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: DIMENSIONAL CHANGES OF COMMERCIAL AND NOVEL POLYVINYL SILOXANE IMPRESSION MATERIALS FOLLOWING SODIUM HYPOCHLORITE DISINFECTION
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1.Few grammar mistakes are there. I have highlighted them and added questions as per the sticky notes  in the content of manuscript where there is doubt.
2. Authors are requested to go through all the highlighted content and make corrections. ADA specifications number needs to be added.
3. Clarify that you are testing for  final impressions for fixed prosthesis in your material & Methods.
4. Post hoc tukey test table is missing.
Experimental design: 1. Explain four figure balance briefly.
2. How was polymerisation of specimens checked.
3. Mention being an in vitro study in Material & Methods.
4. Tables to be included of multiple comparisons. That's vital and needs to be cited in text later.
Validity of the findings: Nicely written except for few changes in grammar that have been highlighted.
2. Legends under the figure needs to be corrected.
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: DIMENSIONAL CHANGES OF COMMERCIAL AND NOVEL POLYVINYL SILOXANE IMPRESSION MATERIALS FOLLOWING SODIUM HYPOCHLORITE DISINFECTION
Review round: 1
Reviewer: 3

Output:
Basic reporting: The submitted manuscript reports experimental data on impression materials treated with sodium hypochlorite disinfection, a very interesting topic, especially during these times.
However, some flaws do not allow me to give a green light for acceptance, but changes are required to improve the quality of the manuscript, to make it more appealing, readable and therefore to contribute fully to clinicians’ practice.
Experimental design: Let’s start from the abstract:
1)	It would be better to specify in the methods what You did and what You used: Rodhasurf indeed it is not specified for example.
2)	In results, Extrude should be with capitol letter and DW should be specified before when You name distilled water
Introduction
Line 57: of impression is repeated
Lines 84-88: literature reference is missing
Methods
Line 108: eighty sample (n 10) numbers does not match, or it seems confusing to the reader. Please rephrase it clearly
Lines 115-120: the paragraph must be rewritten due to the presence of several grammar and punctuation errors
Validity of the findings: Statistics: have You checked the distribution before to perform the ANOVA?
Results: it would be nice to add the microphotographs of the sample
Discussion
Line 145: add Your discussion here must be deleted.
Lines 154-155: the sentence must be rewritten due to the presence of several grammar and punctuation errors
Line 162-166: the paragraph must be rewritten due to the presence of several grammar and punctuation errors
Line 174: the full stop should be placed after the round bracket and after “et al”

The methods are appropriate and well described, and adequate details are provided to replicate the work.

In the discussion, the most important part of the article, its core, some very important concepts are mentioned but not fully and properly discussed.
Indeed, an accurate impression means an accurate prosthetic rehabilitation (I might suggest this article to stress out this concept Traini, Tonino et al. “Esthetic outcome of an immediately placed maxillary anterior single-tooth implant restored with a custom-made zirconia-ceramic abutment and crown: a staged treatment.” Quintessence international (Berlin, Germany: 1985) vol. 42,2 (2011): 103-8.)
Another concept that instead totally lacks is the role of the innovation technology, from the reproducibility performance to the digital format in achieving the ideal “material and methods” to realize the most precise prosthetic rehabilitation (I might suggest these articles to stress out this concept Varvara, G et al. “Comparative surface detail reproduction for elastomeric impression materials: Study on reproducibility performance.” Journal of biological regulators and homeostatic agents vol. 35,1 (2021): 161-169. doi:10.23812/20-561-A, Turkyilmaz, Ilser et al. “Guest Commentary: The Battle of File Formats from Intraoral Optical Scanners.” The International journal of prosthodontics vol. 33,4 (2020): 369-371. doi:10.11607/ijp.2020.4.gc).
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: DIMENSIONAL CHANGES OF COMMERCIAL AND NOVEL POLYVINYL SILOXANE IMPRESSION MATERIALS FOLLOWING SODIUM HYPOCHLORITE DISINFECTION
Review round: 2
Reviewer: 1

Output:
Basic reporting: 1. Most of the changes have been implemented.
2. Slight correction required in a line in discussion which has been edited by me in the file.
3. Commercial spelling wrong in the legend for graphs at 3 places.
Experimental design: All corrections have been implemented.
Validity of the findings: 1. In the end, significant 'p value' of post hoc Tukey test should be written.
Additional comments: Article can be accepted after these minor corrections.


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: LEOPARD AND SPOTTED HYENA DENSITIES IN THE LAKE MBURO NATIONAL PARK, SOUTHWESTERN UGANDA
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is a clear and concise manuscrit, easily followed and understood.
Experimental design: The methods used are adequate for the purpose here.
I would appreciate some details about camera trap placements as well as why no cameras were deployed in the western part of the park.
Validity of the findings: Analyses are straightforward and the result adequately presented.
The quality of the discussion is a bit poor but can easily be improved.
Additional comments: Dear authors,

You present a simple and straightforward ms, not testing any hypothesis but providing first estimated for spotted hyaena and leopard densities in Uganda. It that sense, your work contributes to the global knowledge about these 2 species and is using recognized methods to estimate densities and population size. The language is clear and the ms manuscript well written, easily understandable. The statistical methods employed are also adequate and properly used.

However, I would recommend that you provide additional details in the methods in terms of data collections and SECR models descriptions. Supporting materials also require some work to be truly of value for readers.

I have 2 main concerns.
The first one is about camera trap placement as in the choice of the actual location where cameras were deployed in the landscape and why no cameras have been deployed in the western part of the park (Fig 1). Can you explain why it was not done?
Second, the authors claim in the discussion that one weakness of their work is that it provides no information about the relation between leopards and hyaenas. However, figure 3 shows variation in local density for both species, so possible so correlative analyses would be possible, and I would recommend it to be added to the ms.

Finally, I am somewhat disappointed by the quality of the discussion that often strays for form the actual focus of this paper (eg compensation schemes for livestock losses). I feel the quality of the discussion can be greatly improved and its length shorten to better fit such a concise aim as this work presents. For instance, you never discuss of the variation in local densities shown in Fig 3. Would you have some explanation for such variations?

You will find detailed comments on the attached pdf of your manuscript.

The supporting material 2 & 3 require some work to make a more valuable contribution, especially in terms of formatting. I would recommend to also add an R script, using one of the models as an example so reader could repeat your analyses. This was, you also would not have to provide the lengthy details in the way you did. But should you decide to provide them anyway, I would recommend formatting them in proper table instead of simple copy-paste from the R console.
I also provided comments on these 2 files, all combined in a single pdf with the MS.

I sincerely hope these comments will be helpful.


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: LEOPARD AND SPOTTED HYENA DENSITIES IN THE LAKE MBURO NATIONAL PARK, SOUTHWESTERN UGANDA
Review round: 1
Reviewer: 2

Output:
Basic reporting: I have no comments on the language of the manuscript. It is well written and professional.
There are gaps in the litterature cited and the literature list and tables that needs to be throughly reviewed.
The raw data is shared.
There is no hypothesis.
Experimental design: The manuscript is within the aims and scope of the journal.
There are no research questions defined, but there easily could be and the research is very important for the species and the areas it investigates.
The sampling design appears adequate and there is no ethical concerns.
Validity of the findings: Findings are mainly reporting on densities of leopard and spotted hyenas but no actual investigations into what affects their densities and the conclusions are mainly speculative albeit with revised analyses the authors would be able to make scientific inference.
Additional comments: Comments to the authors

Dear Authors of

I enjoyed reading your manuscript and commend you for your efforts. It is so little science that comes out on large carnivores in parts of East Africa and particularly Uganda. My impression is that you have a good dataset, but I do have a few concerns regarding it and some suggestions for improving it.
Currently your manuscript is a reporting on densities of leopards and spotted hyenas in Lake Mburo National Park, but there is no clear hypothesis stated nor is there any direct conservation implication and finally the use of SECR on a social canid is controversial.

Major comments
Firstly, you have good data and have a conservation approach to your study, but you do not use your data to address conservation issue. SECR is a powerful method not only for estimating densities but also to understand which factors affect the density. It is not a difficult process to add covariates on e.g., distance to national park boundary, a water source, prey density (which you are referring a lot to and must have data for given the maps you provide) to test a hypothesis on what affects densities of leopards and spotted hyenas. This will give you a scientific foundation for making conservation recommendations rather than simply speculate/postulations about them. I suggest you read the study by Havmøller et al. 2019 (which is in your references but not quoted in the text or table…) and Rather et al. 2021 DOI: 10.7717/peerj.10634 for inspiration and insight and use similar metrics and rerun your analyses with questions such as do large carnivore densities decline close to NP boundaries/villages? Are densities affected by distance to water? habitat type? prey densities? Etc.
This would set the foundation for a more insightful manuscript/publication that you can actually use as the scientific foundation for conservation recommendation – as opposed to just speculations.
Secondly, when you create a state space you should only include an area that realistically can include your study area. Right now, you are reporting and drawing conclusion on an area 20x your study site. You should use an appropriate state space and rework your entire discussion according to your new results.
Thirdly, spotted hyenas are known pack-living and occasionally pack-hunting canids. Using traditional SECR with minor changes to estimate densities is not an appropriate method because individuals do not have independent activity centres and thus densities are overestimated. There are very few studied published on SECR densities on social canids, but please read the suggested publications below and reconsider your analysis for the spotted hyenas density estimation. As your manuscript is currently composed, I am convinced that you have overestimated the hyena population.

