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: HYDROCLIMATIC VARIATIONS REVEAL DIFFERENCES IN CARBON CAPTURE IN TWO SYMPATRIC CONIFERS IN NORTHERN MEXICO
Review round: 1
Reviewer: 1

Output:
Basic reporting: Under the consideration that I am not an English native speaker, the paper was clear for me
Experimental design: Methodology seems to me well done
Validity of the findings: Convincing results
Additional comments: Main comments
Convincing manuscript (I liked specially Figures 3, 4 and 5) that finds differences between Pseudotsuga menziesii and Cupressus lusitanica on the Mexican Sierra Madre Occidental, in sensitivity of dendrochronological variables in response to climate variables.
In my view,  considering that  the overall world-wide trend (due to climatic change) is increase mortality (e.g. Allen et al 2010) rather than a beneficial increase of growth of so, based on the findings of the authors, especially the strong sensitivity to winter rain for P. mensiezii , I wonder if the authors wanted to advance the hypothesis that expected increase of tree mortality (linked to climatic change) on Sierra Madre Occidental, might occur if happen one (or more) year(s)  with a winter extremely dry and warm.
Conclusions need to be more explicit about what are those differences in climatic sensitivity between those two species (more details below).
There are minor changes needed indicated below, to improve clarity.
I suggest accepting it with minor changes.

Minor comments
Lines 55-56. “Such information enables the proposal of actions through which to understand the effects of climate change on forest ecosystems”. I believe that suggested actions, derived from gaining understanding of the processes, are for improving management to mitigate climatic change impacts. However, suggested actions are not for “understand” the effects of climate change. The understanding phase is previous to the action phase.
59-60. “when it is associated with density data”. Better: “when it is associated with Wood density data”.
77. “The Sierra Madre Occidental is recognized by…”. Better for an international audience: “The Sierra Madre Occidental along western México is recognized by…”.
83. “while the latter is located in areas close to water bodies”. ?????  I doubt that. Well, not in my limited experience. Perhaps authors aimed to say “while the latter is located in temperate-cold moist areas”.
99-102 and 173-174. Figure 1 Caption. “El Salto meteorological station”. Indicate Lat., Long. and elevation of that station.
320-324. OK, if the overall trend (due to climatic change) is increase mortality rather than a beneficial increase of growth of so, and you found, specially for P. menziesii a strong sensitivity to winter rain, I wonder if you wanted to advance the hypothesis that expected increase of tree mortality (linked to climatic change) on Sierra Madre Occidental, might occur if happen one (or more) year(s)  with a winter extremely dry and warm?
338-344. Conclusions could be more explcity. You says that “C. lusitanica and P. menziesii presented different responses to seasonal climatic variability”. OK, then, say what are those differences! P. menziesii is much more sensitive to previous winter rain (for example). “ and, as a consequence, the conservation and restoration of these species will require different and specific management measures” OK, I agree, but, what kind of specific measurements would you envisioned, given your results? Perhaps develop a bit of that on the Discussion section.

On Figures 4 and 5, I do not see the “Letters and arrows that indicate  growth periods”. They are absent in my available version.


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: HYDROCLIMATIC VARIATIONS REVEAL DIFFERENCES IN CARBON CAPTURE IN TWO SYMPATRIC CONIFERS IN NORTHERN MEXICO
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is the weakest portion of the manuscript. Writing is not clear, and this obscures the relevance of the questions addressed and the importance of the results. I started making notes on the manuscript as I began to read it, but soon realized that I would have to correct most paragraphs to make it readable to an English speaking audience, so I capitulated! I seriously suggest that a professional English native speaker corrects the style throughout the manuscript.
Authors fail to provide references on dendrochronological work conducted in Mexico which has identified climatic signals (temperature, rainfall) on tree growth, or in early vs. latewood. This is unfortunate because one of their studied species showed a pattern which is consistent with the findings of Carlón-Allende et al. 2016 & 2018. None of the references by Cerano or Villanueva are provided, which have also conducted analyses of climatic influences on tree growth for different conifer species in Mexico.
Most sections of the manuscript are adequate, except for the introduction. It fails to provide enough evidence for the relevance of the questions addressed.
Experimental design: As stated above, research questions are not clearly justified in the introduction. Authors should note that they did not measure carbon flows. They estimated carbon and biomass gain through growth in tree diameter, and through the use of one allometric equation. Hence, most of their argumentation about carbon fluxes is irrelevant to their study.

Dendrochronological methods are adequate and clear. However, field and collection methods are not.  There is little explanation on how the 15 individuals for each one of the two species were selected. Was there a criterion to collect cores from the largest and presumably oldest trees within forest stands? Where were the forest stands? Where all trees on south or north facing slopes?
Validity of the findings: Presuming that trees were collected from sites where no site-effect might have modified their results, then the findings are credible. Because C. lusitanica was not very responsive to climatic variation, I am not convinced of the conclusions derived from this study about that species.
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: HYDROCLIMATIC VARIATIONS REVEAL DIFFERENCES IN CARBON CAPTURE IN TWO SYMPATRIC CONIFERS IN NORTHERN MEXICO
Review round: 2
Reviewer: 1

Output:
Basic reporting: English OK
New references were added, as requested by one reviewer.
Structure OK. Raw data available.
Discussion and conclusions are supported.
Experimental design: Methods follows usual methodology of the field
Validity of the findings: Discussion and conclusions are supported by their data.
Additional comments: I suggest to accept the ms.

Minor comments:
Comments on the tracked version.
L 95-97. “such as Cupressus lusitanica (Mill.) and Pseudotsuga menziesii (Mirb.) Franco. The first grows in areas with great water availability, while the second has a wider distribution. A comparative analysis could expand the knowledge.”.
I agree that Pseudotsuga menziesii has a very wide distribution across USA and Canada, but not in México. The sentence refers to Sierra Madre Occidental. Is needed to be more precise.

Comment for the pdf “clean”  version
Figure 7 is absent. There is only the Figure caption.

If the authors made the above mentioned corrections, I do not need to see again 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: HYDROCLIMATIC VARIATIONS REVEAL DIFFERENCES IN CARBON CAPTURE IN TWO SYMPATRIC CONIFERS IN NORTHERN MEXICO
Review round: 2
Reviewer: 2

Output:
Basic reporting: Authors did not make substantial improvements to the manuscript. Writing is very confusing in several portions of the text. I took longer than I would have liked to in reviewing this manuscript because I indicated changes throughout. I hope that authors include my suggestions and re-elaborate entire paragraphs where they introduce concepts that are irrelevant to the main point of the study.
Experimental design: Authors clarified most of my concerns in terms of experimental design. I wrote in the manuscript where further clarification is needed.
Validity of the findings: The main conclusion of the study, that is, that climatic variation can influence carbon uptake by trees, is well justified. Other side discussions, like the comparison of their method with other methods such as Eddy covariance, are unnecessary, unjustified, and only distract the reader from the main point of the study.
Additional comments: The few additions to the manuscript included in the second version did not address most of the limitations detected in the first version. Reviewing an article takes time, and it is done in the best of interests assuming that authors would reciprocate by improving 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: HYDROCLIMATIC VARIATIONS REVEAL DIFFERENCES IN CARBON CAPTURE IN TWO SYMPATRIC CONIFERS IN NORTHERN MEXICO
Review round: 3
Reviewer: 1

Output:
Basic reporting: Basic reporting OK
Experimental design: Methodology used sound
Validity of the findings: Interesting findings that the two conifers have different sensitivity for different climate variables
Additional comments: One main point:
1) I wonder if there is no a mistake on the last paragraph of Discussion section (lines 350-360). They state that:
 "The decrease in the mean annual temperature in the study area (CNA, 2016) that has taken place over the last 30 years seems to have had a positive  impact on carbon accumulation in some tree species, such as Cupressus lusitanica. Moreover, the negative trends of annual precipitation will cause reduced carbon uptake in some species, such as Pseudotsuga menziesii (Figure 6d)."
Really there is a "decrease in the mean annual temperature" ?? With all the ongoing climatic change is that true? Your figure 6d, that you invoke in that paragraph, indicate an increase of  temperature and a decrease of precipitation.
By the way, Figure 6 lacks a figure caption for panel (d).

Minor comment:
On several places of the revised version, scientific species names are not in italics.


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: HYDROCLIMATIC VARIATIONS REVEAL DIFFERENCES IN CARBON CAPTURE IN TWO SYMPATRIC CONIFERS IN NORTHERN MEXICO
Review round: 4
Reviewer: 1

Output:
Basic reporting: New version improved
Experimental design: Methodology OK
Validity of the findings: Conclusions for each species supported
Additional comments: Authors corrected the wrong sentence in the last paragraph of the Discussion section.
I see that there are improvements on the English wording after the comments of the other reviewer.

Only they missed again to provide a  figure caption for Figure 6, panel (d). It could be something like:
"(d) Relationship between mean annual temperature and total precipitation per year ".
or
"(d) Data trend of mean annual temperature and total precipitation per year ".
or
"(d) Mean annual temperature and total precipitation regressed against year ".


