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: HABITAT SUITABILITY OF CETACEANS IN THE GULF OF MEXICO USING AN ECOLOGICAL NICHE MODELING APPROACH
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This manuscript built maximum entropy (MaxEnt) models using oceanographic variables (sea surface temperature SST and chlorophyll-a concentration) and bathymetric variables (depth, slope, and distance to 200 m isobath) to predict the potential distributions of 12 cetacean species in the Gulf of Mexico (GoM), and to identify the most important environmental predictors influencing their distributions.  The paper is interesting and potentially useful, as it demonstrated the importance of depth, bottom slope, and minimum SST in influencing the distributions of cetaceans in the GoM, and made an attempt to assess the habitat suitability of cetaceans along the continental slope of the GoM using MaxEnt.  I think that the combined use of oceanographic and bathymetric predictors in a MaxEnt modeling framework is an interesting advantage of this paper in relation to others that deal with similar topics.  There are some justifications the authors need to include, which will enrich the content of the research while clarifying the selection and implementation of the approaches used.  The specific comments are:

Abstract
-	(1)  Lines 25.  “MAXENT” to “MaxEnt”.

Introduction
-	(2)  Lines 49-54.  This sentence seems too long.  I would suggest rephrasing it into shorter sentences.
-	(3)  Line 52.  “abundance of prey” to “the abundance of prey”.
-	(4)  Line 68.  “can also be found in both” to “can be found in both”.
-	(5)  Line 84.  “Presence-only data” to “presence-only data”.
-	(6)  I would suggest emphasizing somewhere in the Introduction section the significance of the combined use of oceanographic variables (SST and chlorophyll-a concentration) and bathymetric variables (depth, slope, and distance to 200 m isobath) in a MaxEnt modeling framework, because these approaches might help people from broader field find your work useful rather than just people working on cetaceans being interested in it.