Ngoprasert, Dusit, George A. Gale, and Andrew J. Tyre. "Abundance estimation from multiple data types for group-living animals: An example using dhole (Cuon alpinus)." Global Ecology and Conservation 20 (2019): e00792.

Harihar, Abishek, Mousumi Ghosh, Merwyn Fernandes, Bivash Pandav, and Surendra P. Goyal. "Use of photographic capture-recapture sampling to estimate density of Striped Hyena (Hyaena hyaena): implications for conservation." Mammalia 74, no. 1 (2010): 83-87.

Bohm, Torsten. "Population ecology, conservation status and genetics of the spotted hyena (Crocuta crocuta) in the Odzala-Kokoua National Park, Republic of Congo, including an assessment of the status of spotted hyenas in southeast Gabon." PhD diss., 2015.

I am suggesting major revisions to the editor and hope that you find my suggestions useful.
I look forward to reading your revised manuscript and I think it is incredibly important to have these types of studies out from this part of the world - and you have good data so you can really make analysis that can have a valuable conservation impact! You can do this!

Best regards

Rasmus Havmøller

Minor comments
Abstract: The word functionally extinct implies that lions are present, but in so low numbers that they have little or no impact on the ecosystem. Consider whether this is what you actually want to say.

L78: Uganda is a country not a state
L91: comma missing in 1585
L96: eg. Abbrivation incorrect and autocorrected capital letter subsequent
L101: should be e.g. no eg.
L107: why is the scientific name suddenly in parentheses? Check journal format requirement.
L168: female leopard home-ranges have been reported far smaller than 30km2, what is relevant to present is the inter camera trap distance, which gives the reader an idea of how many camera traps you have within a male/female home-range.
L184: half way. It is technically a result that the right flanks were captured most often, I suggest moving it to the results section.
L265: You have not defined what constitutes “temporally independent” in the methods
L268: write juvenile rather than young
L273: Bayesian p-values??? In a Bayesian framework you can only really talk about posterior probabilities to my knowledge, please just stick to that.
L290: a state-space of 6733km2?!? That is an enormous area nearly 20x your study area – is this a typo? Your math is off, 6.31 leopards / 100km2, LMNP is only 370km2, meaning 6.31x370km2 = 23.347 leopards for the entire LMNP. You are reporting +204 leopards for the national park plus 25km buffer? If your statespace needed to be this high it is an indication to me that indication that your models were a poor fit. If you have not performed a sensitivity test of your buffer, then I suggest you do so and choose the lowest possible to add realism to your study.
L294: Same as above, the math is off. If you have a density of ~11 hyenas per 100km2, and your study area/national park is 370km2, then you only have 11x3.7= 40.7 hyenas for the entire national park.
L322: But you have not tested for an effect of prey even though you could easily have done it.


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

Input:
Title: LEOPARD AND SPOTTED HYENA DENSITIES IN THE LAKE MBURO NATIONAL PARK, SOUTHWESTERN UGANDA
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Dear authors,

Thank you for the detailed response to my previous comments and the revised manuscript that is now much improved.

I still feel that the methods section regarding SCR and your model parameters needs some clarifications, maybe a table similar to table 3 to explain each parameter might be helpful?
While I appreciate that you split the discussion into sub-section, it does not really work as you did it. Having sections called Possible reasons for observed leopard and hyena densities and Spotted hyena densities in LMNP and comparisons to other studies is more confusing than anything else. Either change the titles to meaningful ones 'possible reasons for observed densities' is not exactly clear… or omit them.
Your table 2 still introduce parameters such as Nsuper and ψ that are never mentioned elsewhere, since detailed about the models outputs are not given. Consider deleting them from the table if you never mention them…

I attached an annotated version of the ms pdf wit specific comments.

Apart from that, I do not have further comments on your manuscript and commend you for your 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: LEOPARD AND SPOTTED HYENA DENSITIES IN THE LAKE MBURO NATIONAL PARK, SOUTHWESTERN UGANDA
Review round: 2
Reviewer: 2

Output:
Basic reporting: Language is clear, but still with some type-os and insufficiencies as per journal standards.
References are generally fine, but there are error in the reference list and some articles that are cited in main text but not present in reference list and vice versa.
Structure is professional and data shared
No hypothesis
Experimental design: Basic reporting
Basic questions that fills a knowledge gap
Rigorous analysis for leopards, more questionable but acceptable for spotted hyenas
Methods well described
Validity of the findings: Very important study with data from an area that has very little research coming out.
Data analysis is correctly performed, but does not allow for in-depth discussion which makes the discussion and conclusion very speculative
Additional comments: Dear Authors of Leopard and spotted hyena densities in the Lake Mburo National Park, southwestern Uganda

Thank you for the opportunity to once again review your manuscript. From my perspective the manuscript is improved, and I see that you have incorporated large parts of comments provided by Stéphanie and myself.
However, your lack of willingness to expand your SECR analyses to go beyond simple density reporting creates a dilemma.
You spend a lot of effort discussing that human conflict is on the increase around the national park, and then also state in your rebuttal that a visual inspection of the carnivore densities shows no sign of edge effects. This type of non-analytical subjective statements is not good scientific practice, you need the statistics to make these sorts of statements. The same goes for your discussion which is now just speculations, but could easily be a discussion of real results. Furthermore, say that you or someone else in five years repeats your study and find that carnivore densities have changed, but given that you have not investigated which factors impact carnivore densities, then you cannot conclude what has cause the decline. Was it an edge effect? Did prey decline? Did the surrounding human impact increase?
Stating that using SECR on spotted hyenas is becoming increasing commonplace in your rebuttal, is not supported in your manuscript given that the only article that you cite regarding SECR on spotted hyenas is the M’soka et al. 2016, who included a variety of parameters to understand which factors affected hyena densities (Lindsey et al. 2019 is not in your reference list……..). Your elaboration in the rebuttal on spotted hyena ecology undermines your argument for using SECR. Social animals who reside together, but might not forage together, still violates a crucial assumption in the SECR framework which is independent activity centers. The fission-fusion element of hyena ecology further complicates the use of SECR because home-ranges vary. I am all for providing the best possible density estimates of spotted hyenas, through SECR too, but it is imperative that the limitations in using SECR on this species is clearly stated and it is emphasized that further development in the line of e.g., Dusit Ngoprasert´s work is needed for more accuracy.

Minor comments

L35: check capital in species name
L39: should be “have” not “has”
L145: “,” after “e.g.”
L146: country and state might be interchangeable, but for a US reader its confusing as it sounds like Uganda is a state in the country of East Africa. Suggest you rephrase this.
L152: Crocuta Crocuta should be Crocuta crocuta according to nomenclature standards species names are never capital but genus names are.
L159: Double-space after full stop
L169: “,” after “e.g.”
L175: same as lines 35 and 152
L195-197: () missing around scientific names as per journal standards
L212: same as 195-197
L284: same as L169
L383: as above
L426: as above
L505: Lindsey et al. 2019 not in reference list
L597: comma missing after e.g.
L728: error in reference list
L747: missing indent
L801: (still) not cited in main text


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: EFFECTS OF MEDIA MULTITASKING FREQUENCY ON A NOVEL VOLITIONAL MULTITASKING PARADIGM
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript examines the application of the human behaviour of media multitasking to a real-world task that employs media multitasking skills such as cognitive flexibility/task switching. The authors have provided a clearly written overview of the study in much of the manuscript. There are a few areas where the clarity of the information presented could be improved.

The authors have provided a suitable overview of the relevant literature relating to media multitasking and cognitive functions. However, several new papers have been published within this area since 2017 including a 2021 review and it would be relevant for the authors to include some of these newer pieces of evidence within the introduction and discussion sections of the manuscript.

The structure of the article is clear and follows the required journal article conventions. Raw data has been provided in accordance with journal requirements.
It is recommended that Figures 2 and 3 be removed from the manuscript as they do not provide significant value add to the information already presented within the manuscript. Figure 1 is generally clear in providing an overview of the sequence within a trial of the experiment. However, a key is needed to ensure clarity around which responses the key presses represent. For example, is it C = Correct and I = Incorrect? This needs to be clarified in Figure 1.