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: ANALYZING MOISTURE-HEAT COUPLING IN A WHEAT-SOIL SYSTEM USING DATA-DRIVEN VECTOR AUTOREGRESSION MODEL
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comments.
Experimental design: No comments.
Validity of the findings: No comments.
Additional comments: This manuscript analyzes moisture-heat coupling in a wheat-soil system using data-driven vector auto-regression model. The manuscript is not well written. There are some comments as below,

In Introduction part, please add some most recent references regarding the heat and moisture transfer process and summarize their major findings and unsolved critical problems.

Discussion part should be revised thoroughly, the reviewer could not find any deep analyses and discussion in terms of the results obtained in the previous sections.

Conclusion part is redundant and needs revision. Only major findings resulted from the study should be included in the conclusion.

English editing by a native speaker is highly recommended.


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: ANALYZING MOISTURE-HEAT COUPLING IN A WHEAT-SOIL SYSTEM USING DATA-DRIVEN VECTOR AUTOREGRESSION MODEL
Review round: 1
Reviewer: 2

Output:
Basic reporting: This article proposed a new model to coupling the water content and temperature in wheat soil. It is significant to develop this data-driven model to research the interaction of soil moisture and temperature in field.

But there are also some questions and unclear about this article when I read this paper. Some doubts have been marked in the text. Others have been written in the following parts (Experimental design and validity of the findings).
Experimental design: 1. You also said that you did not use other models to verify this new model at the end of the article. How to prove the results you obtained were reliable?

2. In the part “Field experiment on soil moisture and temperature”, the experiment was very clear. In the article you referred the drip irrigation and flood irrigation, and analyzed the influence of two irrigation systems on the coupling of soil water content and temperature. However, you haven’t mentioned the irrigation in the experimental design. Were there two irrigation systems in this experiment? And how-to analysis the different effect of drip and flood irrigation on soil moisture and heat?
Validity of the findings: 1. In this article, the time lag and response intensity are the most important results to indicate the interaction of soil water content and heat at different soil layer. Therefore, in the abstract you should explain the meaning of these results, and how to indicate the effect of soil moisture and heat. (Line18-30)

2. During designed the stochastic data-driven model, I am not very clear the process of developing, and how to calculate the time lag and response intensity using the soil water content and temperature data. Maybe I was not good at math and modeling. So, this part could be more detailed. (Line 81)

3. In the figures, you should be better to specify the horizontal and vertical coordinates, despite you have explain the meaning in text. (Figure 1-3)

4. You must be labeling the units of physical quantities, soil moisture and temperature.
Additional comments: I think it is a good idea to design this new model to analyze the coupling of soil moisture and heat. There are also lack of some data of different year and other depth. We should to verify the new model at different soil texture, depth and irrigation system. In addition, we should utilize other model which have been used widely to test the accuracy of new model.


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: ANALYZING MOISTURE-HEAT COUPLING IN A WHEAT-SOIL SYSTEM USING DATA-DRIVEN VECTOR AUTOREGRESSION MODEL
Review round: 1
Reviewer: 3

Output:
Basic reporting: Theoretically, soil moisture content dependent soil thermal diffusivity affects significantly thermal signals propagation from ground surface, thus soil temperature in soil profile and soil moisture content of corresponding soil layer related closely each other. There are many studies focused on unknown soil temperature prediction from known soil temperature, soil water content and other soil properties, such as Hu and Isram, 1995; Hirota et al., 2002; Holmes et al., 2008; Wang, 2012; Huang et al., 2014. Also many previous studies devoted to soil water content inversion from temperature measurements, like Steele-Dunne et al., 2010; Krzeminska et al., 2012; Bechkit et al., 2014; Halloran et al., 2016; Dong et al., 2015; Bristow, 1998; Ren et al.,2000; Liu,2011; Striegl and Loheide, 2012; Sayde et al., 2014. However due to the relationship between them involved many complicated factors, like soil properties, soil heat and water coupling transport, canopy and so on. A direct relationship between them is difficult to be established. Thus the results like P344-346 and 382-390 stated wrongly.

This manuscript investigates the relationship between present value and past value of soil temperature and soil moisture contents (different depth of soil profile). It provides the opportunity to understand the lagged effect of temperature on soil moisture content, or vice versa. Some results of soil profile during wheat greening period are obtained. In this regard, I like the contribution. However, the paper fails to verify these regression equations, and provides no general relationship between present value and past value of temperature and moisture content. Because the complexity of both crop factor and heat and water transport. Maybe the regression equation is rather empirical, thus all the conclusions are lack of universality. Like statement in the introduction section that “some soil moisture-heat coupling simulation, such as Philip and De Vries (1957), Nassar and Horton (1989), Shang et al. (1997), Bittelli et al. (2008)”. These studies estimates soil water and temperature parameters using numerical simulation of water-heat or water-heat-salt transport equation, which based on soil physical process and thus are a general method. Thus I really worried about the contribution of this paper.

Several issues in the format. (1) There should a space between number and units like h and cm but no space between number and oC. (2) some sentences are lack of a punctuation for broken sentences such as Lines 401. (3) The figures have no axis titles and units.

Finally, the manuscript is poorly organized and expressed. Some sentences in the Discussion and Conclusion section duplicate the information from the Results section. Many Grammatical mistake occurred, for example,

Line 51. What is affected closed soil column.

Lines 52-53. This statement is difficult to understand.

Line 127. Increase the likelihood of what?  Fitting models? Doing so may result in over-fitting? Unclear statement

Lines 131-133. What is estimated model and estimated regression model.

Line 155. The impulse response can be built. Improper statement.

Lines 160-161. The explanatory ability of regression. What is meaning?

Line 186. The time length during which there is obvious response of soil moisture. What is meaning?

Line 400. For the empirical test of this method. What is meaning?
Experimental design: no comment
Validity of the findings: The authors also spent effort on providing suggestions on irrigation using the analyzing results from regression equations. This simple function is far from enough to guide irrigation as it is affected by many factors such as soil and crop properties.
Additional comments: This paper maybe better if focused on analyzing the lagging effect between soil moisture and temperature using mentioned method, and also verify its universality and potential importance using more data of different conditions. The author also should improve the english writting to a greater extent.


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: ANALYZING MOISTURE-HEAT COUPLING IN A WHEAT-SOIL SYSTEM USING DATA-DRIVEN VECTOR AUTOREGRESSION MODEL
Review round: 1
Reviewer: 4

Output:
Basic reporting: Clear and concise. Sufficient literature cited. Professional figs, tables.

Raw data and codes are not shared.
Experimental design: The experiment design is not very sound because the authors have not discussed the heterogeneity of the soil horizontally, and particularly vertically.
Validity of the findings: The authors should mention/discuss how the results discovered here may vary with soil texture and climate conditions.
Additional comments: In this study, the authors used a data-driven vector auto-regression model to investigate the moisture-heat coupling in a wheat-soil system. They found that the time lags and response intensity for moisture and temperature responses were different at different depths. Based on the results, they suggested that surface flooding irrigation is appropriate and the vector auto-regression model can help predict soil moisture response at 10 and 30 cm.

In general, the manuscript is well written. However, some minor grammar mistakes need attention. For example, the last sentence of the abstract and line 146 (tow variables?). I suggest the authors recheck the grammar throughout the paper and improve the readability of the manuscript, particularly the method section.

In addition, I have a few comments on the manuscript.

Lines 183: What are the six impulse response functions? Temperature as shock and moisture as response vs. moisture as shock and temperature as a response? Are the shocks all positive or negative?

Lines 192: why 30 cm? Please describe the irrigation systems first, particularly the depths of the drip irrigator. Did you only have drip irrigation at 30 cm?

Lines 218 to 225: Provide more details on the principles of the sensors. What type of sensors did you use to measure soil moisture and temperature? How did you know they are “highly accurate” and the measurements are free of instrumental drifts? What is the evidence? The measurement accuracy of 0.5 degrees is not very accurate. How about the accuracy of soil moisture?

Lines 246. Please plot the time series after you removed the seasonality.

Figures 3 and Table 3: Please define or plot the shock signals for soil moisture and temperature at different depths for different scenarios. When you say one unit positive shock, what is the unit? What are the units of responses in Table 3?

The results presented here are based on measurements of soil moisture and temperature at one location. How did you deal with the spatial variability of the soils horizontally and vertically? Do you have any physical and chemical analysis data on the soil?

The authors should mention/discuss how the results discovered here may vary with soil texture and climate conditions.

Lines 366 to 372: What are the physical implications of these lags and intensity? Please try your best to explain these results using the previous studies you cited in the introduction such as Liu et al. (2005).

Lines 373-381: This is a key section of the manuscript. Please provide more details on the management issues related to the coupling of soil moisture and temperature in irrigation and discuss more previous studies related to this issue. Why do you want to avoid/trade off the influence of soil temperature on soil moisture when using surface flood irrigation? Would you see the same effect if the soil were within a warming or cooling phase at the time of irrigation? For example, an upward temperature gradient occurs in the winter before the sunrise will affect the water movement in the soil but this will be different after the sunset.