Materials and Methods
-	(7)  Line 103 (and others throughout the manuscript).  “Gulf” to “GoM” or “gulf”.
-	(8)  Line 113.  “with ≥ 30; presence records” to “with ≥ 30 presence records”.
-	(9)  Lines 114-115.  Are there any absence data of cetaceans in the GoM available from the literature or digital databases?  There are some other modeling approaches (e.g., generalized additive models) that have been used in ecology when it comes to predicting species distributions.  Given the potential of species distribution modeling to influence conservation or management, it may be necessary to critically assess the choice of modeling approach for the available data and specific environment considered.
-	(10)  Line 115.  “peer review articles” to “peer-reviewed articles”.
-	(11)  Line 119.  “(Supplemental Data S1)..” to “(Supplemental Data S1).”.
-	(12)  Line 119.  I would suggest using “e.g.” rather than “i.e.”, because there might be other types of potential sampling bias.
-	(13)  Line 122.  It should be “spThin package” rather than “spThing package”.
-	(14)  Line 123.  What do you mean by “records that do not achieve the distance restriction of the nearest neighbor”?  Do you mean records within the distance restriction or records outside the distance restriction?  Please specify that.
-	(15)  Line 127.  “each thinned datasets” to “each thinned dataset”.
-	(16)  Line 131.  “factors that influence on the cetaceans’ distribution” to “factors that influence the cetaceans’ distribution”.
-	(17)  Lines 133-134.  “Dynamic oceanographic predictors such as sea surface temperature (SST, °C), and chlorophyll-a concentration (Chl-a, mg/m^3) were included in three metrics” to “Dynamic oceanographic predictors, such as sea surface temperature (SST, °C) and chlorophyll-a concentration (Chl-a, mg/m^3), were included in three metrics”.
-	(18)  Line 135.  When you examine the influence of SST and chlorophyll-a concentration on the potential distributions of cetaceans, I would suggest also considering seasonal/monthly variables and both concurrent and time-lagged (e.g., one season/month prior) data layers of SST and chlorophyll-a concentration, which may help better understand the distributions of cetaceans.  Adding some discussion on the potential influence of time-lagged ecological variables in the Discussion section would also be helpful.  In some cases, marine processes are better explained by time-lagged ecological variables, such as surface temperature, rather than simultaneous values (Olden and Neff 2001).  Chlorophyll is often considered having a 30-day accumulation period prior to being reflected in higher trophic levels through ocean food chains (Trujillo and Thurman 2016; Wang et al. 2018).
Olden, J.D., and Neff, B.D. 2001. Cross-correlation bias in lag analysis of aquatic time series. Marine Biology 138:1063–1070.
Trujillo, A.P., and Thurman, H.V. 2016. Essentials of oceanography, 12th ed. (pp. 403–444), Boston, MA: Pearson Education, Inc.
Wang, L., Kerr, L.A., Record, N.R., Bridger, E., Tupper, B., Mills, K.E., Armstrong, E.M., and Pershing, A.J. 2018. Modeling marine pelagic fish species spatiotemporal distributions utilizing a maximum entropy approach. Fisheries Oceanography 27:571–586.
-	(19)  Line 140.  “Static layers include three bathymetric predictors were considered” to “Static layers including three bathymetric predictors were considered”.
-	(20)  Line 144.  It should be “raster package” rather than “Raster package”.
-	(21)  Lines 150-151.  I would suggest including the results of principal component analysis (PCA) in the supplemental material, and adding a brief explanation of how you identified predictors that retained a high proportion of the original information based on PCA.
-	(22)  Lines 152-153.  Did you use raw or log-transformed environmental data when applying the modeling approaches?  It would be better to specify a little more even though you have removed the co-linearity among environmental predictors.  Such data transformation may not be necessary for some situations, but it is an important step to make sure the variables meet the underlying assumptions of the algorithms before conducting any statistical analyses.
-	(23)  Lines 164-165.  Some studies have attempted to use a distance-based function to restrict background points more likely to occur geographically further away from the presence records rather than randomly selecting them (e.g., Hengl et al. 2009).  Have you ever considered that?
Hengl, T., Sierdsema, H., Radović, A., and Dilo, A. 2009. Spatial prediction of species’ distributions from occurrence-only records: combining point pattern analysis, ENFA and regression-kriging. Ecological Modelling 220:3499–3511.
-	(24)  Line 173.  Did you use any cross validation when evaluating the model performance?  I would suggest using cross validation when assessing the model performance.  The predictive capability of a model could be overestimated without proper validation, because predictive power is generally highest on the training dataset, followed by approaches based on bootstrapped data resampling, and then on models validated using independent datasets (Wenger and Olden 2012).
Wenger, S.J., and Olden, J.D. 2012. Assessing transferability of ecological models: an underappreciated aspect of statistical validation. Methods in Ecology and Evolution 3:260–267.
-	(25)  Lines 177-178.  The omission rate (OR) is typically threshold dependent.  I would suggest specifying how you chose the threshold for this metric when assessing the model performance.
-	(26)  Line 182.  Do you have any reference for why you chose 50% as the threshold of cumulative percent contribution?

Results
-	(27)  Line 191.  I would suggest adding some explanations of why the sampling bias was persistent in the habitat suitability models of these species in the Discussion section.
-	(28)  Line 197.  “models had the highest number” to “models had the most predictors”.
-	(29)  Line 202.  “habitat-suitability” to “habitat suitability”.
-	(30)  Line 203.  “high-suitability” to “high suitability”.
-	(31)  Line 224.  “the entire Gulf, mainly on areas” to “the entire GoM, mainly in areas”.
-	(32)  Line 278.  “Highly suitability areas” to “Highly suitable areas”.