The authors have provided a comprehensive account of this experiment within the manuscript. The proposed hypotheses stated within the introduction and detailed within the results section are suitable and do follow from the literature review provided. However, there is some further clarification required within the study predictions. It would seem that hypotheses 2 and 3 are stating the same thing? This may not be the case, but rewording would ensure greater clarity. Specifically, this comment applies to this section of the manuscript on lines 154 to 160. “We also expected that participants would show a “return cost”, i.e., respond slower to return to the primary task following a switch to the secondary task that would be negatively predicted by media multitasking. Additionally, we predicted that individuals who media multitask more often would choose to switch to the secondary task more quickly and would have more trouble returning to the primary task after a switch, in line with the suggestion that media multitasking frequency is associated with decreased executive function (Baumgartner, Weeda, van der Heijden, & Huizinga, 2014; Cain et 161 al., 2016).”
It is also unclear exactly how this prediction relates to the concept of impulsivity. This needs to be unpacked to ensure clarity. Lines 161 to 164. “In line with the suggestion that frequent multitaskers show difficulties with filtering or impulsivity, we predicted that MMI score would also show a positive relationship with the amount of interference exhibited on trials where a pop-up was presented, but the secondary task wasn’t chosen.”

One issue that does require modification in relation to hypotheses is the exploratory analyses. While I agree that these are suitable analyses to conduct within the discussion section the outcomes of the exploratory analyses are frequently referred to in relation to predictions or hypotheses being supported or the results of this analysis being consistent with the prediction. Given that this is an exploratory additional analysis, and it does not appear to have specific predictions as would be the case the discussion section needs to be reworded when referring to the outcomes of the exploratory analysis. This revision is required for all instances of the discussion section where this reference is made. (Lines 422 to 605).
Experimental design: The authors have clearly identified the relevant gap within the empirical work on media multitasking research. That is, the area is heavily reliant on standard measures of cognition especially executive functions and has not really examined the link between media multitasking behaviour and performance on a more real world like task that examines cognitive flexibility/task switching.
Statements throughout the manuscript to illustrate good adherence to required ethical clearance standards for the protocol.
The experiment has been well designed and the measures outlined within the methods section of the manuscript. There are a few areas of the method section that could include additional details to ensure full replication of the experiment was possible or to provide greater clarity regarding decisions made about the included measures.
1)	Was the sample size of 90 participants of sufficient power to detect the often-small effects evident in media-multitasking studies? Some clarification about power is required within the manuscript.
2)	All the forms of media included within the MMI need to be stated within the method section detailing this measure (lines 177 to 205).
3)	Within the information presented in lines 177 to 193 a more detailed explanation is required as to why the scale used for participants’ responses differed from the standard MMI measures (line 184 to 205). The current statement to get a more precise measure does not seem to be a sufficient statement to justify this decision. For example, how and why would this 5-point scale provide more precision and also allow cross study comparison compared to the standard 4-point scale that is used within this measure?
4)	Sample items are required for the Multitasking Preference Inventory as well as a clear statement of the scale terms used for the Likert scale.
5)	How was the BIS scored and which scales or sub-scales were used in this study and why? What were the anchors used within the Likert scale for the BIS? Key details are missing for this measure.
6)	It is unclear why participants would have wanted to switch to the secondary task (lines 223 to 235).  Since there was no reward for doing this other than points and it does not seem the points were of use for any reason then why would participants undertake the secondary task at all. Explain how this design decision would not have adversely affected the results of the study in any way.
Validity of the findings: All participant data has been provided with the manuscript submission, thank you.
Clarification is needed to justify the use of the total BIS score within the analysis instead of sub=scale scores.
Lines 291 to 293 note that the MMI mean score is in line with that obtained from a prior study. However, the mean for that study was considerably lower than has been reported in most other studies. Therefore, there needs to be justification as to why this difference in MMI mean scores is suitable and this should be supported with more than one other study used as an example. What method was used to compute the MMI values in this study and is it the same or different to that used in most other studies within this area?
Table 1 requires a note below that has a key to indicate what each abbreviated measure refers to exactly.
Table 2 requires more detail about what the exact measures were that were used on the analysis. The current title is not informative in relation to what factors were included. This same comment applies to Table 6 as well.
Check the z value reported on line 311 as this does not seem to be correct.
The DVs (units of analysis) for the main analysis for the Switch Rate, Return Cost and Interference Cost need to be clearly stated within the text. It is not clear how these variables were measured (e.g., percent correct, percent errors, response time etc.).
In lines 476 to 478 a comment is made the repeating the same task and the link with MMT is explained by attention rather than any other cognitive process such as working memory, inhibitory control (staying on task rather than allocating attention to extraneous thoughts). This needs further clarification to fully justify this point.
Line 492 to 494 suggest that the results could be due to weak effects sizes. There needs to be clear indication that this cannot be attributed to the sample size for this study not being sufficient to examine the possible weak effects that are evident in media multitasking studies examining a link with cognitive function.
Additional comments: Lines 461 to 463. Check expression for sentence starting with “At the same time…”
Lines 559 to 562, check expression in sentence starting with “It is also important to note…”
Was there any analysis conducted between those who undertook both tasks compared to those participants who did not multitask at all for the BIS, MMI or MIP? This analysis could be very informative regarding differences or lack there of between these two groups of participants. This analysis would further add to the overall strength of the study and could be included within the exploratory analysis section of the manuscript.
Check results section as some minor typos (e.g., brackets missing to end brackets) are evident.
Overall this is a very interesting study that informs the literature regarding the link between self-reported media multitasking and cognitive performance.


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

Input:
Title: EFFECTS OF MEDIA MULTITASKING FREQUENCY ON A NOVEL VOLITIONAL MULTITASKING PARADIGM
Review round: 1
Reviewer: 2

Output:
Basic reporting: The idea to assess the relationship between media multitasking habits and voluntary task switching in a setting that somewhat mimics a real-world scenario is of great interest. However, the way the authors frame and introduce their study is rather confusing.

For example, the abstract states that media multitasking has been linked to decreased executive functioning followed by a critique that this finding has been established using “standard” tasks rather than a real-world volitional multitasking environment; which justifies the current study. I must admit that I don’t understand this line of reasoning. First, to use standard executive functions tasks to evaluate the relationship between media multitasking habits and executive functions is a valid strategy in my opinion. Second, if the point is to argue that their multitasking paradigm is a more valid measure of executive functions, this point should be substantiated in the text.

The paper is overall hard to read and lacks precision. For example, the title “real-world media multitasking shows few effects on lab-based volitional multitasking performance” seems to indicate that the authors assessed “real-world” media multitasking (as opposed to the “classic” way) when in fact media multitasking was assessed using the typical questionnaire and the “real-world” aspect refers, in the main text, to their new multitasking task paradigm rather than the media multitasking. Furthermore, the title seems to imply a causal relationship, which is not substantiated by the data.

The multitasking test developed by the authors is in my opinion a misnomer since participants do not perform both tasks at the same time but are required to switch between tasks. I understand the authors may have a different view on these terms (multitasking == task switching) but if so, they should define them.

The coverage of the literature could be improved to be both more to the point and substantive. For example, I don’t see the value of describing “supertaskers” in the context of this study (line 104) and I missed information that there is evidence showing that the link between digital media  consumption and various outcomes is very small (e.g., Orben & Przybylski, 2019). There have also been studies investigating the relationship between media multitasking and multitask performance (e.g., using the operation span task, Sanbonmatsu et al 2013; cited in the paper line 711). It would be useful to explain in greater detail how that task differs from the one presented here and discuss the results accordingly.

The reporting of the results is also confusing and lacks focus. Instead of displaying 13 tables, the authors might display 1-2 figures that emphasise the specific points they want to make; those tables would be more adequately placed in the supplementary material, in my opinion.

Finally, although the data has been shared, it is hard to make sense of that data. No codebook or explanation is provided and it seems that the data is somewhat inconsistent. For example, within file 063process.xls, the “participant” variable takes on values “switchrate”, “totalswiches” but also “63”. More work needs to be done for this dataset to be usable by other researchers. The osf directory also contains a bit of code; but it’s unclear how it relates to the results reported in the paper (it’s not even clear which data is being used for the analyses reported in the paper); providing the code that was used for the analysis in this paper would also help understand what exact analyses were conducted.
Experimental design: The paper seems to be within the scope of the journal (in particular as there have been other papers in cognitive psychology published in PeerJ).

As described in the previous section, the research question has not been presented in a clear and compelling way. I believe the overall design to be interesting but currently poorly justified.