Lines 382-390: How did your results contribute to the current knowledge of coupled heat and water movement in soils as discussed by the previous studies and cited in the introduction? Are you suggesting that it is possible to include the hysteresis effects for an updated coupled heat-water-vapor movement model in the soil as suggested by researchers such as Liu et al. (2005) and Nassar and Horton (1989)?

Since PeerJ is an open access journal, the authors should refer to the online software packages that can be used to conduct this type of analysis or upload a simplified version of the codes they used to generate the results. In this way, more researchers from soil and hydrological sciences can easily include the coupling of soil moisture and temperature for their research. In addition, this will help get the paper noticed by the peers and increase the citation of the work.


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: ANALYZING MOISTURE-HEAT COUPLING IN A WHEAT-SOIL SYSTEM USING DATA-DRIVEN VECTOR AUTOREGRESSION MODEL
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comments.
Experimental design: No comments.
Validity of the findings: No comments.
Additional comments: In the revised manuscript，the authors linked this data-driven model to the physical model, SPAC Continuum, and explained the results obtained from the vector auto-regression model using four equations in the SPAC Continuum. They proved that the results obtained from the vector autoregression model are reasonable with sound physical foundations, especially considering the processes of soil evaporation and plant transpiration.
This aim of the article is to introduce an acceptable method to research the relationship of soil water and heat. Despite the authors has revised the article based on the comments of reviewers, the article is a bit of complicated and verbose. Especially the abstract part, the results is not refined enough. They added much new information to explain the model and others, but this make the process more complicated. So I think it is better to rearrange the structure of the article, and this article can be accepted.
The English writing has improved a lot.


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: ANALYZING MOISTURE-HEAT COUPLING IN A WHEAT-SOIL SYSTEM USING DATA-DRIVEN VECTOR AUTOREGRESSION MODEL
Review round: 2
Reviewer: 2

Output:
Basic reporting: Part of the expression is a lack of linguistic rigor: your study focused on the relationship between the present value of two variables and each other’s past value rather than soil temperature and soil moisture. Thus the expression, such as line 363 and 400, it should be the past value of soil temperature is not help for predicting present value of soil moisture. From physical perspective, soil temperature and soil moisture is related closely each other.
Experimental design: no comment
Validity of the findings: The author still failed to verify the universality of vector autoregression model and conclusion. For the same experiment site but different years, the author obtained different results like lines 395-398 (results of 2016-2017) and lines 411-413 (results of 2017-2018). Thus the author should be cautious about the model’s development, maybe it is very empirical.
Additional comments: In Introduction part, please logically simplify this part about the previous researches and relate it with your study, rather than just a long list.

Double check some problems like:
Line 235, there still lack space between number and unit of cm.
Line 245, volumetric water content unit should be m3 m-3 rather than %
Line 467, unifying the unit of time with before (hours and h).
Lines 367-368, the depth should be 30 cm rather than 10 cm


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: IN VITRO PERFORMANCE IN COTTON PLANTS WITH DIFFERENT GENETIC BACKGROUNDS: THE CASE OF GOSSYPIUM HIRSUTUM IN MEXICO, AND ITS IMPLICATIONS FOR GERMPLASM CONSERVATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: There are some sentences that need to be revised by an expert in English editing and academic writing.
Experimental design: There are some gaps in the methodology. Though the tests implemented to prove the statistical significance of data are right, it is desirable to include the reasons explaining why such models and analyses carried our were used, including examples on the topic recently published.
Validity of the findings: Results are very well supported. Nevertheless, authors may respond some basic question such as: Why did the Wt and Dt display such phenotypes? Which metabolic pathways were changed? ...
Additional comments: The manuscript presents interesting data and fulfills aims and scope of the Peer Journal. Some weaknesses detected and that need to be addressed by authors are:
Line … 81 … “is a plant that has Mexico as its center of origin” … please revise if this sentence is appropriate and grammatically correct
Line 126 … “and 50g” … number and unit need to be separated
Line 126 … “controlled release fertilizer Osmocote), … please provide more details on this fertilizer: chemical composition, manufacturer, country of origin …
Line 134 … “6ml of MS” … number and unit need to be separated
Line 137 … “reached 8cm height” … number and unit need to be separated
Line 141 … “EUA).” … Do you mean USA? If so, please correct
Line 152  … “EUA).” Do you mean USA? If so, please correct
Line 156 … “a negative, and a positive control” … Please provide more details regarding the controls
Line 161 “Cry1Ab/Ac, Cry2Ab,” please provide the sequences of the primers
Line 162 … “CP4EPSPS” … please provide the sequence of the primer
Line 162 … “Eurofins Scientific” … include city and country of the company
Line 166 … “accession #MK089921-30” was not found in the GenBank platform:

Line 194 … “microbial growth” … please explain how you discriminated between contaminations during the preparation of culture and contaminations due to endophytes
Line 204 … “Data analysis” please include some references supporting the statistical tests you applied to analyze your data; other examples applying such tests would be desirable
Line 208 … “R” in italics, to be consistent with R in line 217
Line 227 … “populations,” comma is not needed inhere
Literature cited:
Cross reference all of the citations in the text with the references in the reference section. Make sure that all references have a corresponding citation within the text and vice versa. Double check the spelling of the author names and dates, and make sure they are correct and consistent with the citations.
Spell out all abbreviations in the text the first time they are mentioned in the text.
Spell out all journal titles in the reference section.
Make sure that all figures and tables are cited within the text and that they are cited in consecutive order.
All and all, strictly follow the instruction for authors of the journal: https://peerj.com/submissions/33125/reviews/414730/guidance/
Supplementary Material … “1g per 1lt” … please fix all units and use the SI nomenclature throughout the documents


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: IN VITRO PERFORMANCE IN COTTON PLANTS WITH DIFFERENT GENETIC BACKGROUNDS: THE CASE OF GOSSYPIUM HIRSUTUM IN MEXICO, AND ITS IMPLICATIONS FOR GERMPLASM CONSERVATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is acepted in English language. Authors give sufficient references to describe the field of this study. The hypothesis about effective of transgene presence on cotton biodiversity is an good, but the results can not robust support it.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This manuscript designed the experiment to evaluate effective of transgene presence on cotton biodiversity change. Authors examined the differences of five in vitro culture performance traits between W and D, Wt and W, WT and D, WT and DT through PERMANOVA and NMDS tests. However, the results of statistic tests are simple, and can partially reveal the effective of transgene performance on the G. hirsuturm and wild diversities. Thus other analyses must be added to in detail evaluate the effective.
Some comments followed below:
1.	Based on the statistic tests of ANOVA, authors add multiple comparison tests among individuals of W, WT, D, and DT groups.
2.	The title is unfit for the results, please revise it.
3.	The running title is missing.
4.	Line 99, Gossypium hirsutum should be omitted into G. hirsutum for the second presence in main text.
5.	Line 246 and line 253 and so on, “three out of the five in vitro performance traits ” and “four out of the five analyzed traits” and so on, what are these different in vitro performance traits? Reviewer could not identify them only from Figures.
6.	In Figure 2a, microbial growth comparison is wrong in label line.


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: IN VITRO PERFORMANCE IN COTTON PLANTS WITH DIFFERENT GENETIC BACKGROUNDS: THE CASE OF GOSSYPIUM HIRSUTUM IN MEXICO, AND ITS IMPLICATIONS FOR GERMPLASM CONSERVATION
Review round: 1
Reviewer: 3

Output:
Basic reporting: I suggest the article to be revised by a native English speaking editor to improve the scientific vocabulary and grammatical format used to write.
Experimental design: They use population controls of domestic transgenic and wild type plants that are non-related. Therefore, I recommend using same genetic background samples in experiments.

On the other hand, the authors do not consider position insert of the genome transgene, since a gene doesn’t characterize a specific phenotype. Moreover, there are possible implications on genome variants (SNP) over populations and the possible implications associated to in vitro culture.

As well, it is necessary to determinate the endophytic bacteria or fungus that grew to correctly interpret the results. Research suggests the existence of advantages and disadvantages of the interaction between cotton plants and microorganisms, where there might be different results in in vitro culture.
Validity of the findings: The aim of the article is to evaluate in vitro culture advantages and disadvantages of transgenic and non transgenic cotton populations. However, the results are speculative due to the methods being control lacking.
Additional comments: Because of these reasons, I recommend the results given to be improved before the article is ready to be issued.


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: IN VITRO PERFORMANCE IN COTTON PLANTS WITH DIFFERENT GENETIC BACKGROUNDS: THE CASE OF GOSSYPIUM HIRSUTUM IN MEXICO, AND ITS IMPLICATIONS FOR GERMPLASM CONSERVATION
Review round: 3
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This revised manuscript has been improved in quality. And the explanation and information have been provided as well as the modification of statistics analysis. Now, the manuscript is clearly stated and well organized. There are two questions to be considered in revising this manuscript.
1.	The microoganisms growing the explants are not always endophyte. Thus, authors should give “possible” term to state the performance.
2.	The ELISA data seem to be missing, which should be added in supplemental file.

In fact, the integrated analysis of W, WT, D and DT may be better than by-pairs analysis.


