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: QUANTITATIVE TRAIT LOCI ASSOCIATED WITH SOFT WHEAT QUALITY IN A CROSS OF GOOD BY MODERATE QUALITY PARENTS
Review round: 2
Reviewer: 2

Output:
Basic reporting: I have no further comment
Experimental design: No further comment
Validity of the findings: I have no further comment
Additional comments: No additional comments


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

Input:
Title: THE RISK OF HOSPITALIZATION FOR RESPIRATORY TRACT INFECTION (RTI) IN CHILDREN WHO ARE TREATED WITH HIGH-DOSE IVIG IN KAWASAKI DISEASE: A NATIONWIDE POPULATION-BASED MATCHED COHORT STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: The title of the study does not adequately reflect the contents of this study. This is a follow-up study for children who are treated with high-dose IVIG in KD. It is not appropriate to use the observation results as a title. What about this title: ‘the risk of hospitalization for respiratory tract infection (RTI) in children who are treat with high-dose IVIG in KD.’

  In addition, it is necessary to describe constantly the names of cohort groups in all text and the tables. There are various expressions in the text and the tables, which can confuse readers. For example, it is expressed as ‘KD group’ or ‘IVIG group’ or ‘Patient without KD’ or ‘non-KD’, and so on.
Experimental design: There is a concern about the experimental design.

 First of all, comparing the comorbidity (preterm, heart disease, asthma, allergic rhinitis) of both groups, statistically significant differences are shown. Are these control groups unsuitable for matched cohort groups? In my opinion, that is considered to be the most influential factor in the hospitalization of RTI. Therefore, I would like to ask you to select the control group again or to use another statistical methods (for example, instrumental variable analysis, …) to adjust the bias from confounding factors.

 Second, why did you choose pneumonia, AOM, and bronchiolitis for RTI in this study. It is not clear whether the selected RTI is caused by a frequency of illness, or whether it is based on a common pathogen or anatomical position of respiratory tract. Please add a description for this.
Validity of the findings: There is a mistake in statistics. Eighteen children have congenital heart disease in KD group, which was calculated as 0.35%. It is 0.13% that I calculate. Thus, the expressions of 186 lines and table 1 should be corrected. It also affects discussion, so it needs modification
Additional comments: I think it is an honor to review the paper on interesting research. So far, numerous studies have been conducted regarding the appropriate treatment methods and outcomes, including the pathophysiology in Kawasaki disease (KD). However, except for the prevalence of allergic diseases, there are few observational follow-up studies for patients hospitalized with KD. This study is considered to be very interesting attempt to investigate the incidence of hospitalization by the respiratory tract infection (RTI) in children who are treated with high-dose IVIG in KD.  Particularly, I appreciate the authors ' efforts to explore the vast amounts of data which have been provided by NHIRD.

 Here are some of the following comments as a reviewer to make a more meaningful study.

 Thank you!


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

Input:
Title: THE RISK OF HOSPITALIZATION FOR RESPIRATORY TRACT INFECTION (RTI) IN CHILDREN WHO ARE TREATED WITH HIGH-DOSE IVIG IN KAWASAKI DISEASE: A NATIONWIDE POPULATION-BASED MATCHED COHORT STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1. Table 1: The group of 13709 persons should be "non-KD group".
Experimental design: 1. The patients of Kawasaki disease was recruited by ICD codes only. However, there is a certain part of patients who were admitted with the main diagnosis of Kawasaki disease did not receive IVIG therapy in Taiwan. (J Chin Med Assoc. 2015 Feb;78(2):121-6.) If the patients can be further grouped according to receive IVIG or not, the causal relationship between the decreased risk of hospitalization and IVIG would be further strengthened.
Validity of the findings: 1. From methodology point of view, the authors used age, gender, preterm, heart disease, asthma, allergic rhinitis, and pre-RTIs to build propensity scores. However, they did not describe the detail of the propensity scores, such as the matching method, c statistics, and propensity scores distributions.

2. I would like to suggest the authors to select the control group (1:4 or 1:10) randomly then adjust  age, gender, preterm, heart disease, asthma, allergic rhinitis, and pre-RTIs by traditional logistic models to see if there is different results.
Additional comments: This article is well structured and written in good English.


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

Input:
Title: THE RISK OF HOSPITALIZATION FOR RESPIRATORY TRACT INFECTION (RTI) IN CHILDREN WHO ARE TREATED WITH HIGH-DOSE IVIG IN KAWASAKI DISEASE: A NATIONWIDE POPULATION-BASED MATCHED COHORT STUDY
Review round: 2
Reviewer: 1

Output:
Basic reporting: I think the paper was properly revised and supplemented.
Experimental design: I think the paper was properly revised and supplemented.
Validity of the findings: Additional modifications are recommended as follows:
First, the spell ‘s’ is missing from Table 3 (person months), and must be corrected.
Second, how about you modifying the expression in line 285 as follows?
  from “… but seemed to persist at least for 6 months.”
  to  “… but seemed to be well maintained for at least 6 months and then gradually decreased.
Additional comments: I think the paper was properly revised and supplemented.

As researchers have mentioned, further study into the effectiveness of IVIG’s protection against infectious disease is thought to be interesting; according to the dosages of IVIG, according to the pathogen type (viral or bacterial), and so on.

Thank you for your every efforts!


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

Input:
Title: THE RISK OF HOSPITALIZATION FOR RESPIRATORY TRACT INFECTION (RTI) IN CHILDREN WHO ARE TREATED WITH HIGH-DOSE IVIG IN KAWASAKI DISEASE: A NATIONWIDE POPULATION-BASED MATCHED COHORT STUDY
Review round: 2
Reviewer: 2

Output:
Basic reporting: I have no further comments.
Experimental design: IVIG therapy has strong impact on the subsequent respiratory tract infection. I don’t think it can be ignored in this study. Furthermore, as the authors wrote, some children diagnosed with KD may present with concomitant respiratory tract infections and may pose a higher risk for subsequent RTI-related hospitalizations.
Validity of the findings: I don’t think building propensity score from two cofactors can reduce bias comparing with 7 factors’ model in the previous manuscript. Furthermore, urbanization, allergic disease, and congenital diseases also have strong impact on the subsequent RTI. I didn’t see any effort that the authors trying to control them.
 I still suggest that randomly selecting patients of control group matched by age, gender, allergic disease, congenital disease, and urbanization.
Additional comments: This article in interesting. However, the authors should revise the manuscript  before it can be accepted.


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

Input:
Title: DYNAMICS OF ZIKA VIRUS OUTBREAKS: AN OVERVIEW OF MATHEMATICAL MODELING APPROACHES
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is clearly written in professional English, except some sentences and vocabularies (see comments below). The manuscript contains most of important references in Zika epidemic modeling; however there are still some very significant works missed (see comments below). The structure of this manuscript is very well organized with proper figure and table. Raw data are not applicable for this review manuscript.
Experimental design: The research delivered in this manuscript fits the scopes of the journal. As it is a review paper, methodologies for experimental design are not applicable.
Validity of the findings: I have objections to the conclusion made in this manuscript (see comments below).
Additional comments: As an active researcher in this field, I appreciate the efforts that the authors have made to thoroughly review important works on mathematical modeling for Zika epidemics. However, I have many questions and concerns which needs the authors to address  before I can recommend it for publication.

1. The main problem of this manuscript is it lacks of insights. In the Introduction part, the author wrote this "review was aimed to provide a mathematical modeling concept, particularly, of which developed for Zika virus transmission". After I read the article, I did not see any provided concept. What is the concept here? If the concept only means 5 or 6 types of existent models, the authors should be aware that "a concept" does not mean one or two models.

2. The manuscript is nothing but a pile of existent models. The results part is actually not results, but summaries of models which can be found in other references. The manuscript did not see and understand clearly the current trends. For example, the work by Zhang, et al (2017) is NOT a spatial model. It is a meta-population model based on real-world spatial networks using high-resolution spatial environmental data. Thus, what the authors claimed in the perspective paragraphs that (metapopulation, individual-based and network methods) are only a theoretical framework is not true at all. If the authors carefully examine some other papers on agent-based models like "Spatiotemporal spread of the 2014 outbreak of Ebola virus disease in Liberia and the effectiveness of non-pharmaceutical interventions: a computational modelling analysis", they will also find individual-based models or network methods are not theoretical work at all. The recent trends on "big data" allow modeler to have more realistic models. The manuscript would be much more insightful if the authors focus on the latest development on epidemic modelling and the future outlooks.