I like the idea of their volitional task-switching design but I’m also a bit worried about two aspects. a) it’s unclear to me why some participants decided not to switch at all to the secondary task since this task provided more points. This behavior may perhaps indicate that some people did not engage with the task, did not understand how it worked or simply did not pay attention to the notifications—in which cases the interpretation of the results would be very different. Perhaps a better way to engage participants would have been to offer them the possibility to quit the experiment as soon as they reach a set level of points (in which case abstract points, which some may not value, would translate to time, which most people value).
b) it seems to me that it would have been necessary to also include trials where task switching was required; this would allow for instance to separate “interference costs” due to the processing of the “pop up” (i.e., detecting information on the screen) versus that related to deliberating whether or not to switch tasks.
Validity of the findings: As stated earlier, the data is provided in a way that is not directly usable and the code used to run the analyses reported in the paper has not been shared, as far as I can tell. Hence, it is not possible for me to evaluate the robustness and soundness of the reported analyses.

The validity of the findings is also unclear for reasons already stated in the previous sections.
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: EFFECTS OF MEDIA MULTITASKING FREQUENCY ON A NOVEL VOLITIONAL MULTITASKING PARADIGM
Review round: 2
Reviewer: 1

Output:
Basic reporting: The structure of the article is clear and follows the required journal article conventions. Raw data has been provided in accordance with journal requirements.
The authors have provided a comprehensive account of this experiment within the manuscript.
The overall logic of the study and situating the study within the literature and relevant context has been improved from the previous version of this manuscript.
The clarity of the written document is suitable.
Experimental design: The additional method information provided within the revised manuscript has addressed my comments from the prior version of the manuscript.

The MMI formula alone in Sup Figure 1 is not informative as to how the calculation is actually done this needs to be revised
The BIS measure cannot be included within the supplemental figures as this is a published scale and this would be a copyright issue if it is included without permission. Further it is not needed for this article. This same comment applies to the MPI in Sup Figure 3
Supplementary Figure 2 which is a copy of the MMI is not needed the method information in the revised manuscript now clarifies things around that measure
Validity of the findings: Please check the wording of a two-sided Pearson correlation it is not clear what this actually means. Does it mean two-tailed or something else.
Why were non-parametric tests used for the multitasking performance analysis? This has less power than a parametric test and justification is needed for use of the test.
Figure 5 the correlation should be presented as a Table as that is easier to follow than the Figure currently presented.
Comment on line 578-79 that effects may no longer exist with a larger sample size does not make sense please clarify what is meant by this.
In general I think the length of the discussion section could be reduced. Many of the points made while important could be made more directly and more concisely and still convey the same message for the reader.
This same comment of reducing the word length applies to the conclusion section. State the main aim  and then cover the key significant and non-significant findings. Then focus on the key take home message from the article. This will help improve readability of the last sections of the manuscript.
Additional comments: line 610 serious should be series


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: MAPLE AND HICKORY LEAF LITTER FUNGAL COMMUNITIES REFLECT PRE-SENESCENT LEAF COMMUNITIES
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript submitted by Liber and collaborators examines (1) the fungal communities of two forest trees and compare epiphytic-endophytic-litter- soil communities of five different sites within the forest ecosystem, and (2) the effect of different swab material used in sampling on epiphytic community.

The manuscript is clear and well written; it needs editing for the consistency of subtitles formating, use of italics when is needed  throughout  the text etc.
Experimental design: The manuscript submitted by Liber and collaborators examines (1) the fungal communities of two forest trees and compare epiphytic-endophytic-litter- soil communities of five different sites within the forest ecosystem, and (2) the effect of different swab material used in sampling on epiphytic community. My main concern is related to the experimental approach. As far as I understood, the authors collected  samples from four different substrates and five sites in the forest  for each plant species only once. This means that the  data presented are only a snapshot of the forest fungal communities, thus it is very difficult to conclude on the  characteristics, origin etc. of fungal communities detected. Luckily these concerns/limitations  are discussed by the authors; still I am not persuaded that research questions stated in the introduction  can be really addressed by the presented experimentation.
Concerning the methodology described, it is not clear how many replicates per site and plant are included. Are ten replicates for phyllospheric samples (l 105) and three for the other substrates  (l 108) per site included?  And then where this “ a total of 50 samples were…. analyzed (l 210)” comes from? Please verify the number of replicates per substrate and site for each plant species. Also, there is no information about the similarity of  sample size from the different sites used in the experiment. Please give more details about soil /litter / leaf sampling procedure.
Validity of the findings: No comment
Additional comments: No additional comments


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

Input:
Title: MAPLE AND HICKORY LEAF LITTER FUNGAL COMMUNITIES REFLECT PRE-SENESCENT LEAF COMMUNITIES
Review round: 1
Reviewer: 2

Output:
Basic reporting: In this study the authors aim to (1) compare the leaf, litter, and soil fungal communities of red maple and shagbark hickory; (2) identify the drivers of fungal community composition in temperate forest substrates; and (3) assess if synthetic and cotton swabs provide similar detection of leaf epiphytic fungal communities. To do so, 5 individuals per tree species were sampled in a forest ecosystem in southern Michigan. For each tree, leaves, litter, and soil were sampled. Swabs and leaf surface sterilization were used to distinguish between leaf fungal epiphytes and endophytes.

The document is professionally structured, the text is mostly clearly written, and the scripts and processed data are available on GitHub.

-Missing references to plant and tree fungal community studies
Lines 57-63 are missing background. I believe discussing the findings of the following references could help provide a sufficient field background.
Kembel, S. W., & Mueller, R. C. (2014). Plant traits and taxonomy drive host associations in tropical phyllosphere fungal communities. Botany, 92(4), 303-311.
Whitaker, B. K., Christian, N., Chai, Q., & Clay, K. (2020). Foliar fungal endophyte community structure is independent of phylogenetic relatedness in an Asteraceae common garden. Ecology and Evolution, 10(24), 13895-13912.
Whitaker, B. K., Reynolds, H. L., & Clay, K. (2018). Foliar fungal endophyte communities are structured by environment but not host ecotype in Panicum virgatum (switchgrass). Ecology, 99(12), 2703-2711.
Zimmerman, N. B., & Vitousek, P. M. (2012). Fungal endophyte communities reflect environmental structuring across a Hawaiian landscape. Proceedings of the National Academy of Sciences, 109(32), 13022-13027.
Experimental design: This manuscript provides interesting results that are well aligned with the aims and scope of PeerJ. The research question / hypotheses are well-defined.

The sampling effort is modest (a total of 50 samples), but could provide sufficient information to make a significant contribution to the literature.

Line 101: “A suitable amount” is not a scientific quantity that can allow fellow researchers to reproduce an experiment. Please state with biologically and scientifically relevant terms what represented a “suitable amount”.
Validity of the findings: One of my main concern with the study design/results/discussion is the confusion between "site" and "individual tree" effects. Indeed, the authors consider their design to allow for detecting a "site" effect but since only one individual per tree was sampled at each of their "site", and since it has been shown that there are inter-individual differences in leaf microbial communities, the results are confounding. For example, the authors could code "site" as a random effect or blocking effect in a linear-mixed model or permanova respectively, where each "site" would include the two individuals from A. rubrum and C. ovata sampled.

Overall, the statistical analyses are sound, but way too much results and discussion space is spent on discussing differences in OTU numbers (lines 246-250, lines 358-365), thus providing very little substance to the field and wasting an opportunity to discuss dispersal mechanisms that could explain the leaf-to-soil continuum.

I believe the authors miss an opportunity to situate clearly in the introduction and discussion how their results contribute to our understanding of the dispersal dynamics across the tree leaf-to-soil continuum. Although very modest, this study provides very interesting results of what happens to fungal communities when they return to the soil.
Additional comments: I commend the authors for using both negative controls and mock communities, for adding a technical aspect to their study (testing swab type differences), and most importantly for openly discussing and acknowledging the limitations of their study.
I suggest for future work that the authors consider moving away from rarefaction as it has been shown to discard considerable amounts of information (McMurdie & Holmes 2014) and there are many demonstrated alternatives implemented in QIIME, QIIME2, and DADA2.

Minor comments:
--Abstract
Line 19: In the first sentence, it would situate adequately the readers by contrasting “living plant microbiomes” with “decaying plant material microbiomes”. It is hard to understand that you mention “living plant microbiomes”, which seemed very strange initially, because your project is going to describe senescent leaf microbiomes too.
Lines 26-28: Please rephrase to “Fungal communities were differentiable based on substrate, host species, and site, as well as all second- and third-level variable interactions.”
Line 28: Ordinations are not used for statistical diagnostic but for visual exploration. Please replace “ordinations” with the appropriate statistical tests employed (i.e. permanovas, permdisp).
Line 29-30: This sentence provides very little meaning. There is dispersal between leaf, litter, and soil. I believe the authors could provide a more insightful final statement and suggest pertinent future avenues.