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: IN VITRO PERFORMANCE IN COTTON PLANTS WITH DIFFERENT GENETIC BACKGROUNDS: THE CASE OF GOSSYPIUM HIRSUTUM IN MEXICO, AND ITS IMPLICATIONS FOR GERMPLASM CONSERVATION
Review round: 3
Reviewer: 2

Output:
Basic reporting: I read your new version of the article with great interest and noticed the more adequate title, however, I have two small comments:
1.- I consider the use of superlatives in the abstract to be unusual, therefore I suggest the elimination on line 41 of the word “strongly”
2.- On line 88; I suggest “some authors” to be changed to “an author”, or add other arguments here, because they cited a Hypothesis and Theory Article, lacking any experiments, since I take this information with reserves. I invite the authors to change arguments or add other citations.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: I invite authors to discuss more closely and explain in what way the presence of these transgenic elements cause a detriment to germplasm and its in vitro culture.


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: VARIATIONS IN GUT BACTERIAL COMMUNITIES OF HOODED CRANE (GRUS MONACHA) OVER SPATIAL-TEMPORAL SCALES
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article provides an original investigation into the seasonal and geographical effects on the gut microbiome of wintering Hooded cranes.
The literature and background are sufficient.

There are some grammar and structural issues with the wording of the article (please see comments), but overall the article is well structured.
Experimental design: The originality of the research fits within the aims and scope of the journal and the research is well defined and meaningful and highlights an important knowledge gap.
The experimental design and statistical analysis is appropriate for this study.
Validity of the findings: The conclusions of this study are well stated and linked to previous research and the findings valid. There are some areas that need addressing (please see comments).
Additional comments: Please address the comments highlighted in the pdf copy of your 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: VARIATIONS IN GUT BACTERIAL COMMUNITIES OF HOODED CRANE (GRUS MONACHA) OVER SPATIAL-TEMPORAL SCALES
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1) Detailed editing of the English language and grammar is required throughout the text. Most notably, ensure correct usage of singular and plural forms of words, apostrophes for possession, and pronouns (e.g., within the Introduction, see lines 46, 56, 59-61, 65, 76, 80). One specific example is the inconsistency with which microbiota is used as a singular or plural word.

2) For Figure 3, a heat map with the profile data for all samples (all the individual samples from the 2 sites across the 3 wintering phases) at the family/genus level would be a valuable addition to the manuscript.

3) The LEfSe results are presented in lines 237-241. However, this presentation is minimal. It would be beneficial to further explain the indicator taxa. Of note, the indicator taxa between early and late wintering stages are entirely different for the two sampling locations. This should be explicitly addressed here or in the Discussion, as it does not support the idea that hooded cranes are experiencing consistent shifts in their microbiomes across the winter.

4) In the last paragraph of the Results section, in lines 270-275, it is noted that predicted functional gene profiles of fecal samples differed between sampling sites and wintering phases. However, the indicator genes/pathways/functions for the different sample groups are not currently explained or presented at all. This should be addressed.

5) The Discussion section is currently very general, largely because the focus is on phylum-level variation in fecal bacterial profiles. The Discussion would be more informative if the focus was on more fine-scale taxonomic differences among sample groups (i.e. OTU/genus/family level).

6) It is noted in the Introduction that food density and resources change across the wintering period for these cranes (lines 116-188). This should be further explained here.
Experimental design: 1) The research questions are well defined: Assess if the gut bacterial diversity of hooded cranes 1) differs between two wintering sites; 2) is consistently influenced by seasonal changes over winter; 3) responds to dietary changes. However, the third research question was not specifically addressed in this study because data on dietary resources and consumption were not collected. Therefore, the study actually had two research questions. Inferences are here drawn about the originally proposed 3rd question from the results of the 2nd question.

2) In lines 163-165, it is noted that sequences were processed using a coupled protocol of both mothur and QIIME programs. However, it is not currently clear what this entails, which processing steps were completed with which program, or why this approach was taken.
Validity of the findings: 1) For univariate (ANOVA) and multivariate (ANOSIM) analyses, it is not clear why the authors are not using two-way models (site X wintering phase). Two-way analyses can be run in the same packages the authors have used to conduct the numerous one-way analyses.

2) In line 243, it is observed that there was greater dispersion in the fecal bacterial profiles during the late wintering period at both sampling sites. However, this is not clearly evident in Figure 6. This statement should be statistically evaluated using permutation of dispersions analysis (also available in the vegan package in R).
Additional comments: Include a specific estimate of the time that fecal samples were in the transport cooler between collection and storage in the -80C freezer (see lines 131-133). “As soon as possible” is too vague for the purposes of replication and/or interpretation.

In line 180, it indicates that alpha diversity was characterized using the Simpson Index, however, Simpson data are not included in the manuscript. Either add the data or remove Simpson from the list of diversity measures provided here.

In the legend for Figure 5, panels C and D are not explained and B is currently incorrectly explained (actually C).

In Figure 6, panels A-F are not currently labeled.


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: VARIATIONS IN GUT BACTERIAL COMMUNITIES OF HOODED CRANE (GRUS MONACHA) OVER SPATIAL-TEMPORAL SCALES
Review round: 1
Reviewer: 3

Output:
Basic reporting: This study used high-throughput sequencing of the 16S rRNA gene to analyze the gut microbial communities of Hooded cranes at three wintering stages in the two lakes in China. The study is largely descriptive. I have several methodological questions about the work, which I describe below. In addition, the manuscript contains several grammatical problems, and it should be copy edited by a native speaker of English. It is not clear whether the data have been made publicly available.
Experimental design: Methodological issues in order of appearance in the manuscript

Figure 1 - I am not sure where the study site is located in China. Can you add detail to the legend or the figure itself to explain where the larger map is located in the inset map of China? What is the imporance of the smallest inset map, which appears to be of a chain of islands?

Was a bead beating step included in DNA extraction? Bead beating is typically included in microbiome studies to increase detection of bacteria with cell walls. If a bead beating step was not included, please explain the implications for interpeting your results.

In your pipeline, please explain how many total reads you started with in the raw sequencing data and how many reads were lost during quality filtering steps.

Please describe how you evaluated the quality of your PICRUSt analyses. These analyses rely on several assumptions which may not be sound for your system. See more at:
https://picrust.github.io/picrust/tutorials/quality_control.html

In your analyses of alpha diversity and Figure 2, please explain how you controlled for read count. More diversity is expected with higher read counts; did you control for read count by adding it as a factor in your models or rarefying the data?

Please create a version of Figure 3 that shows how taxonomic composition varies between samples. In the current version, it's not clear how the abundance of phyla and classes varied between different samples. Please revise this figure to make it a stacked bar chart with one bar for each sample in your data set.
Validity of the findings: In the introduction, you specify three hypotheses. Your third hypothesis states that, "Dietary changes in different seasonal affect the gut bacteria of Hooded cranes." However, you have no data on dietary differences between birds and so you cannot test this hypothesis. Please remove this hypothesis from the manuscript.

Moreover, while you should be able to test hypothesis 2 ("Gut bacterial are influenced by seasonal changes and exhibit the same pattern in different wintering location") you do not clearly test any direct predictions of this hypothesis in the results or discussion or state whether this hypothesis was supported or rejected by your data.

The discussion fails to place the work in the broader context of what is known about avian gut microbiota. Please expand your review of the literature in the discussion to compare your results to what has been observed in other wild birds.
Additional comments: Minor comments

Abstract line 21 - "bird" should be "birds"

Abstract line 28 - "ANOSIM analysis explored that" should be "ANOSIM analysis revealed that"

Abstract line 30 - "to shape" should be "in shaping"

Abstract line 31 - The following sentence is missing a word: "In addition, PICRUSt analysis revealed that the predicted metagenomes associated with carbohydrate metabolism, amino acid metabolism and energy metabolism over the entire wintering period at the two lakes"

Introduction line 56 - "birds gut" should be "bird guts" or "the gastrointestinal tract of birds"

Introduction line 59 - this sentence has grammatical problems, "Past decade with rapid development in molecular methodologies, which has been provided new insight for the gut microbial of birds."

The grammatical/language issues in this paper were so numerous that I stopped recording them. This paper will need to be copy editied by a native speaker of English.

Line 100 - did you receive a permit number with the permission to collect samples, or was a permit not issued or unecessary?

Line 190 - Please spell out the full acronym for LEfSe (linear discriminant analysis effect size)

Line 218 - you are missing a comma in "4018,794". Should this number be 4,018,794?


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: GENOME-WIDE ANALYSIS OF THE WRKY GENE FAMILY IN DRUMSTICK (MORINGA OLEIFERA LAM.)
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: In-depth bioinformatic analysis executed by the authors. However, lack of experiment to address functional role of gene of interest.