Discussion
-	(33)  Line 291.  “enriched-nutrients” to “nutrients-enriched”.
-	(34)  Line 295.  “surface temperatures 29-30℃” to “surface temperatures of 29-30 ℃”.
-	(35)  Line 297.  “in the east, these differences” to “in the east, and these differences”.
-	(36)  Line 301.  “than in the eastern” to “than in the eastern region”.
-	(37)  Line 312.  “composed by three species” to “composed of three species”.
-	(38)  Line 315.  “have a different habitat” to “have different habitats”.
-	(39)  Lines 316 and 318.  Do you mean “habits” or “habitat”?
-	(40)  Lines 322-323.  “Both species do not show a dominant spatial pattern” to “Neither species shows a dominant spatial pattern”.
-	(41)  Line 330.  “feed principally on” to “feed primarily on”.
-	(42)  Line 333.  “the Mississippi canyon, and the west Florida and the Louisiana-Texas slopes” to “the Mississippi canyon, the west Florida and the Louisiana-Texas slopes”.
-	(43)  Line 361.  “Presence-only records” to “presence-only records”.
-	(44)  Line 364.  “Those our results” to “Our results”.
-	(45)  Line 375.  “We identified the Mississippi canyon and the west Florida and the Louisiana-Texas slopes as” to “We identified the Mississippi canyon, the west Florida and the Louisiana-Texas slopes as”.
-	(46)  The potential distributions of cetaceans may also be affected by biotic interactions (e.g., predators).  I would suggest acknowledging in the Discussion section these additional factors based on literature and their potential influence on the distributions of cetaceans in the GoM.

Tables and Figures
-	(47)  Table 2 Line 5.  There is no “n” in the table.  Do you mean “Sum” = number of models?
-	(48)  Table 2.  I would suggest adding the “%” symbol to the percent contributions of environmental predictors in each MaxEnt model.
-	(49)  Figures 2-4.  I would suggest specifying in the figure captions what the color range of the scale bar indicates (e.g., red indicates highest habitat suitability, and light yellow indicates lowest habitat suitability), because audience who are not in this field may not be familiar with what the habitat suitability of 0-1 stands for.  A good figure or table caption should make the figure or table understandable without reference to the main text.


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

Input:
Title: HABITAT SUITABILITY OF CETACEANS IN THE GULF OF MEXICO USING AN ECOLOGICAL NICHE MODELING APPROACH
Review round: 1
Reviewer: 2

Output:
Basic reporting: The written language is generally ok but not good. There are a number of minor grammatical errors which may be due to English not being the primary language of the authors (based on the author affiliations). See Line 60, Line 107, lines 140 – 141, line 286, line 291, line 357. These errors generally don’t take away from the manuscript, however there are some places where it makes it difficult to understand what is being argued.

The introduction does an adequate job, however the case for a lack of distribution information for species outside of the northern Gulf of Mexico could be made more clearly. See general comments in relation to my suggestion for a slightly different focus for the manuscript which may require parts of the introduction to be revised.

In my opinion the manuscript would be significantly improved by the addition of two figures: First a figure showing the location of all sightings used as model input (distinguished by species) so the reader can get a sense of the spatial distribution of the sightings used and the biases that may be associated with them. Second, since the results are discussed as regions of the Gulf with highest habitat suitability across all studied species, a figure that presents the cumulative habitat suitability across all species should be presented so the reader can easily identify the high suitability areas rather than having to look at each figure and remember common regions across all figures. This could be something as simple as overlaying all the maps and summing or averaging the values of each grid cell.
Experimental design: The research question is explicitly stated however the justification could use some work. Since the justification is a lack of data outside the northern Gulf of Mexico, throughout the manuscript a better job could be done to distinguish studies/data from the northern Gulf of Mexico from the rest of the Gulf of Mexico/study results. I was often confused why study results were being presented as novel, along side data from the literature that seemed to show the same thing.

The methods used could use some additional detail as described in the specific line comments below. Biases associated with the data and model output should be discussed in more detail either in the Methods or in the Discussion. For example, sampling bias was mentioned on line 191 but no further detail was given about what it may have looked like and what its effects could be. A sample of 30 presence locations compared to 10000 available locations seems very small, so additional detail related to how Maxent performs on low-prevalence data and how model performance measures may be affected should also be added.