--Introduction
Line 33: “Plant and soil microbiomes contribute to critical ecosystem functions and are involved in complex interactions within communities”.
Line 34: “Fungi are important microbial community members […]”
Lines 35-39: This sentence is very repetitive with the one at lines 34-35. I suggest taking out the 34-35 and keeping 35-39 but splitting it in two sentences rather than one very long.
Line 58: “Composition” and “structure” are most often used as synonyms for community ecology. Did you want to say: “composition and diversity”?

--Methods
Lines 102-103: “We selected these tree species as they were consistently found across the forest, providing the opportunity to test site effects.”
Line 105: “Ten fresh leaves (Acer) or leaflets (Carya) per tree per site were collected axenically […]”
Line 111: Sterile plastic bags?
Line 213: Why only forward reads? Did the reverse reads fail?
Line 312: “Leaves and leaf litter were respectively pooled by host species and site.” Otherwise it seems like you pooled leaves and leaf litter together.

--Discussion
Lines 327, 366, 374: Should be italicized.
Line 339: Please define what are "the ecologies"?
Lines 392-393: “Yet, our results provide a significant contribution by describing the drivers of leaf fungal diversity across the leaf-soil continuum.”


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: MAPLE AND HICKORY LEAF LITTER FUNGAL COMMUNITIES REFLECT PRE-SENESCENT LEAF COMMUNITIES
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: No additional comments


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

Input:
Title: MAPLE AND HICKORY LEAF LITTER FUNGAL COMMUNITIES REFLECT PRE-SENESCENT LEAF COMMUNITIES
Review round: 2
Reviewer: 2

Output:
Basic reporting: In this second version of their manuscript, the authors have addressed most of the comments from the previous review. Yet, I still have a few important concerns.

Major comment:
In the previous review, I suggested that the authors situate better their study in terms of literature on dispersal mechanisms of microbial communities. They answered: "We decided to not suggest implications for dispersal dynamics because our sampling design does not assess temporal and functional dynamics, and therefore cannot conclude the direction of dispersal or the activity of organisms in each substrate." Yet the two last sentences of their abstract mention dispersal directly. And then part of the discussion adresses dispersal, priority effects, and other drivers of microbial community assembly at lines 320-322 and 347-349. To do that, the authors need to support their statement by looking at important previous works that can support their claims. Their study should be better situated in terms of literature. Like right after their sentence on the distribution of fungal taxa at lines 47-49. The introduction does not provide the needed context that reader needs to understand the discussion.
Experimental design: Lines 114-116: Should mention that there is no opportunity here to look at site effect since it is confounded with inter-individual variation (host genotype). It is better stated later in the methods at lines 200-202 but the authors shouldn't let the reader think that they are able to measure site effect because of their study design. Lines 407-410 should be placed in methods so that the reader can understand the limits of the study design.
Validity of the findings: Hypothesis 82-84 is opposite to literature just cited. Also opposite to literature cited in discussion when results are stated to be in line with lit lines 322-324.

There is no mention that normality and homoscedasticity of data was checked before testing for differences in alpha-diversity. This should be done. If it has been done then mention it at lines 196-197.

Lines 209-212 are confusing since the authors mention using PCoA then NMDS but we only see NMDS in their study. Is it a mistake? Where are the PCoA? Why use PCoA then switch to NMDS?

Lines 240-242: It's not the dissimilarity index that explains variation, it's the two main axes of the ordination on bray-curtis dissimilarities. Rephrase.

Lines 252-254: Where is the test for normality and homoscedasticity?

Line 255: Where is the information on which statistical test was used to identify indicator taxa?

Lines 354-356: Clustering in an ordination is not a statistical test and doesn't support your statement. Remove or rephrase with permanova.
Additional comments: Minor comments:
Line 22: "[...] as well as to the decay [...]"
Line 24: Why does it require further research? Why not state instead that we still ignore most of these factors?
Line 29-31: Last portion of the sentence on second and third level interactions is weird.
Figures: Most are blurry and tough to read.
Figure 4: Add statistical test and significance results.


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

Input:
Title: CONSERVATION PALEOBIOLOGY ON MINAMI-DAITO ISLAND, OKINAWA, JAPAN: ANTHROPOGENIC EXTINCTION OF CAVE-DWELLING BATS ON A TROPICAL OCEANIC ISLAND
Review round: 1
Reviewer: 1

Output:
Basic reporting: This manuscript focuses on documenting the extirpation (i.e. population level loss) of two species of bat in the genera Miniopterus and Rhinolophus from Minami-Daito Island. These extirpations are interesting from the standpoint of recent changes in the bat community composition of the island, where another bat, Pteropus dasymallus, is now the only extant mammal. The aim of the study is listed; however, given that it is presented in light of previous observations, I feel like this aim could have been better presented as a clear hypothesis. Similarly, the aim only focused on the test of guano-like deposits, yet I feel like there is another hypothesis that was overlooked in the presentation of the introduction that relates to the cause of extinction of these bats. Improving the clarity of how these hypotheses are presented could really help. Overall, the ideas in manuscript are well organized and for the most part the text is written clearly – although there are various suggestions where the writing could be improved for clarity and tidiness of grammar (see attached PDF with comments).
Experimental design: The experimental design used is appropriate to document these bat losses. The multiple evidence approach used combining isotopic, SEM, and radiocarbon data, and the link to local historical accounts of the presence of these bats was well stitched in, and it does provide potential evidence for the influence of anthropogenic change on the bat community of Minami-Daito Island. Refining/clarifying the hypotheses tested would really make the manuscript flow more logically. The methods used were presented clearly and well described.
Validity of the findings: The authors presented a multi-prong approach to document the loss of the bat genera Miniopterus and Rhinolophus from Minami-Daito Island. The evidence presented does support the finding and conclusions that these bats were recently extirpated. However, while the timing for the loss of these bats presented does match with fast anthropogenic habitat transformation, the study does lean a lot on that correlation and not on direct evidence. For example, given the low number of individuals found (i.e. MNI = 17 Miniopterus and 2 Rhinolophus), it could be also possible that these were non-viable drifting populations that naturally died. The direction of the conclusions by the authors is not incorrect, but because there could be other plausible explanations for the extirpation of these bats, perhaps the conclusion should be toned down and balanced by adding alternative explanations.
Additional comments: See line comments in the attached PDF.


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

Input:
Title: CONSERVATION PALEOBIOLOGY ON MINAMI-DAITO ISLAND, OKINAWA, JAPAN: ANTHROPOGENIC EXTINCTION OF CAVE-DWELLING BATS ON A TROPICAL OCEANIC ISLAND
Review round: 1
Reviewer: 2

Output:
Basic reporting: The abstract could use a little rewording, e.g., the first sentence is a little unclear due to word choice of filtration multiple times "With strong environmental and geographic filtration, vertebrates incapable of
flying and swimming are strongly filtered out of island ecosystems." and immediately noting that "the skeleton of an extinct cave-dwelling bat and fossil guano were briefly reported in a previous study" introduces confusion early on and takes away from the potential significance of the new research. I continued to find reference to this throughout the paper a bit distracting, particularly in the discussion when the authors note that taxonomic revision is ongoing.
Experimental design: I appreciate the multi proxy nature of this research and how the authors brought together multiple lines of data to tell a story. I wonder if there is a way to independently validate the historical claims that C4 appeared in about 1900, such as looking at a contemporaneous pollen core, historical photographs, or herbarium specimens? Is there any possibility of a marine influence in the diets of these bats, and if so, could you use MarineCal rather than Intcal?
Validity of the findings: The findings appear valid, though as I mention there are methodological caveats for the authors to consider and elaborate on regarding apatite.
Additional comments: This is a really exciting and well done study. I enjoyed reading the paper and look forward to learning more about this system from the authors! While it is unfortunate that the bones did not yield collagen - which would have been the most accurate choice for radiocarbon dating - I think the authors did the best they could to find other potential constraints on the age of the specimen, and they do a good job acknowledging this methodological uncertainty and downside.

I really like how the authors connected their data to a conservation perspective.

I think a way to improve this manuscript is to incorporate a bit more discussion about the downsides and constraints of apatite in isotopes and be more explicit about their fractionation estimates.


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: BEYOND RUBISCO: CONVERGENT MOLECULAR EVOLUTION OF MULTIPLE CHLOROPLAST GENES IN C4 PLANTS
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is a really interesting and important paper. The findings are fascinating and will be of interest to the C4/photosynthesis community. There are some issues regarding terminology that would benefit from further clarification (e.g. use of convergence/divergence is not formally correct) and there are some issues that need more detailed explanation (better definition of ancestral branches, pairs of branches etc.). An improved and more step by step workflow and analysis figure (like and expanded version of Figure 2) might help the readers to better understand.