3. The authors also wrote that there is a lack of user-friendly interface to translate modeling techniques and modeling results. The GLEAM framework in Zhang, et al (2017)  has provided a user-friendly and easy-to-use graphical tool for general modelers and public health agencies since years ago, please see www.gleamviz.org. The results presented in Zhang, et al (2017) were also delivered in a user-friendly and easy-to-read graphics on a web application: http://www.zika-model.org/ (this is written in the paper).

4. The manuscript has covered many significant works in mathematical modeling on Zika epidemics. However, there are some very significant papers missed. Below are just a few examples:
Perkins, T. Alex, et al. "Model-based projections of Zika virus infections in childbearing women in the Americas." Nature microbiology 1 (2016): 16126.
Castro, Lauren A., et al. "Assessing real-time Zika risk in the United States." BMC infectious diseases 17.1 (2017): 284.

Obviously, the method to filter literature from google scholar and pubmed is not very well established. The keyword searches should not be too narrowed.

5. The title of this paper is misleading. When I saw the title, I thought this would be a paper representing a new model of zika epidemic dynamics. Please re-title the manuscript.

6. English writing in this manuscript in general is acceptable. However, I recommend the authors to revise the manuscript carefully, especially on vocabularies. For example, in line 64, "jump" does not sound scientifically. What does "jump" mean? Similarly, in line 60, "epical", in line 111, "notorious", etc.

7. In table 1, what are those reference numbers representing?


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: DYNAMICS OF ZIKA VIRUS OUTBREAKS: AN OVERVIEW OF MATHEMATICAL MODELING APPROACHES
Review round: 1
Reviewer: 2

Output:
Basic reporting: This literature review article provides a nice introduction to mathematical modeling in the context of Zika. The body of literature that it gathers and synthesizes provides a very useful starting point for anyone wishing to enter this area of research. That said, I think it needs to be improved significantly before it is ready to be published.

Much of the writing is difficult to follow and should be revised and closely edited. The literature is properly referenced in the text, but some important sources appear to be missing (for example Adams and Kapan. 2009. “Man Bites Mosquito: Understanding the Contribution of Human Movement to Vector-Borne Disease Dynamics.” Edited by Alison P. Galvani. PLoS ONE 4 (8).)

The structure is fine, although I recommend making it clearer in the beginning of the Abstract that this is a review article. I am also not sure the authors need to go into such detail about how they selected the articles -- or that they need to limit the literature to that found in this type of methodical survey.
Experimental design: This is not primary research but rather a literature review, summarizing and synthesizing existing work in this area. It appears to fall within the aims and scope of PeerJ. The research question is broad (essentially the article asks what has been done with respect to mathematical modeling relevant to Zika dynamics). It is not entirely clear that it fills a real knowledge gap, although it is surely helpful to have this body of literature synthesized.

The methods in this case are the search criteria. They are clearly described, but I am not convinced that this type of formal survey is needed. I would opt for looser search criteria in order to ensure that all relevant literature has been located. For instance, there are probably important sources that do not contain the term "mathematical model" (even if that is what they provide).
Validity of the findings: The main conclusion is the summary of existing models. From this, the authors note that there has been a lack of application of these models in the field by health professionals, and they suggest some ways in which that might be changed. This is an interesting discussion, but the authors might expand on different ways in which this field implementation could occur, as well as different uses of simple versus complex models.
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: DYNAMICS OF ZIKA VIRUS OUTBREAKS: AN OVERVIEW OF MATHEMATICAL MODELING APPROACHES
Review round: 2
Reviewer: 1

Output:
Basic reporting: The English is acceptable. The structure of this manuscript is very well organized with proper figure and table. Raw data are not applicable for this review manuscript.
Experimental design. For comments on technical details, please see the comment section below.
Experimental design: This is a review article, this part is not applicable.
Validity of the findings: See the comments below.
Additional comments: I appreciate the authors' efforts to improve the quality of this survey article. Unfortunately, the authors did not address all of my concerns and questions. There could be some changes in writing and organization of materials to improve the quality.

Line 754, Determining a “real” network structure requires knowledge of all individuals in a population and all possible relationships among them. In large networks, this is an impractical and time-consuming task.

It is true to get real networks, but now there are so many researches using tons of digital proxies to approximately get the human interacting/contacting networks. e.g., "Kiti, M. C., et al. (2016). Quantifying social contacts in a household setting of rural Kenya using wearable proximity sensors. EPJ data science, 5(1), 1-21."

Such digital proxies or data-driven approach allow agent-based models or meta-population models or other models better simulating the real epidemics, and perhaps this is one important reason that there are so many successful papers on Zika modeling since 2016. If the authors go through early publications on modeling Zika epidemics, it can be easily seen that most of early literatures are theoretical and focus on local regions. Until recently, the availability of large-scale real-world data has made computational models approximating the reality, which should be one of the key findings (or punch-line or insight) in this survey article. For example (and once again), the article by Zhang et al, 2017 is NOT A SPATIAL MODEL. It does not fit any part of equation 5. It is a meta-population model on top of human mobility networks. The model includes (nearly) real human mobility data, population data, high-resolution time-varying temperature data, social-economical data and so on.

I would suggest the authors carefully read the literatures covered in the manuscript (e.g., how the complexity of models has evolved and how the application of real-world data has evolved), and revise the manuscript accordingly.


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: DYNAMICS OF ZIKA VIRUS OUTBREAKS: AN OVERVIEW OF MATHEMATICAL MODELING APPROACHES
Review round: 2
Reviewer: 2

Output:
Basic reporting: The language and style has improved significantly. I now see only minor improvements to be made here, and these can be mostly handled in the final editing stage. A few specific suggestions:

Lines 560-62: What does this refer back to? I don't see discussion of next-generation matrix approach.
Line 831: I find this sentence awkward.
Line 915: imported risk - import risk
Line 966: A part -> Apart

I am glad to see the Adams and Kapan paper discussed although I think the summary misses the main point of their paper, which is not so much about which places are at risk as about the effects of different patterns of human movement between patches on population-level disease dynamics and outcomes. I would revise this, as it also helps to better explain meta-population theory.
Experimental design: I am glad the authors have checked additional search terms. Perhaps that should be made more clear now in the methods section.
Validity of the findings: The expanded discussion of authors' conclusions is useful. However, this raises and issue I had not fully understood from the previous draft and that I think needs to be addressed: the authors seem to be focused on one type of use for all of these models: making specific geographical predictions about disease spreading. The assumption seems to be that if models cannot be used directly in the field by policy-makers or health professionals to map and predict spreading patterns, then they are not useful. This is what leads to the conclusion about the need for better user interfaces. This leaves out that much of the value of mathematical models is in understanding phenomena in a more abstract way that need not be directly mapped to actual geography (even if this understand does ultimately make it possible to make better predictions in the real world). This need not be done -- in fact, should not be done -- by policy-makers. It should be done by scientists, and lack of user interfaces are not really a barrier.

Similarly, the authors suggest that agent-based models are more realistic than simpler models, but I don't think that is necessarily true. Agent-based models can also be used to better understand mechanisms and other more abstract questions that need not translate directly realistic geographic predictions.

I could see keeping the conclusion about the need for better interfaces to facilitate field implementation as long as the authors make clear that this is only one of many uses of mathematical models. However, I think the conclusion itself also requires more support. It is not clear to me from the literature reviewed why the authors conclude that there is a gap here: The literature discussing the models themselves does not comprehensively assess how these models are used in the field, what is to blame for lack of use, or what we would gain from more field use. I think these points require further analysis.
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: DYNAMICS OF ZIKA VIRUS OUTBREAKS: AN OVERVIEW OF MATHEMATICAL MODELING APPROACHES
Review round: 3
Reviewer: 1

Output:
Basic reporting: English writing is acceptable.
Literature references are sufficient and comprehensive.
The organization of the manuscript has been improved and acceptable.
Experimental design: Not applicable for a review manuscript
Validity of the findings: Not applicable for a review manuscript
Additional comments: Thank all authors for their hard working to improve the manuscript, and most of my concerns in the previous review have been clearly addressed. Below please answer some minor questions before the final acceptance.

Title, I would suggest the title changed from "an overview of a mathematical modeling approach" to "an overview of mathematical modeling approaches"

Line 150, "Our review study was performed from April to July 2017." This sentence is a bit unclear. Does it mean the literature reviewed published in this time period? (which I do not think so). or the activity of searching articles happened in that period. It would be better if just simply saying "we have collected research articled that published before XXXX based on our search criteria"

Line 430, "The most prominent advantage of the spatial models is their virtualizing power." What does the term "virtualizing" mean here?

