors did. If I understood the logic correctly, the described approach leads to cyclic reasoning. The problem is that they used one of the studied events as a calibration point, and then from calibrated phylogeny inferred the concordance between branching events and geological events. This impression is further strengthened by extensive discussion on molecular clock, whereas the paleogeographic and paleogeologic events are barely mentioned. The authors can overcome this issue in two ways. First, they can calibrate their phylogeny using some external calibration point (a calibration point outside the studied clade) and thereby assure that the studied events are at least seemingly independent from a priori assumptions used in testing. Alternatively, authors can use any of proposed molecular clocks, and check whether it fits to the data.

Finally, I recommend that authors stick to the questions. They should adjust the methods in order to assure the question is properly address, and in Discussion they should stick to the questions, rather to the methodological issue. I acknowledge that the latter is relevant, but it does not fall into the scope of the paper. The Discussion can be shortened, but I miss e.g. comments on missing species (which may influence the phylogenetic structure), or speciation that took place in the sea, prior the transgression events.
Validity of the findings: I suggest that the analyses are repeated as suggested above and the findings re-assessed.
Additional comments: I have read the MS, a report is appended below, some comments are embedded directly into attached PDF. Overall, I think the MS unveils some new insights  into phylogenetic relationships of the cave shrimps and should be published subject to revision.


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: MULTIPLE TRANSGRESSIONS AND SLOW EVOLUTION SHAPE THE PHYLOGEOGRAPHIC PATTERN OF THE BLIND CAVE-DWELLING SHRIMP TYPHLOCARIS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have revised the manuscript following the indications of the referees, and most of the objections have now been addressed appropriately. There are, however, some issues remaining, but mostly referring to the way results are presented and discussed, and not substantial.
Experimental design: no comment.
Validity of the findings: no comment.
Additional comments: I still find the line of argument of the paper a bit confusing, or at least not very clearly exposed. As I see it, the authors start with two different hypotheses for the origin of the studied taxa, which can be separated by the topology of the tree alone. Their tree supports unambiguously one of the topologies, favouring the pre-Messinian origin of the divergences within the genus Typhlocharis, so that with this the issue of the biogeographic origin is considered to be settled. The purpose of the use of BEAST is thus only to obtain the evolutionary rates of the genes studied under the favoured topology, and compare them with the rates given for Crustacea in other published works - it is not relevant to establish the biogeography of the genus, as the authors already accept its pre-Messinian origin based on the topology alone.  In consequence, they dismiss the dating using the published rates and accept those obtained with the pre-Messinian calibration point without further discussion. If my interpretation is correct, this should be made more explicit through the paper.

And I am still thinking that the link between slow evolutionary rates and "ecology", and more particularly competition, is purely speculative and the authors do not provide any hard data to support it. The Discussion may be open to some speculation, but I would recommend the authors to be more cautious when interpreting their results.


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: MITOCHONDRIAL GENOMES ORGANIZATION IN ALLOPLASMIC LINES OF SUNFLOWER (HELIANTHUS ANNUUS L.) WITH VARIOUS TYPES OF CYTOPLASMIC MALE STERILITY
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is well written and describes the assembly of the mitochondrial DNA of the fertile, PET1 and PET2 cytoplasm in sunflower from next generation sequencing data, which in principle is very interesting and new for PET1 and PET2. However, the assembly of PET2 is not satisfactory. The offer of two circles that cannot be combined is not helpful. It indicates the mtDNA for PET2 is not correctly assembled.
Experimental design: Results for the RT-PCR should be shown and should include the study of fertility restored hybrids.
Validity of the findings: 1. The manuscript requires presentation of one circle for PET2. The coverage might not be high enough or hybridization results might be helpful to solve the problem. The early publication of two premature mtDNA circles for PET2 is not helpful.
2. For claiming an involvement with the CMS phenotype at least the effect on transcripts in fertility-restored hybrids should be shown. It is not enough that an orf is expressed in the male sterile line, but not the fertile line.
3. The sequence of the 5 kb insertion in PET1 is already present in NCBI (accession Z23137.1) and should be mentioned in the manuscript. Homology between the sequences should be discussed.
4. The two open reading frames, orf645 and orf1053, which are supposed to be involved in the CMS phenotype encode proteins of about 21 kDa and  about 35 kDa, respectively. The CMS-specific protein detected by in organello translation for PET2 has a size of 12.4 kDa (Horn and Friedt 1999). This might be an indication that both new open reading frames, only transcription is stated for orf645, might not be involved.
Additional comments: Please take your time to correctly assemble the PET2 mtDNA! I think you do not gain anything by publishing preliminary data even though you put already a lot of work into the the manuscript.