The only major criticism I have is that the claims concerning differences in number of convergent/divergent changes between cannot be upheld. The data is phylogenetically structured and has differences in sampling and branch length between groups. These three factors confound and invalidate the statistical tests that are used. However, even if these claims are removed this is a fantastically interesting paper. It doesn't need the difference in number/rate claims to be really interesting to the community. The finding that there are convergent/parallel changes in multiple chloroplast genes when plants evolve C4 photosynthesis will be very thought provoking.

Other comments are provided below.

Abstract
terminology “pairs of branches” is not clear and is important to understand to enable the reader to understand the results.

Introduction
General point: The authors dont distinguish between convergence and parallelism. Moreover, throughout this article convergence is used to describe parallelism. The authors should probably tighten these descriptions up so that they match something like what is put forward in Stern 2013 Nature reveiws genetics 14:751. This would avoid some confusion.

Line 74: replace “the few slightly different variants of the C4 photosynthesis type originated” with “C4 photosynthesis evolved”

Line 85: It would be good to cite the Heckman model of C4 evolution here and separate the desrcipriton of the liekly order of events from the amino acid changes.

Line 93: change “initiates” to catalyses. Also remove “limited produciton of energy” as it doesnt produce energy per se.

Line 99-112: Its probably worth mentioning the high throughput study of positive selection from the brutnell group in this context. Particulalry given line 130-132. It sort of has been done for a very limited species set.

Line 107: Might be worth citing Bouvier et al 2021 MBE for evidence for convergent adaptation of ribisco kinetics in C4s.

Line 175: As written it sounds like you identified the origins/transitions to C4. I think these were already known.

Line 181: delete remarkably

Line 183: I dont think the statement regarding interactions is true. I do think it has implications for our understanding of photosynthetic adaptation in C4s. I dont think they will be critical for engineering C4 into C3 crops. They may be useful in finetunig C4 function, but not critical for its engineering… the C3 C4 hybrids in Moricandia, alloteropsis etc prove this.

Line 205: what flavour alignment for TranslatorX (MAFFT? If so what mafft method).

Line 223: more details needed for ancestral state estimation. Individual alignments? Which guide tree? With sites removed?

Line 230-237: I think this needs a dedicated figure. Its conceptually complicated to understand and not labelled in Figure 1 to a level that its sufficient to understand what the authors have done. In the tree there are multiple origins of C4 annotated to monophylletic clades (e.g. alloteropsis, or paspalum and axonopus). Why is this the case? Should they not be annotated as single origins of C4?

Line 239: I dont understand what a “pair of ancestral branches” is.

Line 240-241: That is the definition of parallelism and not convergence.

Line 244: I think this is a little unfair. If two different states evolve to two other non-identical states they are no more or less divergent than before and so that should not be counted as divergence. Non-convergent or non-parallel changes would be a good name for the category.

Line 246: Time steps and time stamps are not precise terminology here. Refer to most likely ancestral sequences.

Line 251-257: I know its a pain but the authors need to change their terminology C4-C4 C3-C4 etc as C3-C4 is a widely used defined term in the literature that means something else. Perhaps just replace them all with “C3 to C4” or equivalent.

Line 269-276: It would be good to mention if you phylogeny disagrees with the APG grass phylogeny. Yours is more data rich and more likely to be correct. But ti would be good to know what the differences were and where those differences are.

Line 275-277: I have difficulty reconciling the number of C4 origins claimed with the toplogy of the tree. There seems to be some over counting here.

Line 280-355: There is a small problem with stats here. Because there are more C4 species and a larger number of C4 origins there is an inherent higher probability of observing a C4 convergent/parallel change. (i.e. if the probability of observing a convergent change on a branch is the same then if you if you increase the number of branches being analysed you are more likely to observe a convergent change). This needs to be correctly accounted for in the statistics to validate the claims of a higher occurrence. The length of the branches also needs to be accounted for here if a claim re rate or frequency of occurrence is to be supported. i.e. if probability of a convergent change is a function of time, and branch length is a function of time then the longer the branch the more likely you are to observe a convergent change. I have no doubt that the convergent changes observed by the authors are real. Its really interesting and exciting. I just think the claims about frequency and rate are not supported as the number of taxa and their phylogenetic distance and position and the number of C4 origins have not been taken into consideration in the statistical tests. i.e. Boschloos test is not valid as the data is phylogeneticaly structured. Some sort of phylogenetic comparative method will need to be used here if claims concerning relative numbers of changes or  frequency of changes between groups of species are to be upheld. It should be noted that even if the statistics prove challenging and the authors remove all of the comparative data and claims (i.e. C4s have more changes than C3) then this will still be a really nice paper as provides a really nice list of convergent changes in the evolution of C3 to C4.
Experimental design: See above
Validity of the findings: See above
Additional comments: See above


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

Input:
Title: BEYOND RUBISCO: CONVERGENT MOLECULAR EVOLUTION OF MULTIPLE CHLOROPLAST GENES IN C4 PLANTS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The study by Casola & Li presents the results from an empirical approach to test molecular convergence in C3 and C4 taxa testing if convergence occurred more frequently in C4 compared to C3 lineages using multiple chloroplast proteins beside the large RuBisCO subunit.
Overall, the manuscript is well written and easy to read. The structure of the article and the quality of the figures are good and the authors also provide several supplementary data to support their findings.
The Introduction section considers a sufficient literature to justify the study carried out by the authors, whereas authors must include more references in the Discussion section to discuss their findings. The methods used are valid and appropriate to provide results for testing the experimental hypotheses of the study.

Some concerns arise regarding the use of terms such as "ancestral branches" and "pairs of branches" that need to be better clarified in the text to improve the reading and understanding of the article.

MINOR EDITS:

Line 199: use superscript for "e-10"

Line 294: "Showed" must not be capitalized

Line 318: Correct as follows: "higher number OF convergent vs. divergent replacements"
Experimental design: The experimental design is adequate for the purposes of the study and has been endowed with a sufficient level of scientific novelty. Indeed, the comparative analysis performed in this study is satisfactory for evaluating convergent and divergent amino acid substitutions along the C3-C4 phylogeny.
Validity of the findings: Overall, the findings of this study are well supported. In addition, these findings can be of great interest in the understanding of C4 photosynthesis evolution, possibly promoting future research in this topic. However, I suggest to revise the assertions regarding the differences in convergent/divergent changes between groups considering possible confounding results due to the differences in branch length between groups included in this study.
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: BEYOND RUBISCO: CONVERGENT MOLECULAR EVOLUTION OF MULTIPLE CHLOROPLAST GENES IN C4 PLANTS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors did a great job in revising the manuscript. I'm not completely aligned with the way in which the data was analysed to account for phylogeny, however I accept the authors arguments and that their approach has validity. This should be published. its really interesting.
Experimental design: See above
Validity of the findings: See above
Additional comments: The authors did a great job in revising the manuscript. I'm not completely aligned with the way in which the data was analysed to account for phylogeny, however I accept the authors arguments and that their approach has validity. This should be published. its really interesting.


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: BEYOND RUBISCO: CONVERGENT MOLECULAR EVOLUTION OF MULTIPLE CHLOROPLAST GENES IN C4 PLANTS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors satisfied the requested revisions.
Experimental design: The authors satisfied the requested revisions.
Validity of the findings: The authors satisfied the requested revisions.
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: COMPARISON OF THE BLEACHING SUSCEPTIBILITY OF CORAL SPECIES BY USING MINIMAL SAMPLES OF LIVE CORALS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper is pretty well written, the references are adequate and the hypothesis is clear.

The structure is overall ok, however several parts of the paper (see additional comments) need rephrasing, more information and justification (specially in the methods) and more clarity in the results interpretation and discussion.

Data were made available as supplementary material.
Experimental design: The research is original, important and very interesting, specially by proposing a feasible and applicable method to evaluate coral bleaching, which is a serious issue all over the worlds.

Sadly, there are a lot of information missing in the methods (such as experimental conditions and the relationship to natural field conditions), which are very important to better understand, replicate and ground the study.

Besides, there are a very confusing factor in the study design (variable colored background among species and between heat treatments) that should be performed different or at least deeply explained to convince the reader that it is not a great flaw of the study.
Validity of the findings: The results are very interesting, clear and important.

However the way some of them were obtained is not clear, and also some interpretation is not possible to be made by the reader because it is not clear how authors get to them as they seem not to relate to one or more of the figures. Besides, some results do not have a clear point of what they mean or why they are important.