Regarding to "epidemic management" or intervention, in the scenario of Zika epidemics, the authors could consider this working paper to gain some insights https://www.biorxiv.org/content/early/2017/09/18/187591


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: DYNAMICS OF ZIKA VIRUS OUTBREAKS: AN OVERVIEW OF MATHEMATICAL MODELING APPROACHES
Review round: 3
Reviewer: 2

Output:
Basic reporting: All of my previous suggestions have been addressed.
Experimental design: All of my previous suggestions have been addressed.
Validity of the findings: All of my previous suggestions have been addressed.
Additional comments: The authors have done a great job of addressing my previous suggestions.  I have attached a marked-up PDF with some very minor additional edits.


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: DYNAMICS OF ZIKA VIRUS OUTBREAKS: AN OVERVIEW OF MATHEMATICAL MODELING APPROACHES
Review round: 4
Reviewer: 1

Output:
Basic reporting: English writing is acceptable.

Literature references are sufficient and comprehensive.

The organization of the manuscript is well structured.
Experimental design: NA
Validity of the findings: NA
Additional comments: Thank all authors for their efforts in improving the quality of this manuscript. The authors have addressed all my questions.


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: WILL THE CALIFORNIA CURRENT LOSE ITS NESTING TUFTED PUFFINS?
Review round: 1
Reviewer: 1

Output:
Basic reporting: This manuscript is well-written and has a clear and timely conservation application. The introduction does a good job in laying out the climate change threats to the tufted puffin and the relevance of species distribution modeling for informing the Endangered Species Act listing decision and conservation actions in the face of population declines and colony losses.

The Figures and Tables are generally useful and well-described, with the following recommendations:
--Tables 1 and 2 could be converted to supplemental tables.
--In Figure 4, the green color used for a higher probability of occupancy is too difficult to distinguish from the green background shading of the map; I recommend changing this green to a different shade or making the continent a single color that can be distinguished from the legend colors.  It’s also not clear why there are 4 occupancy categories in panel A and only 3 in panels B and C.
--In Figure 5, I recommend shading the histogram bars with stippling or striping rather than using solid colors so that the bars for the different model algorithms are easier to see.

In the Supplemental excel spreadsheet showing the data for the Tufted Puffin colonies, data from different sources are merged in a sloppy way, so that the data don’t match with the column headings.  This should be fixed so that there is a single set of headings in the top row, and data throughout the spreadsheet conform with these headings, with blanks or N/A for cases where there are no data for that column heading in that dataset.
Experimental design: SDM is an important tool for assessing potential climate impacts on species distributions, and this manuscript provides an important application of this tool for the tufted puffin, which is suffering from significant declines in occupied colony sites.

SDM has well-known limitations that can influence the model results (see for example the discussion in Porfirio et al. 2014, Improving the use of species distribution models in conservation planning and management under climate change, PLoS ONE 9(11): e113749).  The authors do a good job trying to account for some of these limitations, for example by using three different statistical models as well as an ensemble model, reporting two model performance metrics, and the selection of bioclimatic variables by eliminating variables with high collinearity as well as a basis in puffin ecology.

However, I recommend that the authors also justify the selection of the three GCMs that were chosen, particularly because GCMs can vary widely in precipitation projections, although less so in temperature projections. Do these GCMs represent a representative spectrum of future precipitation and temperature projections from the larger GCM model set?

In addition, using the ensemble mean of projected climate variables as the input into an SDM can be problematic, and it is recommended that multiple SDMs be run using a range of climate models as input, producing a range of species distribution maps which must then be combined (see Porfirio et al. 2014). One useful way to combine these maps can be to produce a map showing the agreement between the models—for example, pixels where all models agree a potential suitability above a threshold of 0.5. It’s not imperative that the authors do this exercise, but it’s something to consider.

It was unclear how you handled colonies that were extirpated during the current time period (1950-2008). Did you rank colonies that were extirpated during the current time period as absent?

I was glad to see that you estimated the correlation between SST and air temperature since studies of puffins (and related seabirds) indicate that SST has an important influence on nesting, typically through effects on prey.  Your method appears to assume that SST in the 10km x 10km marine pixel nearest the colony site provides a good representation of SST in the puffin foraging range from that colony site, which, as you note, can extend to 40 km. However, I imagine a single pixel is a good enough representation of the marine foraging range, without the need to do additional analysis.

The methodological description of the PCA that you use to compare variance in environmental variables between areas where colonies collapsed in recent years to those that persist could use a bit more explanation.  Although you say “recent years,” are you using the occupancy and climate data from the current period from 1950-2009?

Model calibration: You state that you constructed 20 models for each algorithm, but you should add more explanation of what the model structure for the 20 models looks like.
Validity of the findings: The results are interesting and informative as to the projected changes in nesting habitat suitability under rising temperatures, and are useful for informing conservation action for puffins.

There is a big difference in the percent range change projected for the California Current between the GLM compared to the GBM and RF approaches (-89 compared to -30). It would be helpful if you could comment on why there may be such a large difference in the results from these statistical methods.

There is also no difference in the ensemble range change projections for the California Current between the RCP 4.5 and 8.5 emissions scenarios, which is surprising and could also benefit from some proposed explanation.

You briefly acknowledge that that the range change modeling results show little agreement among model pixels in future suitable habitat.  Because one of your stated purposes of the SDM exercise is to identify priority areas for conservation protection, it would be appropriate to add a note of caution since there appears to be little agreement in model results on the exact locations that are likely to remain suitable, although there is a trend of decreasing suitability in the southern portion of the range. In other words, it may be premature to deprioritize certain areas for conservation efforts given this uncertainty in model results. It might be worthwhile to show areas that had high agreement on future habitat suitability across models.

The moderate suitability of some colony sites in southern and central California under the RCP 4.5 and 8.5 projections is interesting, and I’m wondering what allowed those particular sites to stay somewhat suitable. It might be worthwhile to discuss the concept of climate refugia for those sites.

In terms of the potential for range expansion, it may be worth noting that puffins most often breed on offshore rocks and islands, as well as cliffs on the mainland, because of the absence of mammalian predators, and that predator presence provides an important limitation on suitable breeding habitat for puffins.
Additional comments: This manuscript makes an important contribution to understanding the potential consequences of climate change for tufted puffins, and has a timely and direct conservation application for this declining species.

I made some minor text edits in the attached manuscript.


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

Input:
Title: WILL THE CALIFORNIA CURRENT LOSE ITS NESTING TUFTED PUFFINS?
Review round: 1
Reviewer: 2

Output:
Basic reporting: This study uses species distribution models to evaluate projected changes in suitable habitat for Tufted Puffins under 2 climate scenarios, and explores the potential drivers of population declines.  Results suggest that most habitat in the California Current will become unsuitable for nesting Tufted Puffins, driven primarily by rising summer temperatures. This information will be extremely valuable for prioritizing long-term conservation actions, but also for regulatory processes that aim to protect species across their range.

I found this manuscript to be very well written making rather complex modeling procedures relatively easy to understand and evaluate.  The introduction adequately describes the challenge of linking species declines to climate change, but also the importance of doing so for the purposes of both conservation planning and regulatory decision-making.  Some specific comments on Tables, Figures and supplemental material follow (and see annotated pdf attached to this review).

If space is an issue, I think both Table 1 and Table 2 can be removed as they can easily be described in the text.

Figure 2 – I would like to see consistency in terminology used.  In the figure title you use “occupied” and “unoccupied” but in the figure legend you use Absence and Presence.  I suggest one or the other.

Figures 3 and 4 – I’m not sure whether this would add value to the Figures or not, but I would be interested in seeing a composite panel whereby you combine say Panel A (current projection) with Panel C (worst-case scenario) highlighting areas that decline in Probability of Occupancy (colour red) and those that increase in Probability of Occupancy (colour green?).  Those areas that don’t change would be some neutral colour.  I wonder if this type of figure would highlight better the specific areas in need of priority conservation actions?