Manuscript needs to further discuss and enrich the functional role of MoWRKY genes and specific motifs in relevance to its genome distribution.
Validity of the findings: To enhance impact and novelty of their study, the current version of manuscript needs minor revision.
Additional comments: In the current manuscript by Zhang et.al. “Genome wide analysis of WRK gene family in Drumstick (Moringa oleifera Lam.)”, authors discuss the role of MoWRKY genes importance using bioinformatic tool complemented along with differential expression profiling under different stress conditions.
WRKY gene family is assumed to have different function in diverse plant function and process. However, authors do not discuss the precise and specific role of WRK gene family in Drumstick. To consider the manuscript for publication quality authors should emphasize and clearly discuss the role and function of such gene in Moringa oleifera. Having redundant expression and functional activity, it is not clear how MoWRKY gene is regulated under different stress condition. What is the functional relevance of such differential expression and having diverse functional role? It should be discussed in detail in context to their structural analysis.


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: GENOME-WIDE ANALYSIS OF THE WRKY GENE FAMILY IN DRUMSTICK (MORINGA OLEIFERA LAM.)
Review round: 1
Reviewer: 2

Output:
Basic reporting: This sections seems fine
Experimental design: Need to work on Experimental design ---especially for expression of the mentioned genes
Validity of the findings: WRKY proteins are DNA binding proteins, characterized by presence of WRKY motif and ZnF. WRKY proteins constitute one of the largest family of transcription factors and have been attributed to many functions in plant such as stress response and signal transduction. The present manuscript describes the identification and classification of WRKY gene family in drumstick. Authors have also reported the stress effects on the expression of these genes. The abstract and introduction sections are nicely written. However, authors need to work on method and figures. I have following major concerns:
1)	Why authors haven’t shown the clustalW data? It would be good to see how they are conserved.
2)	Variant WRKYGKK seems to be particularly interesting as it is not expressed in any tissue in any of the studied conditions. It would be interesting to know how a single residue (Q to K) mutation leads to complete abolishment of the function. Does this variant evolve to behave as paralogue?
3)	In Figure 6, Y-axis is unlabeled. What is the proxy for expression measurement? If the numbers on Y-axis are normalized, it should be clearly mentioned in legend and methods.
4)	Line 252  “Nine MoWRKY genes from different subgroups were selected…”. What was the basis for selection of these genes? Authors should clearly mention that and should be justified (supplementary?).
5)	How were the error bars calculated in Figure 6? This should be clearly stated in method/legend.
6)	What is the error range in Figure 5? What do Ka and Ks stand for? It would be difficult for readers to follow these.
7)	Resolution of Figure 2&3 is very poor. The labels are barely clear.
8)	Method section should be more elaborated.
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: GENOME-WIDE ANALYSIS OF THE WRKY GENE FAMILY IN DRUMSTICK (MORINGA OLEIFERA LAM.)
Review round: 2
Reviewer: 1

Output:
Basic reporting: Revised manuscript is address clearly.
Experimental design: Experimental design is executed well to address the objective.
Validity of the findings: Well defined.
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: GENOME-WIDE ANALYSIS OF THE WRKY GENE FAMILY IN DRUMSTICK (MORINGA OLEIFERA LAM.)
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors have addressed majority of my concerns and hence can be accepted.
Experimental design: The authors have addressed majority of my concerns and hence can be accepted.
Validity of the findings: The authors have addressed majority of my concerns and hence can be accepted.
Additional comments: The authors have addressed majority of my concerns and hence can be accepted.


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: ASSOCIATION BETWEEN VDR GENE FOKI POLYMORPHISM AND RENAL FUNCTION IN PATIENTS WITH IGA NEPHROPATHY
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1. I would advise the authors to consult a native English speaker to strengthen the manuscript, as there were some grammatical errors;
2. It would be better if the discussion concluded other genes polymorphism in IgA nephropathy, and the clinical influence of the Fokl polymorphism was limited;
3. The authors provide a very large baseline table, with a great number of variables, of which only a small percentage is significantly different.It should be reconstructed;
Experimental design: I suggest that authors improve the description in Subjects part, like what is the meaning by "patients with multiple failure"(Line 70)?
Validity of the findings: 1. It is questioned with some data in Table 1, like iPTH. In general, iPTH is abnormal distribution，is not appropriate showed as Mean±SD, and I found that in the detailed data author provide, even in eGFR<60ml/1.73m2, no elevation in iPTH was founded, which is not assistant in clinics;
2.In clinical grouping (Line 85-88), I would suggest the authors clearly state the GFR equation used in this study;
3. In discussion part, I would advise the author to potential reasons for the outcomes with more detailed and newly literature reviews;
4. Althought the authors provide a new gene polymorphism, but no further relationship with clincal dicisions were discussed, and also its advantage and disadvantage with other knowned gens.
Additional comments: I read with interest this manuscript describing a promising gene polymorphism in IgA nephropathy. As described in this manuscript, TT genotype were independent risk factors for renal dysfunction with a dramatic increase. However, the authors do not clearly describe the rationale and  also its potential molecular mechanisms and applying prospect.


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: ASSOCIATION BETWEEN VDR GENE FOKI POLYMORPHISM AND RENAL FUNCTION IN PATIENTS WITH IGA NEPHROPATHY
Review round: 1
Reviewer: 2

Output:
Basic reporting: Man-Qiu Mo et all conducted cross-sectional study in order to investigate the association between VDR Fok I gene polymorphisms and renal function in IgAN patients.
Experimental design: The author conducted cross-sectional study in patients with IgA nephropathy.
Validity of the findings: The results of study is that Fok I TT type have an increased risk of renal dysfunction.
Additional comments: I think this study is meaningful for nephrologist and the results of this study is interesting. On the other hand, this study contains several problems in study design, method, and result.

[Major problems]
1. the author concluded that FokI TT type is the risk factor of renal failure in IgAN patients. However, some former studies reported that other FokI type, CC or CT, is associated with kidney worse kidney function. Is there any reason these differences?
Clin Interv Aging. 2017; 12: 1673–1679.

2. Table 3 showed linear regression analysis for renal function (sCr or eGFR). I think this regression analysis included too many factors to analyze. It is necessary to select adequate factors for regression analysis in this study. In addition, is it appropriate that in regression analysis for sCr, eGFR is selected for explanatory variable?. I think as sCr and eGFR are same meaning, this analysis is inappropriately. In addition, age and age>40 contains multicollinearity.

[Minor problems]
1. PTH is not usually regarded as normal distribution variables. It is necessary to check normality of PTH in this study and correct table 1 appropriately.

2. Is there any information about hematuria?


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: ASSOCIATION BETWEEN VDR GENE FOKI POLYMORPHISM AND RENAL FUNCTION IN PATIENTS WITH IGA NEPHROPATHY
Review round: 2
Reviewer: 1

Output:
Basic reporting: Man-Qiu Mo et all conducted cross-sectional study in order to investigate the association between VDR Fok I gene polymorphisms and renal function in IgAN patients
Experimental design: The author conducted cross-sectional study in patients with IgAN.
Validity of the findings: The results of study is that FokI TT type have an increased risk of renal dysfunction.
Additional comments: I think this study is meaningful for nephrologist and the results of this study is interesting. The revised manuscript is well corrected and  worth publishing.


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: TIMING AND ECOLOGICAL PRIORITY SHAPED THE DIVERSIFICATION OF SEDGES IN THE HIMALAYAS
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1.	The text well-structured and  is written in reasonably good English with the following minor problems noted:
Grammar, phrasing and word usage
Line 147:  species of specimens?  27 specimens representing 21 species is clearer.
Line 149:  comprising not bringing
Line 152:  plural noun for singular verb: should be “repository… was retrieved”; also line 240-41 should be “data…were retrieved”
Line 168: why does the sentence start with However?  This is confusing because it implies a comparison which doesn’t seem to be there.
Line 175: However makes more sense here, but is still unnecessary.  Two-step not two-steps amplification.
Line 222:  presence or absence, not and absence; a species can’t be both
Lines 280-282: Verb tenses don’t agree within the sentence and anagenetic should not be capitalized.  The sentence is also unclear as written.
Line 287: explain rather than explaining
Line 290: use for rather than of
Lines 293-295: The sentence has many grammatical problems and the meaning is not at all clear.
Line 368: another problem with agreement between subject and verb (singular/plural)
Line 371: present tense preferred here
Lines 381-384: noun/verb agreement problems (twice):  should be “number…was”
Lines 385-389: This need to be rewritten to improve clarity.
Line 418: The “however” in the middle of the sentence needs to be removed to make the sentence work.
Line 421: “regions” should be indicated as possessive (regions’) or say “ between the lineages of the two regions”.  A verb is also missing on this line.
Line 421: Change the comma to a semi-colon.  The words after the comma are an independent clause.
Line 485: part of the verb is missing
Line 486 also seems to be missing a verb.
Line 516:  presumably you mean “ nor to” rather than “as well as to”
Line 526: verb missing
Line 539: sentence is awkward, but “versus” would be better than “than” for the comparison
Line 547: Use twice as high as instead of twice higher than
Line 553: Remove “all the”
Missing articles (a, an, the):
Lines 150, 237, 270, 278, 280, 282, 293, 422, 555 and elsewhere.
2.	The introduction and background are sufficient, interesting, well-referenced and well-organized.  The four specific questions that organize the project are clearly presented.
3.	The structure conforms to standards in the field.  I did not take the time to check detailed compliance with PeerJ rules for formatting sections or for formatting references.
4.	The figures are mostly clear and informative, but I noted the following problems:
a.	The caption for Fig. 2 appears to be the wrong caption and has numerous grammatical problems.  It refers to arrows, circles, blocks and abbreviations that I didn’t see on the figure, and it does not explain the significance of the circles labeled 15 and 30 (presumably dates in Ma?)
b.	Fig. 3 caption states speculations as fact, as does the text (see below).
c.	Fig. 4 caption has grammatical problems (indeed used instead of a verb; compare should be compared).  It would be preferable to have the units for Rate given directly on the figure.
5.	Tables are well laid out but there are the following problems:
a.	Tabl Table 1 has values that are incorrect for the number of informative sites based on checking the original data in the supplemental files (see details below)
b.	Table 2 should give standard deviations on the estimates as well as the mean.
c.	Table 3 caption needs punctuation.  Last line is unclear.  Table 3, line 7:  Kobresia not Kobresian.  Also, there is no indication of what the * means. Table 3, line 8: I don’t understand what this line means.
6.	Raw data were available
Experimental design: 1.	This original research is within the scope of PeerJ
2.	The research questions are clear and relevant, addressing an issue that has not yet been considered for this geographic region.
3.	The authors present results from a series of sophisticated analyses designed to rigorously test questions related to evolution and biogeography.  The problem is that they do this with a data set that is, in my view, not adequate to achieve their goals.