The discussion needs a great restructuring because some interpretation are not clear in terms of how they were performed or why they are important. Additionally, several times authors discuss some points, although very important, that do not seem to relate to their study or results.

The conclusion is pretty clear though and I suggest to the authors to focus on it to build their discussion and select the necessary results that need to be shown and interpreted to this study.
Additional comments: Dear authors, I really appreciate to read the manuscript and the main ideas investigated in the study. The proposed method for easily evaluating bleaching through time under different conditions or among different species is really interesting, important, and feasible. However, there are some issues that need to be addressed in order to provide a better and understandable manuscript: 1) a lot of information that is needed to understand how the experiment conditions mimic those in the field is missing; 2) the colored background in the photos, which varied among species and between heat programs, may interfere in the results, which I think it is a great flaw if not properly explained/justified; 3) several results are not clear on how they were interpreted or what is their relevance; and 4) the discussion also need more work in the structure and on better connections and interpretation of the necessary results instead of general discussion about some other important related topics but that were not originate in the results of the study.

Detailed Comments:

Abstract
L24-26 – After reading the paper I realized that authors did a standardization of the greyscale by setting the grey-scale value of a given nubbin during acclimation as 100% and the grey-scale value after bleaching as 0%. It is important to rephrase this part to let it clear that 100 and 0% corresponds to a standardization and not to the real grey-scale values, which would mean total black for 100% and total white for 0%.
L31-32 – This part brings some confusion because short/long bleaching time may give the idea of time necessary to bleach (which I think is the correct) or the duration of bleaching. I suggest rephrasing it properly.
L33-34 – Why? What does that mean? Was it a decision that emerged from the experiment or something that the authors had imposed?
L34-36 – I agree that the proposed method for bleaching evaluation is better than quantifying zooxanthella density because it is easier and less time-consuming. And that it requires less replicates for studies considering several data points collected in different times. However, this must be clear here. Otherwise, the reader may think that the authors are talking about accuracy and precision of the different methods.

Methods
L104-106 – What were the total replicate? I guess it was 5 species x 5 colonies x 2 nubbins, totalizing 50 replicates, is that right? Were half of them assigned to one of the experimental tanks, so 5 nubbins of each species per tank? This information must be made clearer.
L108-110 – Authors should use ‘mol’ instead of ‘E’, once the first is part of the SI and the second is not. How does this PAR value compare to natural PAR in the field? Additionally, was any dawn/dusk simulation performed? These are important information to be mentioned because bleaching response could be triggered by the wrong amount of PAR reaching the corals. Since the proposed method is to be used in studies with an aim of selecting resistant corals or comparing different species susceptibility, experimental conditions must be as similar as possible to natural ones.
L110-114 – How was temperature increase performed? Thermostats? Where were they inside the tank? This is important to let it clear if some nubbins/species were closer to the heating source when compared to others.
L114-115 – 35 °C is a considerable high temperature. What are average, maximum, and minimum temperatures in the field? As for the PAR (mentioned before) temperature in the field is also important to be mimic in the lab to obtain more reliable results. If 35 °C is not a possible temperature to be reached in the field or considering future projections, authors must justify their choice of heating up to 35 °C.
L121-122 – I would add here a couple more words letting clear to the reader that it is because of this criterion (stop taking pictures when the entire nubbin was pale) that for each species time range with data points in Figs 2 and 3 differ among species.
L125-127 – It was surprising for me that the grayscale was estimated considering the square surrounding area instead of the exact coral area. That brought some questions to me. First, how was the greyscale estimated in Photoshop? Was it an average value considering all the pixel inside the squared area? A value of what? Does the software return somehow this average value? This information would be interesting to be mentioned in the main text for further studies using this approach. Second, the squared area instead of the exact area would be a lesser problem if all the plastic backgrounds were the same color, but even though, it would add differently to the final grayscale value depending on the coral nubbin shape. However, as shown in the supplementary figure, the background color varied both among species in a given heat treatment and also between heat treatments for a given species. Clearly each background color returns a different grayscale value, and this probably add some noise to the coral color estimate. The question is, how much noise does it add and how much that noise may change the final results?
L147-148 – Why not using a two-way ANOVA to insert the heat program as a factor as well? One of the goals of this study is to compare the heat programs, so they would be formally included as a factor in the analysis.

Results
L156-164 – It all seems methods to me.
L166-171 – Call Fig 2.
L171-173 – How did authors interpret these results? In which figure or table could the reader reach the same interpretation? Thus, I suggest to clearly refer to the figure necessary to the reader to get to the same conclusion.
L180-185 – Again, this part fits better in methods than in results.
L185 – …bLeaching…
L185-187 – How did the authors concluded that? Was there a formal test? Examining Fig 4, it seems that there are great differences among heat treatments for a same species considering the different BTI. This is particularly true considering that the y-axis scale is different for each heat treatment (maximum of 18 for FHP and maximum of 30 for SHP).
L187-190 – Was this visually or formally evaluated with some statistical analysis? If yes, where are the results? Additionally, the one-way ANOVA tables comparing the BTI among species in a given heat program was not shown.
L196-199 – What does this result indicate biologically? Is it relevant somehow? If yes, authors should explain this rationale in the methods, besides saying that the regression was performed, which it is not mentioned before. Additionally, why is only BTI30 shown in Fig 5?
L200-206 – This part is very confusing and I did not get what this result indicates.

Discussion
L212-223 – Although I agree with the idea, it has nothing to do with the study. The main results compare different species and do not evaluate colony-based variation.
L223-227- This is a very confusing part, and I did not get the point of it. Why is the SHP ‘superior’ than the FHP when comparing bleaching susceptibility if they return similar results? Actually, the SHP return only 3 groups on the susceptibility ranking, therefore, FHP seems more adequate to me. Actually, the authors end this paragraph saying that FHP is better, however without grounding this conclusion considering the previous statements. I suggest a complete rephrase and restructure of this paragraph. Besides, I suggest to move the discussion comparing heat programs to after the paragraphs discussing the comparison of susceptibility among species, it seems more logical and aligned with the aims of the study.
L228 - … of the STONY CORAL species…
L228-241 – I really appreciated the comparison with the literature, this is important. However, I missed more discussion about why the fire coral may be more resistant and why it actually even increases the greyscale value at some point during the experiment.
L242-248 – I did not understand why authors here discuss other factors that may modulate bleaching susceptibility if they have not yet discussed any factor that could explain the susceptibility rank obtained in this study (see previous comment about the previous paragraph).
L255 – merge with the previous paragraph.
L268-271 – Was it done in this study? How? If so, it wasn’t mentioned in the methods.

Figures
- It would be very useful to have the name and a small photo of each species in the respective graph in Fig 2, 3 and 4.


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: COMPARISON OF THE BLEACHING SUSCEPTIBILITY OF CORAL SPECIES BY USING MINIMAL SAMPLES OF LIVE CORALS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Please see the following comments:
Line 19: Nubbins-  I strongly suggest using the word fragment instead throughout the text.
Line 25-26 - Unclear sentence: The average grayscale obtained for the samples during the acclimation period was 100%, whereas those obtained for the samples after bleaching were 0% for each species.
Line 31- Millepora is not a scleractinian coral, maybe distinguish in the abstract.
Line 35-  zooxanthella- Add e throughout the text
Line 40-49- add to abstract what is bleaching?
Line 94- I suggest distinguishing more between scleractinian corals and “hydrocoral”.
Line 104-  illustrates THE procedures
Line 122: did you use the RAW images? This is important to say here.
Line 137- This thus. Remove thus, explain more on the problem?
Line 149-151: can you please elaborate on this point?
Line 206-  I suggest to add one sentence summary of the results
Line 212-213: Perhaps add another reference to strengthen this statement?
Line 219: does this not contradict the previous paragraph?
Line 223: FSP? Not FHP?
Line 225-227: not clear. Why is the FHP superior?
Line 241: what do you mean, assessments by divers in Situ?
Line 274: Consider adding a figure of the workflow on the computer- how you sample an area of the fragment?
Line 285: Adaptation or acclimation?
Line 287: Please correct the sentence

Figure 2 and 3: consider adding titles to the subfigures. Also, in the text state clearly if there was more variance between colonies or between treatments. This is mentioned, but needs to be more clear.
Figure 4 caption: reverse sentence, try decrease in the relative grayscale, based on… Also consider adding the number of fragments n for box plots.
Figure 5: caption is missing the conclusion of the figure.
Supplementary figure S1 needs a caption or to add on the image the coral names
Table 1: last line jumped (page 27 on PDF)
Experimental design: I strongly suggest to use RAW images in this protocol, which is not stated in the text.
Validity of the findings: See comments on section 1 (Basic Reporting).
I strongly suggest to add a figure of the workflow on the computer- how do you use a gray scale image and subsample pixels. This will be very helpful for those who wish to employ this method in their research.
Additional comments: Dear authors. I enjoyed reading the manuscript. However there are some grammatical issues as well as semantics such as the use of the word nubbins. Personally, I find automatic grammar correction tools such as Grammarly very useful in checking final drafts before submission.
I look forward to reading an improved version of this manuscript and seeing this paper published.