Supplemental Material - Compiled Tufted Puffin colony survey data – file may be corrupt?  I can’t seem to open this.
Experimental design: Research question was well defined and the results highly relevant to regulatory process related specifically to Tufted Puffin.  Methods could also be applied to other species if quality and time frame of data were of similar quality as those of the Tufted Puffin.  I do not have experience with computing SDMs myself, so cannot comment/review on the details of the analyses, however, the description of the methods was clear and on the surface sounded logical and robust. My only suggestion would be to add some of the text described in the supplemental material related to the ‘past model’ projection into the main manuscript as I was not clear of its relevance on first reading.
Validity of the findings: Conclusions related to range contractions in the south and potential expansion in the north are well presented and could have significant application to both short-term and long-term conservation actions.  I would be interested to know whether there exists the detail to examine site-specific information.  For example, the maps presented are at a scale where one would have difficulty identifying a specific colony that might be destined for extirpation.  Although it gives a great overview what the species range might look like in another 20 years, could priorities be set based on the information presented here or would we need access to better spatial resolution?   The findings also provide some evidence that temperatures in particular are driving the Tufted Puffin declines, although the relationship between temperature and puffin prey remains one worth increased attention.
Additional comments: This is a very well written paper that should be published with some minor edits.  It will provide valuable information to regulatory agencies trying to assess the status of the species (both in the US and Canada), and may help direct colony-specific conservation actions in the future.  Great 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: WILL THE CALIFORNIA CURRENT LOSE ITS NESTING TUFTED PUFFINS?
Review round: 1
Reviewer: 3

Output:
Basic reporting: This is a well-written manuscript overall.  Following are comments focused on the background context provided in the Introduction and some more general editorial comments:

While I appreciate the concision of the opening paragraph, it would be helpful to broaden it slightly by including illustrative examples for the results of warming climates that you provide.

Line 58: Write out US Fish and Wildlife Service before providing the acronym.

Lines 82-84: It would be helpful to have the conservation actions specified for WA and Japan.  State that it has been listed as Endangered at the state level.  This is a stronger statement than how it is currently phrased.

Line 106 and 108: It should be “fledging” success unless you are specifically referring to the success of fledglings, which the Gjerdrum et al. paper does not emphasize.  Does this need to be defined for a general scientific audience?  And “Sea Surface Temperature” does not need to be capitalized.

Line 116: add the acronym “ESA” following your mention of the Endangered Species Act.  The acronym appears later in the text but is not introduced previously.

Lines 143-144: I would suggest rewording the final phrase of the sentence to improve concision, as follows: “… can be used in both regulatory (e.g., Endangered Species Act listing decisions) and conservation planning contexts.”

Line 203: capitalize “puffin”.

In the Discussion, "auklet" needs to be capitalized in the common name of Cassin's Auklet.

This is a minor editorial point, but the word “data” is plural.  The text should be edited to reflect that.

There is some inconsistency in tense in both the Methods and Results sections, moving between present and past tenses.
Experimental design: In general, the Methods section is well structured and thorough in its description of the modeling approach used in the study.  Although the modeling presented in this study is beyond my expertise, the authors explain the process thoroughly and helpfully include justifications for various decisions they made in building the models run.

I have a couple of comments to offer for the Methods section:
Lines 151-152: It might be helpful to explain your process for determining factors relevant to Tufted Puffin breeding phenology.  Someone who is not an expert on the species might really benefit from an expanded explanation here.

Lines 160-161: While I understand the idea behind the cropping process, using locations within 200 km of the ocean seems to be overly generous given that they are obligate coastal/island breeders.  Shouldn’t the scale be more restrictive, possibly using the linear dimensions of your grid cell size of 10 km?  If 200 km makes more sense from a model construction perspective, it would be helpful to have that explained explicitly.
Validity of the findings: The results are robust and presented in a clear and compelling manner.  The figures are well-designed and contribute to both the Results and Discussion.

The major points in the Discussion are both compelling and appropriate and are completely consistent with the findings presented in the Results section.

The authors effectively frame the implications of their work not just in the context of the focal species but also as a general analytical approach applicable for many other species of conservation concern.
Additional comments: This is an impressive body of work represented in the manuscript.  In addition to it being useful for researchers interested in state-of-the-art ways to model species responses to climate change, the results are particularly timely for conservation planning for the focal species, Tufted Puffins.


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: WILL THE CALIFORNIA CURRENT LOSE ITS NESTING TUFTED PUFFINS?
Review round: 2
Reviewer: 1

Output:
Basic reporting: I support the authors' revisions.
Experimental design: I support the authors' revisions.
Validity of the findings: I support the authors' revisions.
Additional comments: The authors did a thorough job responding to and addressing my concerns and suggestions, as well as those of other reviewers.  I support the authors' revised analyses and edits which have made the study clearer and analytically more rigorous.  I recommend this revised article for publication.  It will make an important contribution to the scientific literature and to advancing conservation action for this threatened seabird.


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: HIGH RESOLUTION CRYSTAL STRUCTURES OF THE RECEPTOR-BINDING DOMAIN OF CLOSTRIDIUM BOTULINUM NEUROTOXIN SEROTYPES A AND FA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper is generally well written, with only a few minor errors that need to be corrected. Literature cited properly. Figures are good, although the main difference compared to an existing structure of HC/FA, namely the presence of the electron density for the loop 1261-1268 is not illustrated.
Experimental design: Nothing novel in the presented results compared to those already available in the literature, but the experiments have been done well.
Validity of the findings: Data are sound, conclusions well stated, although nothing novel has been presented.
Additional comments: The main difference between the structures described here, namely the visibility of the loop 1261-1268 in HC/FA, is of only limited interest, since conformations of flexible loops, even those involved in biologically relevant interactions, are not very illuminating unless they are seen in a proper context, and not as crystal contacts. Similarly, the presence or absence of disulphides is also simply related to conditions of crystallization.

A few minor errors that should be corrected:

Lines 32-33 "The toxins target...through a dual receptor binding model". No, they don't do it through a model, but through binding to two receptors. Please rephrase.

Line 37 "A through to /G" - please make it "A through /G"

Line 115 remove comma after "group,"

Line 159 is "invaluable" the best word here?

Legend to Fig. 1 5MK1 is probably in error, 5mk6 meant


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: HIGH RESOLUTION CRYSTAL STRUCTURES OF THE RECEPTOR-BINDING DOMAIN OF CLOSTRIDIUM BOTULINUM NEUROTOXIN SEROTYPES A AND FA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is well written.
Experimental design: No comment.
Validity of the findings: The structural analysis is overall robust, although some additional information about the findings is requested as described in the general comments.
Additional comments: The manuscript describes the high resolution crystal structures of the receptor binding domain (Hc) from two botulinum neurotoxins (BoNTs), Hc/FA and Hc/A1.  These structures can potentially provide insights into the binding specificity of these BoNTs in recognizing particular receptors.  The main new findings include the observation of an Hc/FA loop conformation that was disordered in a previous structure, and the discovery of a disulfide bond in both Hc/FA and Hc/A1 that was not observed in previous structures. The structural data are technically sound.  However,  multiple structures of both Hc/FA and Hc/A1 had been previously determined either for the domains themselves or as part of the whole protein.  Therefore there need to be more discussion of the new scientific insights gained from these structures, in comparison to the previous structures, for both Hc/FA and Hc/A1.

1) One of the main new findings is the R1261-R1268 loop conformation in Hc/FA, yet there is no figure showing its electron density or  relating this loop to receptor binding (a role suggested by the authors) by comparing the current structure to previous complex structures.

2) In Fig. 1, it will be useful if the authors could show the locations of the disulfide bonds and the R1261-R1268 loop. In addition, it may be worth indicating the N and C-termini on the structure.

3) Table 1,  the Rwork and Rfree of the 1.45 Angstrom resolution structure seem high, relative to its resolution.  It will be informative if the authors can comment on this, particularly compared with the other two lower resolution structures.  Did the refinement use anisotropic B factors?

4)  line 134, the average B factor of the loop should be provided.


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: HIGH RESOLUTION CRYSTAL STRUCTURES OF THE RECEPTOR-BINDING DOMAIN OF CLOSTRIDIUM BOTULINUM NEUROTOXIN SEROTYPES A AND FA
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript is well written and easy to follow.
Experimental design: The experiments are well designed and well performed. The structure of the receptor binding domain from BoNT/FA has been reported before. The authors do however provide new insight and clearly reference and compare to the previous study. The structure of HcA has been reported, however an interesting difference in a disulphide bond and the resulting structural rearrangements is reported.
Validity of the findings: All statistics look good and the data is of good quality.
Additional comments: This is a solid study reporting a some new observations. The paper is well written and should be accepted after minor revisions.

The contouring level and type of map (Fo-Fc?) for figure 2 should be added. A description of how the map was calculated should be added to material and methods (what program was used).

P422 is an unusual space group. Alternative space groups should be examined and the possibility of twinning should be considered (could give false high symmetry).

A sequence alignment between subtypes and serotypes should be included to visualise and discus the conservation of the cysteine.

The position of the cysteine and the loop that is discussed, should be indicated in the figure 1.

A picture shoving an overlay with the ganglioside complex should be included to clarify the role of the loop in BoNT/HA that is discussed.