 I see three distinct problems with the data set:

First, only 3 genes are used and two of them are nuclear ribosomal spacers which can sometimes be misleading due to incomplete lineage sorting, divergent paralogues, etc., and almost 50% of the data are missing. In checking the data, it appears that 65 species, including 13/38 of those in the Kobresia clades, which are the main focus of the paper, are represented only by one of the three genes (usually ITS, or sometimes ETS).  Furthermore, Genbank numbers are given only for the new data gathered for this study (40 species).  The other data come from a Dryad repository from an earlier paper and it is not clear whether these sequences have Genbank numbers.

Second, although the level of variability for the 3 genes appears to be very high in Table 1, these numbers do not appear to be correct.  The percentage of informative sites seemed extremely high, so I checked the supplemental data files and found that ETS had 501 informative sites (that is, with a mutation shared by at least two species) rather than the 720 specified in Table 1; ITS had 359 informative sites rather than the 590 specified in Table 1; and matK had only 190 informative sites rather than the 319 specified in Table 1.  The numbers given in Table 1 are substantially higher than the total number of variable sites, so it is unclear where they came from.  In total, there are only 1050 informative sites for resolving 970 species, so it is not surprising that the support values are weak for most clades even in the combined gene tree (supplemental file S8).  The authors state on line 337 that the topology is “supported at most major clades”.  While it is true that the five major clades of Carex are well supported, the topology within these clades receives only weak or no support, with the exception of  sets of two or three closely related species scattered through the tree, a very few well-sampled mostly North American clades (e.g. the Griseae-Careyanae-Granulares group and the Laxiflorae-Paniceae-Bicolores group), and groups that have been the topic of recent study (e.g. the Racemosae clade and the Spirostachyae-Echinochlaenae clade).

Third, the choice of species appears to be geographically biased toward North America.  Based on the color-coding in Fig. 2, a large proportion of the species are from the Nearctic and many of those from the Eastern and Western Palearctic are species that also occur in the Nearctic. Few Neotropical species are represented and most of them also occur elsewhere. Similarly, except for African species in the Siderostictae clade and an early-diverging Core Carex clade (primarily section Indicae), only a few species from the Afrotropic and Indo-Mayalan regions are not also distributed in one or more other regions. Most troubling is that nearly all species coded as Indo-Malayan are also coded as Himalayan, even though there are likely to be species in the subtropical Indo-Malayan region that would not occur in the Himalayan region, but these are not included in the sampling. Carex is diverse in the Eastern Palearctic (hundreds of species, many endemic) but this diversity is not reflected in the sampling. Ideally, inference of origins of the Himalayan species and patterns of dispersal between regions, as well as questions related to speciation and extinction rates in different regions should have complete or at least unbiased representative global sampling of species in proportion to their abundance in each region. My concern is that the bias in the sampling may have a strong influence on the results of the study and undermine confidence in the conclusions.

In short, the initial phylogenetic analysis using all 3 genes shows a topology that is largely unsupported except for the major clades, and the choice of taxa is biased rather than representative of the diversity in all regions. All other analyses depend on the same data and topology.  How can the conclusions be valid if the tree topology is not supported, except for the 5 major clades?

Problems with dating: Dates are treated as fixed even though the variability associated with estimates in the papers they cite is high.  Dating the crown age was based on two papers that used the same fossil calibration.  Curiously, another paper on Cyperaceae with Hipp as a co-author found a younger estimate for the crown age of Carex.  That paper (Escudero, M. and Hipp, A. 2013. Shifts in diversification rates and clade ages explain species richness in higher-level sedge taxa (Cyperaceae).  American Journal of Botany 100: 2403-2411.) is not cited.  Two cited papers by Spalink et al. (2016a,b) using additional fossils within Cyperaceae for dating found an even younger mean estimate for the crown age of Carex.  This estimate is dismissed as different on lines 354-357, and not used because “we use a calibration based on a more recent date according to Escudero et al. 2012 and compatible with the fossil record (Jimenez-Mejias et al. 2016)”.  This is very confusing because Escudero et al. 2012 use an older fossil for dating than the other papers, not a more recent one, and the older fossil they use is treated by Jimenez-Mejias et al. as doubtfully Carex.

4.	Most of the methods are described in enough detail but I noted some serious and not so serious omissions of information that should have been included in Materials and Methods and Results sections.  These are detailed here:
•	Reference is missing for the R packages on line 248.
•	The number of species in each category should be given on lines 258-259, and it should be specified whether the software is sensitive to species sets that are drastically different in size (as they likely are here) and accounts for such differences. From first principles, it seems likely that estimating rates from a large sample would be more accurate than estimating rates from a small sample size and the variances would not be homogeneous.
•	On line 330, it states that the “phylogeny obtained from ITS (…) showed phylogenetic incongruence”.  It is not clear what it is being compared with and the nature of the incongruence should be specified. Supplemental file S4 shows a very different arrangement of the major clades ((Core Carex + Vignea (except C. gibba)) sister to the Core Unispicate clade with the Schoenoxiphium clade nested within it), but this arrangement has no significant support.  Given that, there should be some justification given for combining the ITS data with the other data into a single analysis.
•	On line 350-353 it says the data calibrations are “based on the same sources” as those in 3 references.  It should be clarified what this means:  trees based on the same data (which does not appear to be true), based on the same fossils?  Based on the same dates obtained in earlier studies?  I checked the references and I could not find a dating analysis in Waterway et al. 2009.
•	Lines 373-377 are poorly written to the extent that the meaning is not clear.
•	Lines 379-81: It would be useful to show the percentage of them in each major clade here.
•	Lines 392-394: variability estimates should be given with the means for the estimated dates.  They are certainly large enough to put all of the dates into the Miocene.
•	Lines 390-end of paragraph:  The mean estimates for the dates are treated as ‘truth’ here despite the known variability of the estimates and the many issues related to dating both in terms of the fossils used and methods followed. This section should be rewritten to acknowledge that the dates are  really ranges and that what is being interpreted is the relative order of events.  As noted elsewhere, the biased sampling of species in the data set makes all of these reconstructions potentially suspect.
•	Lines 454-455: This distribution may be true of the dataset, but there are many species in the Decorae and Indicae clades in subtropical southern China and SE Asia that were not included in the dataset, so this is misleading.
Validity of the findings: Due to the problems listed above with the data set, I cannot say the data are robust and statistically sound.  Fairly strong conclusions are drawn but I don't think the data support such strong statements, particularly when the dates are treated as being without error variation.

Lines 509-512:  This categorical statement needs to be qualified. Given my various concerns about the data and geographic sampling, I think this is a speculative statement, not a conclusion that is warranted by the data and analyses presented in this manuscript.
Lines 515-520: This statement is also speculative and quite likely incorrect.  Sampling omissions from these regions can account for the results, so it is speculative to attribute biological reasons. Carex are quite frequent in SE Asia, often in montane regions, which do not appear to have been sampled for this data set.
Lines 538-540: Comparison with previous estimates of diversification rates in Carex and Cyperaceae  should be made somewhere in the discussion (e.g. Escudero and Hipp 2013 and other Escudero papers, Spalink 2016)
Lines 546-549: The higher dispersal rate out of the Himalayas than diversification rate within the Himalayas is at odds with the previous statement that the Himalayas were an evolutionary dead end.  This result could also be explained by biased sampling that failed to include an appropriate proportion of Himalayan endemics, which are more difficult to sample because of their endemicity.
Additional comments: This is a very interesting project with some sophisticated analyses and approaches to the issues, but several issues with the data need to be addressed.  The tree on which all other analyses are based has so little support except for the five major branches that I don't think the conclusions are valid.  I think it would be a stronger paper with fewer species chosen to have an unbiased geographic distribution and  more genes to assess the relationships.  Data for additional genes is available on Genbank for many of the species in your analysis.