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: COMPARISON OF THE BLEACHING SUSCEPTIBILITY OF CORAL SPECIES BY USING MINIMAL SAMPLES OF LIVE CORALS
Review round: 1
Reviewer: 3

Output:
Basic reporting: This is a well written paper with an appropriately detailed methods and results section. It provides context on both the ecological importance of coral blecahing/color change and the development of techniques to measure it, alongside their strengths and weaknesses. The manuscript has appropriate figures.
Experimental design: The authors use the first several time points as the control for their color scores and, I believe, have a single tank replicate for each temperature control (this could use some clarification). While i agree that this is probably an acceptable approach for the type of methods development they are doing, I think it would be appropriate to more explicitly address their lack of tank replication and a baseline control.

It would also be nice to see (in text or figure) that there is a stable (absolute? relative?) grayscale during the acclimation period, both to ensure that a week was appropriate and that the use of these in place of a proper control is approriate.
Validity of the findings: I have one primary question about a detail that may actually be importnat for the overall direction of the manuscript. Why is there an increase in figure 3f (m. intricata)? The authors mention this in the results, but what is the actual cause of this likely to be and what does it mean for the use of this method? I also think the wording on line 179 ('period of acclimation') is confusing since it appears during this point the corals were reaching max temperature, not acclimating.

The conclusions and discussion of this paper are appropriate and are nicely matched with the figures. The only thing i would like to see the authors add is a bit more discussion of the fact that the SHP can likely be used to select genotype level differences (different colored points), making it a better approach and strengthening the utility of this method. If so, the authors may elect to add some analysis of this, which i think would benefit the paper and its citability.
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: COMPARISON OF THE BLEACHING SUSCEPTIBILITY OF CORAL SPECIES BY USING MINIMAL SAMPLES OF LIVE CORALS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript was improved on these points.
Experimental design: From my prior comments:
did you use the RAW images? This is important to say here.
Re: We used jpg files as correction against color cards and our formula render everything relative. Using RAW does not have the benefits of giving true color anyway, this is especially true when the method is employed by different people/teams. We chose calibration against the same color card, this is more practical and is also easy to use.

I still think it is important to note that you used JPG. It is a nonlinear compression that affects the grayscale values. It is still acceptable but I strongly suggest to mention this in the discussion.
Validity of the findings: Figure S2 helps to replicate this study.
Additional comments: Dear authors, you have substantially improved the manuscript, great work.! Please note my comment about image acquisition.


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: DIVERSITY AND STRUCTURE OF THE MICROBIAL COMMUNITY IN RHIZOSPHERE SOIL OF FRITILLARIA USSURIENSIS AT DIFFERENT HEALTH LEVELS
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: 1 The health status of Fritillaria ussuriensis varied greatly in different plots. Please describe the geographical differences between different points.

2 How to distinguish between three different levels of health of rhizosphere soils. Please explain this in manuscript.

3 In figure 7, the significantly higher abundances of Massilia and Fusarium with stronger correlations with other genera were found, but couldn't indicat that these two genera played a dominant role in the pathogenesis of Fritillaria ussuriensis. Which is more important, environmental factors or microbial factors?

4 Please add references about the explain that "The soil environment could have been changed due to the death and decay of a large number of Fritillaria ussuriensis plants, which in turn affected the variation in the soil microbial community."

5 Is it the co-correlation networks or co-existence networks?
Validity of the findings: no comment
Additional comments: no comment


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

Input:
Title: DIVERSITY AND STRUCTURE OF THE MICROBIAL COMMUNITY IN RHIZOSPHERE SOIL OF FRITILLARIA USSURIENSIS AT DIFFERENT HEALTH LEVELS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Introduction section:
Please revise the section of introduction to clarify these issues:
1) There is little here which is intrinsically novel or insightful.
2) Why should this research be conducted on the study site (i.e., Hailin Forestry Farm)?
3) There are no robust hypotheses or mechanistic insights provided which further inform the discipline of soil biochemical cycles in a general sense. In short, the authors are not unravelling relevant mechanisms that reported from other researches, nor put forward their own hypotheses.
5) Line 51-54: Please add the references here.
Experimental design: Materials and methods section:
1) A map with geographical location of the study site will be more intuitive for readers.
2) Please provide some basic information on soil (e.g., the soil water content, temperature and soil porosity), the specific sampling date or season and the course of the disease.
3) Please describe clearly the differences among the health, pathology and blank levels. It would be better to provide some pictures that present different levels.
Validity of the findings: Results section:
1) Line 108: The rarefaction curve was just used to identify the validity of the data, and it was a stage of data processing, I recommend to put the Figure 1 into the supplement materials.
2) Line 217-220: Which sample did the data refer to? Please rephrase these sentences to clarity your meaning.
3) Figure 5: ‘bacterial phyla’ change to ‘bacterial genera’. Please mark the differences among the three disease levels and unify data format of P-value.
4) Is there any difference in the fungal and bacterial community network between the diseased sample and the healthy sample?
5) Line 295-298: Please rephrase this sentence to clarity your meaning.
6) I recommend to use the structural equation modelling (SEM) to evaluate the relationships among soil properties, microbial communities and treatments.

Discussion section:
The logic of this section was poor, please revise as suggested below:
1) Line 300-309: Delete these sentences as they are the content of introduction part.
2) Line 320-323: This sentence is confused, please rephrase it to clarity your meaning.
3) Line 324-326: The ‘soil microbial community’ was not appropriately used here, please change it to microbial diversity or a specific index.
4) Line 330-333: The author report: ‘…. the soil microbial diversity was related to the differences in crop species, soil types, and environmental factors…’, How are they related with each other, and why, please clarify them in detail or set some examples.
5) Line 343-346: Same issue with 4), please clarify your point in detail.
6) Line 365-366: Delete this sentence, it is useless.
7) Line 371: Should be ‘relative abundance’, and be careful to check the use of ‘abundance’ and ‘relative abundance’ in the whole MS, and revise the mistake.
8) Line 371-375: What is the authors’ intention of this sentence?
9) Line 384-386: This sentence is confused, please rephrase it to clarity your meaning.
10) Line 392-394: Please add the references here.
11) Line 402-433: This paragraph should illustrate the mechanisms with respect to how environmental factors affect the microbial community structure in different levels of disease. Obviously, it failed. The authors only provided a series of related researches (some of them may be not appropriate) and make the comparison with them. Please revise this paragraph carefully.
12) In the Discussion section, the author should also reply the important problems: what are the limitations of this study and what are the implications for future research, such as the prevention of the disease.

Conclusion section:
The conclusions are not at all conclusive, but yet another summary of the findings and other content in the paper. Please revise this section.
Additional comments: no comment


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

Input:
Title: DIVERSITY AND STRUCTURE OF THE MICROBIAL COMMUNITY IN RHIZOSPHERE SOIL OF FRITILLARIA USSURIENSIS AT DIFFERENT HEALTH LEVELS
Review round: 1
Reviewer: 3

Output:
Basic reporting: English writing is terrible and the authors should substantially improve. the background of the research is provided. the article structure is reasonable.
Experimental design: the research question is meaningful for the understanding of the effects of soil microbial community on plant health. The experimental method is suitable for this study and could provide support for the conclusion. the authors should explain why did not determine the bacterial and fungal diversity using the same soil sample at each healthy level.
Validity of the findings: the main findings of this study should be refined. the authors should tell what is the most important finding in the conclusion section.
Additional comments: I suggest that the authors should refine the main finding of this research and tell a attractive story. In addition, the authors should substantially improve English writing and I therefore recommend it for publication after 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: DIVERSITY AND STRUCTURE OF THE MICROBIAL COMMUNITY IN RHIZOSPHERE SOIL OF FRITILLARIA USSURIENSIS AT DIFFERENT HEALTH LEVELS
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This manuscript has greatly improved following the careful responses to the first round of reviews. I don't have any further concerns.


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

Input:
Title: DIVERSITY AND STRUCTURE OF THE MICROBIAL COMMUNITY IN RHIZOSPHERE SOIL OF FRITILLARIA USSURIENSIS AT DIFFERENT HEALTH LEVELS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The English writing has been improved.
Experimental design: Research method section has also been revised.
Validity of the findings: The conclusions have been refined.
Additional comments: No additional comments