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: NECESSITY OF ELECTRICALLY CONDUCTIVE PILI FOR METHANOGENESIS WITH MAGNETITE STIMULATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: 1. I am not convinced that G. metallireducens and M. barkeri were closely associated by TEM in  Fig. 3A. It is too dark to figure out what are they. This is important to the conclusion.

2. In the co-cultures of G. metallireducens and M. barkeri with ethanol as the substrate in the absence of magnetite, the dynamic concentrations of methane, ethanol and acetate are not well matched (pink lines in Fig.1).

3. line 188: magnetite was firstly reduced by G. metallireducens... Check your data in Fig.1, the changes in Fe(II) concentrations are insignificant during the first 10 days.
Additional comments: Using the co-cultures of M. barkeri and wild-type G. metallireducens or a PilA-deficient strain, the authors demonstrated that the presence of magnetite accelerated the conversion of ethanol to methane in defined co-cultures of G.metallireducens and M. barkeri. More importantly, they found that magnetite could not substitute for e-pili to promote DIET between Geobacter and Methanosarcina. This is a fair contribution to DIET research. Paper is well written, the enhanced quality of figure is need to support results, and the data interpretation should be more rigorous.


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: NECESSITY OF ELECTRICALLY CONDUCTIVE PILI FOR METHANOGENESIS WITH MAGNETITE STIMULATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: I read the manuscript without any language problem. I found the literature review was complete and references were properly cited. The layout of the presentation including main text and figs is acceptable.
Experimental design: The work represents a piece of original primary research. The question, whether magnetite can substitute e-pili for direct interspecies electron transfer (DIET), was well defined. To answer this question, the defined cocultures were established using the wild type Geobacter metallireducens that produce e-pili or its mutant that can not produce e-pili with Methanosarcina barkeri. These cocultures were used to test the effect of magnetite.
Validity of the findings: My major concern is the reduction of Fe(III) in magnetite by G. metallireducens. It was clear that G. metallireducens can use both ethanol and acetate to reduce Fe(III) from magnetite (Fig. 1C and Fig. 2). When the wild type coculture was tested with ethanol, acetate was produced and used by methanogen. Oxidation of one ethanol will produce one acetate plus two electrons released. The stoichiometry (line 155) and data in Fig. 1D indicated that the acetate produced was completely dismutated into CH4 and CO2. This reaction was completed by M. barkeri alone and should be nothing to do with DIET. Apparently, the addition of magnetite promoted the activity of G. metallireducens by providing a proper electron acceptor. Without clarifying this fact, the statement that magnetite promoted DIET (from line 157 to 161) can be misleading.
The test on mutant coculture suggests that the e-pili is essential for the reduction of (Fe(III) from magnetite. Thus, reduction activity appears dominating the conversion from ethanol to acetate and then to CH4 and CO2 in the wild type coculture. The reduction activity makes the explanation complicated and eventually can end up a completely different story from DIET. The statement about the effect of magnetite on DIET can be valid only if this reduction activity can be quantitatively clarified or excluded.
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: NECESSITY OF ELECTRICALLY CONDUCTIVE PILI FOR METHANOGENESIS WITH MAGNETITE STIMULATION
Review round: 2
Reviewer: 1

Output:
Basic reporting: My comments have been addressed properly.
Experimental design: My comments have been addressed properly.
Validity of the findings: My comments have been addressed properly.
Additional comments: My comments have been addressed properly.


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: NECESSITY OF ELECTRICALLY CONDUCTIVE PILI FOR METHANOGENESIS WITH MAGNETITE STIMULATION
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The manuscript is greatly improved. But some data still look odd to me and I shall appreciate if authors can give more explanations.  First, based on Figure 1A, the production of CH4 from the coculture of G. metallireducens and M. barkeri without magnetite indeed indicates DIET in syntrophic interaction. In this case, however, only about 0.5 mmol of CH4 was produced. If this CH4 was produced solely from CO2 reduction by the electrons released from ethanol oxidation, 1.0 mmol of acetate should be produced which can be either used by the methanogen or accumulated in medium. The ethanol concentration for this treatment is slightly different from the earlier version, perhaps due to some mistakes. But in the absence of magnetite, it should be easy to calculate electron balance which shall help to better understand what is really going on. Second, based on Figure 1C, the treatment of Geobacter monoculture plus Fe3O4 indicated that a lot of ethanol (from 1.2 mmol decreased to about 0.4 mmol) was oxidized by Geobacter with Fe3+ in magnetite as the only electron acceptor. This indicates a substantial reduction of Fe3+ in magnetite. With this reduction activity involved, it is hard to image why DIET is still necessary for the living of Geobacter and if acetate is released by Geobacter during ferric iron reduction, DIET would be also unnecessary for the living of Methanosarcina.


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

Input:
Title: THE CONTRIBUTION OF EARTH OBSERVATION TECHNOLOGIES TO THE REPORTING OBLIGATIONS OF THE HABITATS DIRECTIVE AND NATURA 2000 NETWORK IN A PROTECTED WETLAND
Review round: 1
Reviewer: 1

Output:
Basic reporting: The hypothesis that land abandonment causes change in vegetation structure was not properly tested.
Classification maps should be presented. Figure 1 and 4 need improvement, see general comments.
Experimental design: The classification scheme proposed in this study seems not standard and transferable for other sites. The sampling strategy was not mentioned and sample size was not sufficient enough to derive a reliable result. Compasion among different classification algorithms need further statistical test. See general comments for details.
Validity of the findings: The authors drew conclusion that EO-based approach could be used to monitor the conservation status of natural habitat types defined by European Union Habitat Directive, which was not supported by this work. The classification in this study only focused on several groups of land cover classes,  while mapping detailed habitat types can be very challenging  with conventional remote sensing image classification methods due to their spectral similarities.
Additional comments: Dear authors,

The work presents an Earth observation method to address relevant aspects of reporting obligation towards the Habitats Directive and Natura 2000 network regarding wetland ecosystems. Specifically, the performance of 10 classifiers are compared, the uncertainties in the classification output from these algorithms are explored and an ensemble approach of multiple classifiers is proposed. The case study monitors habitat changes in a single site at local scale by post-classification comparison. I find the topic very relevant, and the manuscript is clearly written in professional, unambiguous language. However, the study shows several limitations that need to be addressed:

•	The classification scheme proposed in this study consists of eight classes, and some are grouped categories of detailed habitats defined by European Union Habitat Directive. The definition of the classes (so-called ‘environment unit’ in the manuscript) seems not standard, and it may not be applicable for other sites of Natura 2000 network and hence is difficult to evolve from site-specific research into operational application. I would suggest the authors to adopt a more standard land cover classification scheme and wetland typology (e.g., Ramsar Convention).
•	The sample sizes used for training and testing classification are small, especially for reedbed class, which affects the reliability of the high mapping accuracy. In principle at least 30-50 samples should be used for either training or validation. Moreover, I missed the sampling strategy in the manuscript, which needs to be clarified. As Table 2 shows, equal number of samples for each class were used for validation, which may not be representative of the population and causes sample bias. I suggest the authors to adopt proportionate stratified random sampling, and make sure sufficient samples are selected for each class.
•	Regarding accuracy assessment, it is also useful to show producer’s and user’s accuracy for each class, especially when you made an inference of overestimation in a certain class (line 248). To compare the performance among different classifiers, differences in overall accuracy is not enough to indicate the superiority. Additional statistical test, such as McNemar’s test (Foody 2004; De Leeuw et al. 2006), is needed to assess the significance of the differences in accuracy. It also provides evidence for the selection of algorithms for ensemble rather than using some arbitrary threshold of 85%.
•	For the ensemble approach, majority vote considers different classifiers with equal weights to make the decision regardless of their respective abilities to classify properly. As Du et al. (2012) recommended, weighted vote that uses specific accuracy obtained by individual classifiers as weights would be more suitable in this study.
•	It is good that the authors tried to explain some ecological and socio-economic phenomenon related to land cover change. However, the hypothesis that land abandonment causes change in vegetation structure was not properly tested. Plausible explanation of abandonment of traditional agropastroral practices in discussion (line 284) is speculation and inference. Current analysis could not support the hypothesis.
•	As a study of land cover classification, it is unprofessional that not a single classification map was included in the manuscript. Besides, it is not clear where the classification was performed even with Figure 1.

References:
Foody GM (2004) Thematic map comparison: Evaluating the statistical significance of differences in classification accuracy. Photogramm Eng Rem S 70: 627–633.
De Leeuw J, Jia H, Yang L, Liu X, Schmidt K, et al. (2006) Comparing accuracy assessments to infer superiority of image classification methods. Int J Remote Sens 27: 223–232.
Du P., Xia J., Zhang W., Tan K., Liu Y., Liu S. 2012. Multiple classifier system for remote
379 sensing image classification: A review. Sensors 12:4764–4792.