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: TIMING AND ECOLOGICAL PRIORITY SHAPED THE DIVERSIFICATION OF SEDGES IN THE HIMALAYAS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper is clearly written in general. But I have some concerns.
Citations need to be checked more carefully. For instance, they cited Xie et al. 2014 for geological history of this region. But none of the authors in this paper are geologist. The format of the citation is not consistent and strange. Some “et al.” are in italic and some are not. They should check the formatting guidance carefully. For instance,” van Hinsbergen et al., 2011; van Hinsbergen et al., 2012” should be van Hinsbergen et al., 2011, 2012.
Some figures are not informative or not nice-looking. In my opinion, fig 1 is not necessary and they could merge fig 3 to fig 2.
Experimental design: The diversification history of Himalayan flora is crucial for our understanding of mountain diversity. The authors investigated the biogeographic and diversification pattern of a diverse group, Carex in this region by using comparative phylogenetic methods. They found that the Himalayan radiation may date back the late Oligocene and the success of Kobresia might due to competitive exclusion. This provides new insights into the diversification of Himalayan flora.
Validity of the findings: there are some technical problems in their analysis which I listed in the comments to authors.
Additional comments: The diversification history of Himalayan flora is crucial for our understanding of mountain diversity. The authors investigated the biogeographic and diversification pattern of a diverse group, Carex in this region by using comparative phylogenetic methods. They found that the Himalayan radiation may date back the late Oligocene and the success of Kobresia might due to competitive exclusion. This provides new insights into the diversification of Himalayan flora.
The paper is clearly written in general. But some issues need to be addressed before publication. My concerns are listed in the following.
1.	You used “narrow sense” and “broad sense” for biogeography and GeoSSE analysis, but you did not point out in the GeoSSE method part. I was confused which is which in the Results and Discussion part. For instance, when you say the radiation of Kobresia date back to late Oligocene, do you mean the “broad sense” Himalaya? In my opinion, the diversification history of the broad sense Himalaya might be totally different from the “true” Himalaya. This is because your broad sense Himalaya includes three distinct geological entities, the Himalayas, the Tibetan Plateau and the Hengduan mountains. They have different uplift history. This matters when you interpret the biogeographic history. For instance, you said that the Himalayan Kobresia was dispersed from the Nearctic region, but it is also possible that the “true” Himalayan Kovresia may arise from the Tibetan Plateau as it is older than the Himalayas.
2.	For your GeoSSE analysis, you interpret the dA and dB as dispersals in the Himalayas and non-Himalayas. This is not correct. You made it clear that dA means the dispersal rate from the Himalayas to non-Himalayas, not within the Himilayas.
3.	Please check your citations more carefully. You cited Xie et al. 2014 for geological history of this region. But none of the authors in this paper are geologist. The format of the citation is not consistent and strange. Some “et al.” are in italic and some are not. When you have references by the same authors from different years, you only list author names once. For instance,” van Hinsbergen et al., 2011; van Hinsbergen et al., 2012” should be van Hinsbergen et al., 2011, 2012.
4.	Please replace “Late Miocene” or “Late Oligocene” to “late Miocene” or “late Oligocene” as late Miocene is not a formal geological epoch any more.
5.	Some figures are not informative or not nice-looking. In my opinion, fig 1 is not necessary and you could merge fig 3 to fig 2.


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: TIMING AND ECOLOGICAL PRIORITY SHAPED THE DIVERSIFICATION OF SEDGES IN THE HIMALAYAS
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This is an exciting manuscript on the diversification and biogeographical history of the Himalayan species of Carex. The authors have compiled an excellent dataset to investigate a series of questions related to the origin, adaptation, and rate of diversification Carex lineages in the Himalayas. Their main conclusions are that Himalayan Carex are the result of many instances of migration from outside sources; detectable in situ radiations was largely limited to a single clade; that rates of diversification in the Himalayas was low; arrival of Carex in the Himalayas postdates orogeny and uplift; and lineages that entered the Himalayas were possibly preadapted to alpine-type climates.

The writing is generally clear and the manuscript is easy to follow. My suggestions for improvement are mostly minor; some re-analyses may be required unless the authors can provide sufficient justification for their choices.

Molecular Dating: Given their reliance on a single calibration point for a 900+ taxa tree, I spent a bit of time comparing the various recent Cyperaceae dating analyses. Interestingly, their calibration point is the Carex crown age (42.8 Ma; Mid Eocene) obtained by Escudero et al. 2012, whose sole Carex calibration is a fossil whose veracity has been previously questioned by an author of this study (Carex tsagajanica). If my reading of Jiménez-Mejías et al (2016) is correct, the oldest verifiably Carex fossil is from the late Eocene, with fossils becoming increasingly common into the Miocene and on. Thus, while the date of the Carex crown in this study is consistent with the fossil record, the younger dates obtained by Escudero and Hipp (2013), Spalink et al (2016), and Léveillé-Bourret et al (2018) are not inconsistent with the fossil record.

With the exception of the set 42.8 Ma Carex crown, most other dates on their chronogram are older than previous studies – even those that have used the same calibration, e.g., the Siderostictae crown is 15 Ma in this study, 10 Ma in Spalink 2016, and 5 Ma in Escudero 2012; unispicate clade crown is 30 in this study, 18 in Waterway, 22 in Escudero, and 15 in Spalink; the core Carex clade is 28 in this study, 18 in Waterway, 21 in Escudero, and 15 in Spalink.

This is not to say that the dates in this manuscript are wrong, but as the timing of events is important for many of their conclusions, it would be helpful if the authors could address these concerns and decide if any re-analyses are merited.

Other suggestions:
Line 82, e.g.: sometimes the authors refer to the Tibetan-Plateau, other times to the QTP – are these the same?

Line 104: “This high variation in … vegetation types.” This is the first time vegetational diversity is mentioned – please rephrase or provide background information.

Line 114: “Disproportional” relative to what?

Line 116: “which are sister to smaller clade” – please clarify.

Sentence beginning Line 125: 40 species is not a majority of 189 species – please clarify.

Line 133: it is a bit confusing to refer to “former genus Kobresia.” Since you have already established that Kobresia is no longer a genus – but presumably refers to a meaningful clade – perhaps you could say something like “(hereafter Kobresia) the first time you mention this issue.

Sentence beginning Line 135: Please clarify this sentence – the meaning is unclear.

BioGeoBEARS analysis: please provide a sentence or two describing why the assumptions of DEC (as opposed to DIVE or BAYAREA) were appropriate for your analyses. Also, there do not seem to be any dispersal constraints in this analyses – meaning that migration from South America to the Himalayas is as likely as migration from adjacent China to the Himalayas.

Line 499: I don’t see where the authors tested for competitive exclusion. Please revise.

Line 533: Are there other undersampled sections of the phylogeny that could impact the interpretation of the results?

Line 540: was there any actual statistical significance?

Line 547-8: please provide units.

When referencing preadaptation: it is important to mention that climate is only one aspect of niche.


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: TIMING AND ECOLOGICAL PRIORITY SHAPED THE DIVERSIFICATION OF SEDGES IN THE HIMALAYAS
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors did great job in revising the manuscript. The manuscript has been improved substantially. I only have one minor comment.
L472-473: delete ", during which time the Indian Tibetan continent collided with Asian plates, causing the initial uplift of the Tibet plateau".  Because the collision between Indian and Asian plantes was much earlier than 25 Ma.


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

Input:
Title: A BEHAVIORAL AND GENETIC STUDY OF MULTIPLE PATERNITY IN A POLYGAMOUS MARINE INVERTEBRATE, OCTOPUS OLIVERI
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment in general but I suggest to add these references and add in the introduction some issues about the stimuli that can guide the animals in the choice of the partner Frontiers in Physiology
Volume 7, Issue SEP, 28 September 2016, Article number 434
Neuroendocrine-immune systems response to environmental stressors in the cephalopod Octopus vulgaris(Short Survey)
Di Cosmo, A.Email Author,  Polese, G.

Role of olfaction in Octopus vulgaris reproduction	Polese, G., Bertapelle, C., Di Cosmo, A.	2015	General and Comparative Endocrinology
210, pp. 55-62

Olfactory organ of Octopus vulgaris: Morphology, plasticity, turnover and sensory characterization

Polese, G., Bertapelle, C., Di Cosmo, A.	2016	Biology Open
5(5), pp. 611-619
Experimental design: no comment
Validity of the findings: no comment
Additional comments: My comment and suggestions to the AA is fo add major informations  and references about what are the stimuli that can guide the animals in the choice of the partner.


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

Input:
Title: A BEHAVIORAL AND GENETIC STUDY OF MULTIPLE PATERNITY IN A POLYGAMOUS MARINE INVERTEBRATE, OCTOPUS OLIVERI
Review round: 1
Reviewer: 2

Output:
Basic reporting: "Who's your daddy" absolutely must be removed from the title. The use of this phrase is unprofessional and tone deaf at best, as it can be HIGHLY offensive to female readers. Look up the phrase in Urban Dictionary or Wikipedia to learn what it means to most people in the US.
Experimental design: While the experimental design appears to be sufficient, sample sizes need to be explained more clearly both in the methods and the results. The authors do not address how the reuse of males in different trials was treated in the statistical analyses. By using the same males with different females, the replicates were not independent, and it's possible assumptions of the statistical tests could have been violated. Please clarify.