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: MITOCHONDRIAL GENOMES ORGANIZATION IN ALLOPLASMIC LINES OF SUNFLOWER (HELIANTHUS ANNUUS L.) WITH VARIOUS TYPES OF CYTOPLASMIC MALE STERILITY
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper should be seen by a native English speaker or a technical editor. There are multiple typos and unnecessary punctuation signs. For example, " revealed two single nucleotide insertion: thymidine insertions in 35690-35691 and 129368-129369 positions of NC_023337" should be " revealed two single nucleotide thymidine insertions: in positions  35690-35691 and 129368-129369 of NC_023337".  And the following sentence " Considering that due to 2 SNP is not reasonable for appending current data (HA89 fertile line complete mitochondrion sequence) in the NCBI databank" should also be completely reworked. "MC2 cyclization was failed" -> :"MC2 cyclization has failed"
Experimental design: The PET2 genome used is not fully assembled. It would be desirable to produce the entire genome. I do not anticipate this task to be theoretically or practically challenging
Validity of the findings: There was a new open reading frame orf1053 described in the genome. This in silico discovery should be supported by RNA seq data. This may be a chimeric gene or assembly artifact,etc. The authors need to analyze structure of promoters and distribution of TBFS to support the function of the identified genes.
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: MITOCHONDRIAL GENOMES ORGANIZATION IN ALLOPLASMIC LINES OF SUNFLOWER (HELIANTHUS ANNUUS L.) WITH VARIOUS TYPES OF CYTOPLASMIC MALE STERILITY
Review round: 2
Reviewer: 1

Output:
Basic reporting: I think the manuscript has been significantly improved. The circular assembly of PET2 mtDNA looks much better now. It represents a unique contribution and should therefore be published. The other two assemblies for the fertile and the CMS PET1 are also of public interest. In the latter two it would be nice if the nad5 would be given with its location. The PET2 DNA assembly also supports the data obtained by Reddemann, Horn 2018. Orf228 represents orf231 without counting the stop codon and orf246 corresponds to orf288 (without stop codon and the possible elongation at the 5’ end of the atp9 gene). However, in our fragments nad5 was on the same fragment as atp9 and the split atp9 was on the fragment together with the orf2565 (DNA polymerase type b homology). This might be looked into it again.
Experimental design: no comment
Validity of the findings: Next generation sequencing data allow assembly of whole mtDNA genomes, which has been done in this manuscript. The coverage was sufficient for obtaining the results. Duplications were detected.
Additional comments: In Table 1 amplicon size needs to be corrected. Either use bp than some values have to be changed from 0.9 to 900 or use kbp but then other values have to be changed from 162 to 0.162. Please correct one way or the other!
The manuscript still needs some improvement with regard to the English language. Some corrections are suggested here and should be made in the manuscript:
Line 17: 	is often associated
Line 18-19:	Investigations of the CMS phenomenon also promote understanding of fundamental
		issues of
Line 21:		Helianthus annuus in italics
Line 45-46:	large sizes….. sequences which can result in complex sub-genomic structures
Line 52:		Leclercq in an interspecific
Line 55:		11-kb-inversion and a 5-kb-inversion
Line 56: 	Those rearrangements
Line 61+62:	16-kDa-protein
Line 67:		Interestingly, stable transgenic
Line 72:		restorer
Line 78: 	Leclercq (1969)
Line 113: 	from five plants
Line 186:	which has already been available in
Line 192: 	in the NCBI databank
Line 197:	both, large-scale
Line 199: 	one translocation, two deletions and three insertions were determined.
Line 208:	we could demonstrate that the mtDNA in sunflower can also form a 154-kb sub-genomic
		circular molecule
Line 211: 	makes the cyclization of ……..molecule possible. …………….sub-genomic circular molecule
Line 215+216:	The orf777 codes for a putative …..function, which shows no similarities
Line 218:	……..noncoding sequences. Notably the insertions
Line 221:	…..resulted in a translocation, as described above.
Line 223:	… most likely not involved in the origin of the CMS phenotype.
Line 228: 	orf645 putatively translated into a polypeptide……. Twenty-three amino acids at the N-
		terminus
Line 230:  	transcripts of orf645 in PET2 CMS line by qPCR, using specific primers (Table
                 1). 	However, mRNA of orf645
Line 241: 	for Helianthus (in italics) mitochondrion
Line 246:	this part of the insertion …… coding sequences.
Line 252:	….domains. The opposite is the case for the atp6 gene.
Line 264+265:	at the C-terminus of the ATP6 protein.
Line 269:	nearly
Line 270:	atp6 in italics
Line 271:	Interesting to note is that
Line 276:	probably associated
Line 277+278:	is a 1558-bp-insertion localized between the genes nad5 and ccmFc. The 14330-bp-
		insertion as well as the 1558-bp-insertion have a complement to another part of the
                genome and a unique sequence.
Line 283:	in two new ORFs
Line 284+285:	Orf228 encodes a polypeptide of 76 aa, of which 75 are identical
Line 286:	resulting
Line 286:	…..lacks four amino acids
Line 293: 	Add: The orf246 corresponds to orf288 (Reddemann, Horn 2018), which takes a possible
		elongation at the 5’-end of the atp9 gene in sunflower into account.
Line 299:	Interestingly PET1


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: MITOCHONDRIAL GENOMES ORGANIZATION IN ALLOPLASMIC LINES OF SUNFLOWER (HELIANTHUS ANNUUS L.) WITH VARIOUS TYPES OF CYTOPLASMIC MALE STERILITY
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors fixed the majority of the typos and significantly improved presentation of the material. Mathematical formulas (such as 1+E^ΔCt formula) should be typed using an appropriate equation editor.
Experimental design: The authors assembled the genome and, therefore, the manuscript does not look like a dump of half-cooked results anymore
Validity of the findings: qPCR and Sanger validation of discovered rearrangements was conducted.
Additional comments: The paper was significantly improved. The authors took all suggestions into consideration. I recommend to accept the manuscript in its current form, except for minor formatting changes as described above.