Detailed comments:
Line 76: “RAMSAR” should be “Ramsar”-named after Ramsar City in Iran
Lines 196-197, the authors mentioned the grouping of natural habitats into environmental unit based on some expert criteria, which needs further clarification. The reference is in Spanish that can be difficult to understand for general readers.
Line 210: what are lower and upper accuracy values?
Line 248: Could it be other algorithms underestimate this class? With producer’s and user’s accuracy presented, it is more clear to see which class is overestimated/underestimated.
Line 291: “Nature” should be “Natura”
Figure 1: The format of lines needs to be changed for a more clear illustration of the study area. The blue arrow line is not friendly, especially for the west part, and the areas outlined by the blue arrow were not displayed completely.
Figure 4: It is not necessary to use circular plot to show conversion among land covers. It is complex and difficult to estimate the numbers, and similar colors used makes it even difficult to read. Transition matrix can directly and clearly shows the information you need to present.


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

Input:
Title: THE CONTRIBUTION OF EARTH OBSERVATION TECHNOLOGIES TO THE REPORTING OBLIGATIONS OF THE HABITATS DIRECTIVE AND NATURA 2000 NETWORK IN A PROTECTED WETLAND
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is a well done research article which describes an ensemble mapping approach based on satellite images to assess habitat and land cover changes in a Natura 2000 site. This research is indeed quite relevant to help EU member states with their reporting obligations under the EU nature directives. The paper is well written in clear and concise style. Although it could be easily accepted in its present form, I still have a few suggestions which could improve the paper.
Experimental design: No comments
Validity of the findings: No comments.
Additional comments: Line 50 and also the discussion. I agree that your approach could be helpful for the three objectives mentioned but the sentence suggests you actually demonstrated the usefulness of the methodology to provide policy support ("our approaches were found to be useful to help …"). However you did not investigate the usefulness of your approach by surveying potential users so I would slightly reformulate this conclusion in the abstract and also in the manuscript.

The COPERNICUS land product has a high resolution land cover land use data set which has been specifically developed for Natura 2000 sites. However, not all Natura 2000 sites are covered at this point in time. It may be worth checking if data for the site under study is available as an alternative way to validate the outcomes of this study. Or the authors could refer to it in the article. https://land.copernicus.eu/local/natura/natura-2000-2012/view

Figures 2 and 3 are not particularly helpful. I would convert them to tables. In addition I would replace figures 2 and 3 with boxplots with the average and standard deviation calculated over the different EO methods.  Also Figure 4 is quite different to read (even if it is nicely designed). Again, habitat conversion and the resulting land flows from one type to another may be best presented in a matrix.

Minor comments:
Line 331: In the EU species are only protected under the Birds and Habitats directives. I have no knowledge of other directives which protect species. For some species, such as Anguilla Anguilla, specific regulations may exist.
Throughout the text: "State Members" should read "Member States" and "benefits and services" should read "services and benefits" (following the order of the ecosystem services cascade model).


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

Input:
Title: THE CONTRIBUTION OF EARTH OBSERVATION TECHNOLOGIES TO THE REPORTING OBLIGATIONS OF THE HABITATS DIRECTIVE AND NATURA 2000 NETWORK IN A PROTECTED WETLAND
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript has been much improved since last revision. Some figures and tables need  further improvement.
Experimental design: No comment
Validity of the findings: The challenges and limitation in mapping Natura 2000 habitat using remote sensing should be further highlighted in the discussion.
Additional comments: The authors did a good job reworking the manuscript. I only have a few additional minor comments.

1. The authors adopted a more standard classification scheme and wetland typology based on the habitat types defined in the Annex 1 of the directive. I was wondering why reed red was considered as a separate class from salt marshes and meadows. Is the habitat defined in the report by Ramil-Rego et al. 2008? Additionally, in line 342, the authors mentioned that Phragmites australis reed bed was not listed in the habitat directive. But in the Interpretation Manual of European Union Habitats, the plant is included in several habitat types, such as 1130 estuaries, 1150 coastal lagoons and 1340 inland salt marsh.

2. There are several challenges in mapping these Natura 2000 habitats using remote sensing, such as the spectral difference of the covers belong to the same habitat type and the spectral similarity of the covers belong to different habitat types. Detailed habitat mapping may require hyperspectral remote sensing or LiDAR remote sensing. These limitations should be further highlighted in the discussion.
Reference: Borre, J. V., Haest, B., Lang, S., Spanhove, T., Förster, M., & Sifakis, N. I. (2011, 15-17 Sept. 2011). Towards a wider uptake of remote sensing in Natura 2000 monitoring: Streamlining remote sensing products with users' needs and expectations. Paper presented at the 2011 2nd International Conference on Space Technology.

3. Figure 4 caption: user’s accuracy (UsA), but in the figure: UrA

4. Figure 5: since the authors did not intend to differentiate between individual algorithms and between ensemble algorithms, it is better group the legend accordingly (e.g., individual algorithms and ensemble algorithms), otherwise it is a bit confusing showing different items with the same color.

5. Figure 6 and 7 map legend needs improvement, the continuous bar makes it difficult to relate one color to the corresponding class.

6. Dataset S1: EnvUnit should be updated to new habitat class.


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: STABLE ISOTOPES OF HAWAIIAN SPIDERS REFLECT SUBSTRATE PROPERTIES ALONG A CHRONOSEQUENCE
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is written in English using clear text and and appropriate structure.
Experimental design: The manuscript meets the aims and scope of the journal and the hypotheses are clearly stated. My largest concern about the paper is about the sampling design. There are no replicas of each chronosite (Upper Waiakea, ‘Ola’a and Laupāhoehoe). In addition:

Lines 215-216: I suggest to describe in more detail the laboratory procedures. Different parts of the spider's body may show variations in isotopic compositions. In addition, were gut contents removed before grinding spiders?

Lines 242-244: The criteria for grouping the isotopic samples are extremely important because they directly influence the results of the study. I suggest the inclusion of a scatter plot for each functional group at each collection site so that the variation of the data can be verified.
Validity of the findings: This manuscript demonstrates how the biogeochemistry of the food web is determined by ecosystem succession of the substrates on which the organisms have evolved. In this case, the data strongly show that the isotope values of the organisms reflect the chronosequence.
Additional comments: The manuscript entitled “Stable isotopes of Hawaiian spiders reflect substrate properties along a chronosequence” by Kennedy et al. is very interesting and presents important information concerning how different functional groups of spiders reflect the successional changes in the soil stoichiometry of the island chronosequence. This manuscript was previously submitted to Ecography and has been revised following the suggestions of the reviewers. The authors answered adequately the great majority of the questions asked by the reviewers. This fact made it possible to improve the manuscript.
In my opinion, the manuscript can be accept for publication since some essential minor revisions.


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: STABLE ISOTOPES OF HAWAIIAN SPIDERS REFLECT SUBSTRATE PROPERTIES ALONG A CHRONOSEQUENCE
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: The authors could describe their one negative result in more detail in the Discussion. See below:

Line 277-282: This is true except for Ola’a vs. Laupāhoehoe within Ariamnes, as was mentioned in the Results (Line 244), correct? This neutral result is interesting. Can the authors elaborate on it more in the Discussion? I think there is a great opportunity to contrast Arimnes with Tetragnatha  at the end of Line 301, as you have just described the implications for the results with respect to Tetragnatha. But what do the results mean for Ariamnes, given the ecology of Ariamnes?
Additional comments: The manuscript is much improved and clearer from the versions that I read from the previous submission to Ecography. The authors reframed the manuscript such that many of my initial concerns have been addressed. Below are a few more suggestions and questions about the study.

In the Discussion, it would be nice to emphasize that the results of this study are even more exciting because they were found in mobile predators. One could argue that the chronosequence would be more clear in more sedentary, herbivorous organisms and thus, seeing them in mobile predators makes this finding even more compelling. This was touched upon a bit in the Introduction, but it might be nice to emphasize in the Discussion as well, if space permits.

Line 69: Consider saying something along the lines of “disappearing” as opposed to “collapsing”. I found “collapsing” to be confusing.

Line 105: Change “one” to “within” so it reads “within stick spiders.”

Line 106-119: There is much more information about the Tetragnatha group compared to the Ariamnes group. Is all of the information about this group necessary? It seems like the relevant information is that some are web builders feeding on a mixture of insect herbivores and predators while others are cursorial predators.

Lines 302-312: I t might be worth explicitly stating that d15N seems to be reflecting nutrient differences while d13C in plants does not.