Animal sizes (wet weight of individuals, and relative masses of mating pairs) were recorded but not reported given, which is unconventional for mating studies conducted in the lab.

Data are not made available, though this is not unusual for mating experiments.
Validity of the findings: no comment
Additional comments: Overall this is an interesting study about the mating behavior and fertilization patterns in Octopus oliveri, and an important paper in the field of cephalopod behavior. It contributes to our understanding of the complex relationships between mating behavior and fertilization patterns, which is a very new avenue of research for cephalopods. Overall this study appears to be well designed, though important details will need to be included in the revision, because it's possible the experimental design limits the statistical analyses that can be used appropriately.

In the detailed comments below I have suggested papers the authors might like to read to provide additional context for interpreting their results, in particular the similar studies by Morse. The authors might also find Itawa's works on squids relevant to their discussion of sperm competition.

Detailed comments:

Abstract:
While it becomes more clear later in the text, as it's worded here, it's not clear whether the entire study is based on the same three males and six females, or whether each experiment had its own 3 males and 6 females. Please clarify. It's not clear from the abstract (or the main text) what the four sets of experiments were. Were they separate experiments or were they replicates? If they were replicates, did they use the same or different individuals?

Line 27: Replace find with found. Here and throughout, all methods and results should be given in past tense, not present or imperfect.

Line 30: Replace may with might here and throughout.
Are the female sperm limited if the eggs are still fertilized? Maybe the wild females are guarded.

Line 32/33: I'm curious to see how you showed this in this experiment. Otherwise it is speculation that should not be included here.

Introduction paragraph 2: Sneaker males were described for Octopus cyanea in 1997. Other relevant references: Cigliano, J. A. (1995). Assessment of the mating history of female pygmy octopuses and a possible sperm competition mechanism. Animal Behaviour, 49(3), 849-851.
Morse, P., Zenger, K. R., McCormick, M. I., Meekan, M. G., & Huffard, C. L. (2015). Nocturnal mating behaviour and dynamic male investment of copulation time in the southern blue-ringed octopus, Hapalochlaena maculosa (Cephalopoda: Octopodidae). Behaviour, 152(14), 1883-1910. Morse, Peter, Christine L. Huffard, Mark G. Meekan, Mark I. Mccormick, and Kyall R. Zenger. "Mating behaviour and postcopulatory fertilization patterns in the southern blue-ringed octopus, Hapalochlaena maculosa." Animal Behaviour 136 (2018): 41-51.

Line 54: Replace males with male's and another with another's sperm

Line 62: Cigliano's work showed behavioral evidence of sperm competition, but no evidence of sperm precedence.

Discuss this work here, but word accordingly.

Line 68: Another relevant work to consider reading is Morse, Peter, Christine L. Huffard, Mark G. Meekan, Mark I. Mccormick, and Kyall R. Zenger. "Mating behaviour and postcopulatory fertilization patterns in the southern blue-ringed octopus, Hapalochlaena maculosa." Animal Behaviour 136 (2018): 41-51.

Lines 72-75: Redundant with previous paragraph

Lines 91-108: This information should be incorporated into the introduction.

Lines 111, 116: Give lat and long of collection site, and full location (state, country) for both.

Line 115: Sample sizes are not described clearly. Give total number of animals collecton. Are the same 6 + 3 used for all trials, or different 6 + 3 sets used in each of the four experiments? I assume different, but use/reuse of individuals is not entirely clear.

Line 119: Delete HIMB because this acronym is not used elsewhere.

Line 122: Spell out NOAA

Somewhere in the methods or acknowledgements, mention the collection/research permit situation (agency, issued to whom)

Lines 130-135: add a diagram showing sample sizes/uses of individuals in experiments

Line 132: Describe the three experiments. The abstract mentions four experiments.

Line 134: Give actual sizes of males and females.

Lines 150-154: Do you know of any work looking into spermatophore regeneration, because that's what is most important here? Perhaps from squid work?

Line 155: replace with "The trial history of each female was recorded to..."

Line 159: It's not clear how the experimental design yielded sixty-two trials. 3 males x 4 females x 4 experiments (abstract) or 3 experiments (methods). Similarly, it's not clear what the final sample sizes were for the statistical tests.

Line 179: Would it be more accurate to say that fighting was followed by mating? Or were these examples of forced copulation in your view? Please specify.

Line 192: Clarify in the diagram requested above how these DNA-sampled individuals fit in with the experiments described above.

Line 196: Do you mean "and" instead of "or"?

Results section: Consider moving the behavioral data analysis section to before the paternity analysis section.

Lines 231-232: This is a lot of factors for such a small sample size.

Lines 237-238:  These sample sizes are helpful. Please list them for all tests.

Line 242: List the R version and cite the software.

Lines 291-293: Interpretations should be moved to the discussion.
Replace the citation of Huffard 2007 with the more appropriate Huffard, C. L., Caldwell, R. L., & Boneka, F. (2008). Mating behavior of Abdopus aculeatus (d’Orbigny 1834)(Cephalopoda: Octopodidae) in the wild. Marine Biology, 154(2), 353-362.

Line 300: Interesting!

Lines 300-302: This is a bit redundant with methods.

Line 314: The data...were...(datum is the singular).

Figures: Include either Figure 1 or Figure 2 (and accompanying results) based on which you think gives the most accurate representation of your experimental results.

Lines 415-422: Will you publish a general account of these behaviors and how common they were?  Did beak-to-beak mating also involve enveloping of the male by the female as described in Caldwell, R. L., Ross, R., Rodaniche, A., & Huffard, C. L. (2015). Behavior and body patterns of the larger pacific striped octopus. PloS one, 10(8), e0134152? What is it about these two species that leads to beak-to-beak mating when it's so rare otherwise?

Lines 433-443: Strong evidence of males investing more mating effort in larger females, and time spent by females mating, is also discussed here: Huffard, C. L., Caldwell, R. L., & Boneka, F. (2008). Mating behavior of Abdopus aculeatus (d’Orbigny 1834)(Cephalopoda: Octopodidae) in the wild. Marine Biology, 154(2), 353-362.

Lines 453: Earlier in the paper you mention analyzing the broods of females caught but not mated in experiments. These serve as your controls for this discussion on sperm limitation. Please present the results of those paternity runs more thoroughly. I lost track of them. They are an important part of your study and should be highlighted.

Lines 446-466: Consider combining and streamlining the first two paragraphs of the female mate choice section.

Lines 518 and 523: Replace "In contrast" with "By contrast"

Line 531: Replace "our first males" with "the first males in our experiments"

Lines 437-438: This statement is not consistent with the results presented in lines 401-401


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

Input:
Title: A BEHAVIORAL AND GENETIC STUDY OF MULTIPLE PATERNITY IN A POLYGAMOUS MARINE INVERTEBRATE, OCTOPUS OLIVERI
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: In the post-copulatory sexual selection (sperm competition and cryptic female choice), it is important to know how many males copulate with a female and what is important to decide the fertilization success. Sperm precedence is one of the important factors in the fertilization and last copulated males sired more offspring in general “refer to last male precedence”.
Cephalopods have various sperm storage organs and mechanisms in their reproduction, which suggest the reproductive traits originally evolved through post-copulatory sexual selection. Nevertheless, there are few studies to exam what are important to decide their reproductive success, especially in Octopus.
This study conducted a sequential mating experience in Octopus oliveri and showed mating order did not relate with fertilization success. This result would contribute to the knowledge of cephalopod reproduction. And one behavioural report, spermatangia reject by females, is important for considering cryptic female choice. However, I have to write the quality of this manuscript is quite low. The authors should check their text at least twice before submitting because their manuscript has so many grammatical and logical problems. They also have to study more in cephalopod reproduction, sexual selection and statistics. There were many problematic descriptions throughout. At first, they have to read a recent paper written by Morse et al (2018) which is a study of paternity analysis in blue-ringed octopus. This paper would be a good sample to make their draft. The authors should re-submit it considering what is a new for their study. Unfortunately, I cannot recommend to accept this manuscript without major 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: A BEHAVIORAL AND GENETIC STUDY OF MULTIPLE PATERNITY IN A POLYGAMOUS MARINE INVERTEBRATE, OCTOPUS OLIVERI
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Thank you for tracking changes in the review file. This is very helpful. These changes improve the manuscript. Great paper.

You should remove the “Who’s the daddy” question from the title for a few main reasons. This question makes no intellectual contribution to the title. As catchy as the phrase might sound in some circles, many people in the world will have no understanding of the tongue and cheek reference you make,  and the use of the colloquial term daddy risks confusing or alienating people who do not use English as their first language. It’s best to stick to the terms most often used in the scientific literature for this reason.  On the other hand, some people will get this reference, and you risk offending these readers. It’s best to omit, as you are open to doing.

Line 179: Provide a citation for this literature.