Lines 345-348: Are there published trophic discrimination factors for spiders? If so, it would be worth including them here. Post 2002 is also based on aquatic food webs. Citing a terrestrial study on invertebrates along with Post 2002 would also be useful.


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: CONSERVING RELICS FROM ANCIENT UNDERGROUND WORLDS: ASSESSING THE INFLUENCE OF CAVE AND LANDSCAPE FEATURES ON OBLIGATE IRON CAVE DWELLERS FROM THE EASTERN AMAZON
Review round: 1
Reviewer: 1

Output:
Basic reporting: I thought the authors did an admirable job of reporting their results and I had few comments (on annotated pdf file)
Experimental design: I found the statistical methods to be both thorough and innovative.  My only suggestion of substance was to consider using a weighted richness measure where each occurrence for a species occurring n time is weighted 1/n.  This weights species equally.
Validity of the findings: As the authors point out, the findings are novel, especially with respect to spatial structure.
Additional comments: Iron caves are small.  I have generally thought that the primary habitat was the MSS (canga?) and that caves were sampling sites.  I realize the importance of caves under Brazilian law, but I wonder if you could comment on this in the discussion.  It actually ties in quite well with your findings.


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

Input:
Title: CONSERVING RELICS FROM ANCIENT UNDERGROUND WORLDS: ASSESSING THE INFLUENCE OF CAVE AND LANDSCAPE FEATURES ON OBLIGATE IRON CAVE DWELLERS FROM THE EASTERN AMAZON
Review round: 1
Reviewer: 2

Output:
Basic reporting: This manuscript represents an attempt to document the spatial and disturbance variables that might affect troglobitic communities and their constituent species in the iron caves of eastern Brazil. The manuscript is well-written and mostly unambiguous. I have uploaded a version of the manuscript with a few small suggestions highlighted. The context is clearly explained, and the literature cited seems comprehensive.
Experimental design: I am not fully conversant with the statistical packages used in the study, but I cannot detect any major flaws. The research questions are well defined.
Validity of the findings: This is a novel study centered on the controversial topic of the conservation of trogolobitic communities in the face of anthropogenic land uses changes. The findings appear to be well supported and do not over-reach the data or the analyses.
Additional comments: No additional comments


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

Input:
Title: THE SYSTEMATIC POSITION OF THE ENIGMATIC THYREOPHORAN DINOSAUR PARANTHODON AFRICANUS, AND THE USE OF BASAL EXEMPLIFIERS IN PHYLOGENETIC ANALYSIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is generally clear and well written, appropriately structured, with sufficient background information and figures. Raw data has been uploaded.
Experimental design: The article represents a piece of original primary research, and addresses a well-defined question (the phylogenetic position of the dinosaur taxon Paranthodon). Methods are generally appropriate and well-conducted, with some minor concerns (see comments for the author, below).
Validity of the findings: Results generally appear well supported and are adequately and carefully discussed, with some minor reservations (see general comments to the author, below).
Additional comments: This paper aims to reassess the phylogenetic position of Paranthodon, a putative stegosaur dinosaur from the Cretaceous of South Africa. It provides a redescription of the type material, and tests the phylogenetic position is a large number of different datasets. It concludes that a stegosaur identity is most likely, but also provides an excellent case study of the importance of including multiple species-level exemplars to represent major clades in phylogenetic analyses, rather than just a single basal taxon. I recommend publication with some minor revisions, and have only a couple of substantial concerns, around the association of the vertebra with the rest of the type material, and the conclusions drawn about ankylosaur phylogeny. These and additional points are explored in more detail below:

Line 32: ‘parasagittal’ is misspelled

Lines 46–48: You state that ‘The lithologic description of the upper unit by McPhee et al. (2016) matches the matrix of NHMUK R47338, and thus it is likely that Paranthodon is derived from this unit.’ I think this statement should be unpacked in a bit more detail. What is the matrix present with NHMUK R47338, and how exactly does it compare with that of the upper member of the Kirkwood?

Line 88: You state that the holotype includes a dorsal vertebra, and elsewhere say that this was mentioned by Galton & Coombs. I have checked Galton & Coombs, and they do not mention any vertebra as part of the holotype material of Paranthodon africanus, but they do mention ‘three vertebrae in matrix’ with the specimen number NHMUK [BMNH] 47337a, which is similar to the specimen number for the holotype of the pareiasaur Anthodon serrianus (holotype NHMUK 47337). Owen also does not mention vertebral material as part of the same specimen as the type of Paranthodon africanus. I think you need to provide more details on this vertebral fragment: has it been mentioned in the literature previously, is it really from the same locality as the holotype etc.? I am slightly concerned about the association, given that Owen mixed together Permian and Cretaceous material when describing Anthodon serrianus, and given that this vertebra appears crucial to determining the phylogenetic position. I don't know enough about pareiasaur vertebrae to draw any comparisons with them.

Lines 90–94: You list the teeth as referred to Paranthodon, but at the same time say that they are indeterminate thyreophoran remains. These two statements are incompatible. Do you mean to say that the teeth are “previously referred specimens”?

Lines 114–115: Galton & Coombs (1981: fig. 1A) show a large posterior process of the premaxilla, and also describe it on page 301. Are you to correct to say that they misidentified this process as the nasal?

Line 154: is Butler, Porro and Norman the correct citation for an observation of Hypsilophodon?

Line 156: you need a full stop or semi-colon after “Leahey et al., 2015)”

Line 312: Same comment as above – call them “previously referred specimen”

Line 317: Details of the CT scanning should be provided in a methods section. What was scanned, where was it scanned, and what settings were used? What software was used to analyse the data, and where is the data archived?

Lines 340-341: Barrett et al. (2014) is not an appropriate citation for this tree-searching approach. This is a widely used method and does not require a citation.

Lines 448–458: I have two substantial concerns here. First, Arbour & Currie reported a minimum tree length of 420 steps, whereas your minimum tree length is 421. This suggests that you have not hit the minimum length trees in your analysis, despite using the New Technology search strategy. Second, New Technology searches tend to find a lower number of MPTs than ‘Traditional’ searches, and this is one reason why they should be followed by a round of TBR branch-swapping. The higher resolution in the strict consensus tree of your reanalysis of Arbour and Currie (2016) when using New Technology probably merely reflects the fact that you have not fully explored tree space and have not therefore collected all enough of the MPTs to adequately estimate the strict consensus. Your statement that ‘TBR branch-swapping on RAM trees was not possible due to computational limits, although this would not change the topology of the strict consensus’ is not strictly correct – adding this extra procedure will very likely reduce the resolution in the strict consensus tree, because you will explore more of the tree space and collect more MPTs. This extra procedure should therefore be implemented, and is unlikely to be hugely onerous in terms of computing memory requirements.

Line 520: Marginocephalia cannot be basal to Cerapoda, because Cerapoda is defined effectively as Marginocephalia + Ornithopoda. I’m not quite sure what you mean here.

Lines 630–631: How do we know that the topologies producing using supraspecific taxa by Butler et al. (2008) are correct?

Lines 750–770: This section is quite problematic for the reasons noted above (lines 448-458). You need to check that you are indeed hitting minimum length trees and that you are adequately exploring tree space.


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

Input:
Title: THE SYSTEMATIC POSITION OF THE ENIGMATIC THYREOPHORAN DINOSAUR PARANTHODON AFRICANUS, AND THE USE OF BASAL EXEMPLIFIERS IN PHYLOGENETIC ANALYSIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Excellent and detailed description of an important fossil. References up to date. Wonderful to see this important , but obscure taxon, refigured so well!

Lines 180 - 187 should be re-examined, I know I state, relative to Europelta, "such that the palate would not have had a pronounced hourglass appearance typical of derived nodosaurs such as Pawpawsaurus, Edmontonia, and Panoplosaurus [73–75]. "

I think the introductory part of the abstract could be tightened up a bit and the confirmation of another Lower Cretaceous stegosaurian occurrence on another continent given a bet more emphasis.
Experimental design: The phylogenetic analysis is very thorough. I particularly like their observation that higher taxonomic units used in a phylogenetic analysis need to be represented by both a basal and derived taxon.
Validity of the findings: In a descriptive paper such as this, exceptional figures are critical in evaluating the descriptions. Only 3D models of the described elements would have yielded more information.

On carefully reading the report, this reviewer is convinced as to the importance of this fossil material.
Additional comments: no additional comments


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

Input:
Title: THE SYSTEMATIC POSITION OF THE ENIGMATIC THYREOPHORAN DINOSAUR PARANTHODON AFRICANUS, AND THE USE OF BASAL EXEMPLIFIERS IN PHYLOGENETIC ANALYSIS
Review round: 1
Reviewer: 3

Output:
Basic reporting: See general comments.
Experimental design: See general comments.
Validity of the findings: See general comments.
Additional comments: Many thanks for the opportunity to review this manuscript – Paranthodon is a biogeographically significant dinosaur that is frustratingly poorly preserved, so any new insights into the evolutionary affinities of this taxon are sorely needed. I have a few comments that I hope will improve the manuscript, and also attach a marked-up PDF with other minor comments.

1. I think it would be helpful to introduce Isaberrysaura as another potential Gondwanan stegosaur – it jumped immediately to mind when I read “The geographic location of Paranthodon is particularly significant because it represents one of only two Gondwanan stegosaurs”. I know you discuss this when you get to your phylogenetic analyses, but I think others may notice its absence in this spot too, and it would be good to briefly mention it.

2. I appreciate the use of multiple analyses and comparisons to try to figure out just what Paranthodon really is, and I like the approach you’ve taken here. One thought I had while reading your discussion of exemplar taxa is that one of your main questions boils down to ‘is Paranthodon a stegosaur or an ankylosaur’ but you don’t have a dataset that will easily answer that question – you’ve got matrices that heavily sample ankylosaurs but lightly sample stegosaurs, and matrices that heavily sample stegosaurs but not ankylosaurs, but not an overall Thyreophora dataset. I know it’s not as simple as mashing together two character matrices and calling it a day, but perhaps there should be a coming together of Team Ankylosaur and Team Stegosaur to do just that and find out what some of these weirdo taxa are once and for all – sound like a plan for the future? In the meantime, I think there should be a comment somewhere in your methods section noting that there isn’t a comprehensive Thyreophora matrix at the moment and creating one is outside the scope of your project.

3. Relatedly, you might want to try sticking Paranthodon in the Arbour, Gates & Zanno 2016 dataset that included more comprehensive nodosaurid sampling in the ankylosaurid characters (and got pretty good resolution within Nodosauridae), especially as a comparison to the Thompson et al. matrix.

4. In the “Importance of Paranthodon” section, I think you need to be careful with the word ‘confirmed’. I think you can discuss which hypotheses of relationships for Paranthodon you can reject, and which are best supported, but since Paranthodon wanders around within Thyreophora a bit, I don’t think you can say you’ve confirmed it’s a stegosaur.

5. The photographs of Paranthodon are excellent but I think the figures could use a few more labels, or perhaps a more complete skull as reference just to orient readers who are less familiar with isolated thyreophoran skull bones.

6. You’ve got a figure summarizing the previously published phylogenies used in your analyses, but not one summarizing the results of your own analyses! I know you ran so many that it would be hard to fit all in one figure, but I think you could choose some exemplar results to summarize in one figure, with Paranthodon in bold, to help show how its position varied.

All in all a welcome addition to the thyreophoran literature, and I look forward to seeing the final version 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: SQUEEZING WATER FROM A STONE: HIGH-THROUGHPUT SEQUENCING FROM A 145-YEAR OLD HOLOTYPE RESOLVES (BARELY) A CRYPTIC SPECIES PROBLEM IN FLYING LIZARDS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The basic reporting in this article is generally very good, but some improvements could be made to the data sharing and transparency. Details can be found below.
Experimental design: The experimental design presented in this article is generally good, any shortcomings are primarily due to the nature of the historical sample.
Validity of the findings: The validity of the findings presented in this article is generally good, but some extra findings could be reported to support the authenticity of the data. Details can be found below.
Additional comments: Dear authors,

Thank you for your submission on Draco taxonomy, I think you make an important point in showing that the sequencing of holotypes can resolve taxonomic and nomenclatural issues. I have to commend you for your generally well presented publication. Please find below the comments I have relating to your submission.

Please make sure that you have accession numbers for the deposited sequence data on re-submission, these data can be uploaded to genbank with a hypothetical release date, and genbank staff will release the data earlier if appropriate.

I don’t think this paper qualifies as a “major revision”, but I would like to verify some of the changes before publication hence the recommendation as such (the requested BLAST and ancient DNA stats may or may not support the authenticity of the recovered sequences).

Yours sincerely.

-------------

Some more “major’ issues:

On many occasions the paper refers to unpublished data/findings or data/findings that will be published in the future, this does not improve transparency or the reproducibility of the research, from what I can find PeerJ does appear to approve this type of referencing though.
Line 104. “subsequent paper”, the reader can not verify your taxonomic findings and just has to assume these findings are true. But, as the section mentions this is not related too much to the objective of this paper, so leave as is.
Line 188. “unpublished data”. Again the reader just has to assume this method has been tested and can not verify its validity; the reader can not form an opinion on whether it was the extraction method or the sample that caused the lack of sufficient DNA.  At least give more detail if you refer to this unpublished data/experiment.
Line 203. “unpublished data”. Exactly what part did Cotoras et al. contribute?
Line 232. “customized”. Exactly what part of SeqPrep was customised?
Line 245. “in prep”. This seems fair enough, but again please realise that the reader can not verify the  validity of methods and results of this experiment because it hasn’t been described in detail.
Line 292. “unpublished data”. Please describe briefly in which way both methods contribute.
Line 304. “unpublished data”. Because Cotoras et al is not described in detail; does it actually (pr likely) improve extraction? The reader can’t verify this.
Could you please improve this overall lack of transparency?

Concerning you BLAST results I would like to see some more details.
Line 312. Here you mention 2 libraries from the same extract, but this is not mentioned in the methods section, could you please clarify? In what way do these libraries differ?
If there is only the smallest difference between these libraries (except for index adapters), could you  please provide the the BLAST results per library?
Also, could you please report the BLAST results exhaustively? e.g. could you please list all organisms that received a hit? If lizards get significantly more hits than other random vertebrates this is an indicator that the sequences you have recovered are genuine and this finding should be reported. If the exhaustive list gets too big please include as supplemental material.

To further support the authenticity of the recovered ancient DNA sequences please provide some appropriate statistics. What is the average length of the recovered D. cristatellus sequences and how does this compare to the rest of the library (i.e. the contaminants). Could you give some detail as to how many and which mutations you see at the ends of the sequence reads compared to 56763? Please reference an ancient DNA paper on cytosine deamination to support your findings.

Table 1. Please remove the Total and % columns. These genes do not have equal evolutionary rates, these statistics are therefore biased due to the recovery of different regions per sample. Instead you could list the percentage for each independent measurement, e.g. “12/79 (15.2%)”. For this reason you also can’t refer to the percentages/total numbers mentioned in the paragraph starting line 339, instead you would have to mention the values per gene, this paragraph requires rewriting considering this information. Please also correct the value mention in line 356 so that you compare ND2 vs ND2 values rather than “mitochondrial genes” vs ND2 values; please also mention the values for D. punctatus.

Some minor issues:

Line 60-65. This is perhaps a matter of opinion but since your paper’s main focus is not the effect of ethanol preservation I would avoid ending your abstract on this subject. I would suggest you finish on the big picture finding i.e. your taxonomic findings and the fact that sequencing holotype specimens is important in resolving these issues.

Line 85. It is not clear what “10 of 21 specimens” refers to in this instance.

Line 158. Please do not use the word “sensible” as it expresses an opinion.

Line 216. I don’t understand how you get to 50ml, please clarify. I see 0.5 ml, 13ml, 30ml, 25ul, 25ul. Which does not add up to 50ml, is the rest lysate?

Line  277. Please rewrite this sentence, you are correct to not use ML or Bayesian approaches, but the mentioned branch lengths are not informative because your alignment is gapped, e.g. the D. cristatellus sequences appear closer to each other because of limited sequence data and therefore fewer distinguishing substitutions.

Line 281. Please also make the HTS data available. I understand that you may prefer to hold on to the capture data for release with its respective paper, so you may want to release just those sequences that mapped to the mitochondrial genome. All data from the historical specimen could be deposited in the Sequence Read Archive.

Line 282. Is it really necessary to upload this distance matrix elsewhere? I think it may be more convenient for readers if it was included as online supplement.

Line 377. Please use initials rather than “senior author”.

Line 412. “denatured”, is "degraded" perhaps more appropriate?

Line 421. I am sceptical about this conclusion. Please find some more papers that compare DNA preservation in formalin and ethanol and amend/reference this statement accordingly.

Figure 1. Although this may be obvious please describe in the figure legend which animal is depicted in the lower left picture.

Some other remarks:
I suggest using BWA instead of Geneious in the future as the algorithms employed in the latter are not sufficiently described.