The lack of a temporal aspect to the environmental predictors used is also problematic. The modeling area is described as ‘dynamic’ but no effort to capture its variability was made. Further, some species being modelled may shift their ranges seasonally (as mentioned in the discussion). So the inclusion of parameters like min SST could actually be representing the suitability of an area for only a portion of the year, rather than for the entire year. These kind of issues should also be addressed in the section describing biases, etc, and ideally an explicit statement would be made about why the temporal aspect was not considered.
Validity of the findings: It doesn’t sound like model performance was tested on an independent data set. This is problematic and its implications should be discussed in the manuscript as you would expect the model to perform well on the data used to formulate it. If the input sightings did not represent all possible habitats of a species (likely given some species with relatively few sightings) the results may not be all that informative. With that said, if no other data truly exist for the non-US EEZ waters, any results may be a starting point to work from.

The interpretations of effects plots are strangely limited. Gradual increases in predictive value with decreasing min SST (Fig S2) are presented as essentially the same as strong increases in predictive value of min SST (Fig 3) by general statements like ‘… favored temperatures < 25 degrees’. I encourage the authors to give a little more consideration to what the results may mean.

Much of the discussion confuses this study’s correlative results with causation. Maxent only finds correlations in the data it is given and the actual process driving any observed trends is not addressed (and may not actually be observed). So results should be discussed based on their correlation with cetacean occurrence, rather than how SST/Depth/etc ‘drive’ cetacean occurrence.
Additional comments: General Comments:
The vast majority of marine mammal studies in the Gulf of Mexico have been limited to the US EEZ. This study sought to use a variety of sightings data to build habitat suitability maps for a wide range of cetacean species to define areas of suitable habitat throughout the Gulf of Mexico. This has the potential to be an interesting study, however, in my opinion, the way it is currently presented is challenging to understand and much of the methods need additional description or discussion of biases and related caveats so the reader can better understand how the results should be interpreted.

The discussion of areas of ‘high habitat suitability’ is confusing because the term seems to be used for both habitat suitability of individual species as well as areas of habitat suitability for multiple species. It seems like what is really being described are areas that are capable of supporting high cetacean biodiversity. Managing and conserving biodiversity is an area of emphasis throughout the world, so focusing on this terminology (identifying areas in the GoM that could support high cetactean biodiversity) will make the results more readily interpretable and of interest to a broader range of readers. The ‘suitable habitat’ terminology could then be used to describe individual species-level habitat associations, making a clear distinction between the two types of ‘high habitat suitability’ being discussed in this study. I personally think the identification of areas that could support high biodiversity is the most interesting aspect of this study but it is not covered very well. I would also suggest the authors consider focusing their language on ‘the distribution of suitable habitat’ rather than the currently used ‘potential distribution’ of a species as Maxent pretty explicitly states the output is not related to species density or probability of occurrence and in my opinion, nothing is gained by the use of potential distribution.

Line Comments:
Lines 22 – 24: This makes it sound like no SDM’s have been made for cetaceans in the GoM. Also, it doesn’t really make sense to mention 20 cetacean species if you are only looking at 12 of them
Lines 29 – 30: The most consistently significant predictors? Or supported? Constant isn’t quite the right word here
Lines 33 – 36: Were these ‘high-suitable regions’ identified that way because they were suitable for many species? I assume a separate model was fit for each species? So maybe they are highly suitable areas for cetacean biodiversity?
Lines 80 - 83: It is unclear if this is referring to high habitat suitability for each species or areas of high suitability for many species. Consider presenting the results in a biodiversity context where regions with high habitat suitability for many species would be considered regions capable of supporting high cetacean biodiversity. Then ‘habitat suitability’ could be reserved to discuss habitat of individual species. Also consider revising the wording related to geographical regions for clarity as it is often difficult to distinguish between what is known/being discussed about the northern Gulf/US EEZ and the rest of the GoM.
Lines 91 – 94: Why do the figures (except Fig 1) show just the GoM when the modelling area was the whole warm-temperate north west atlantic? Was this done to expand the number of sightings used as model input? If so it should be explicitly stated.
Lines 95 – 104: This would probably fit better in the introduction
Line 107: ‘As we mentioned’. It is unnecessary and can be deleted
Lines 112 – 113: I suggest starting the paragraph with this line (only selecting species with > 30 records) and then follow up with a justification for that threshold and what species that removed from the total.
Line 127: A map showing all sighting locations would be helpful to orient the reader and give the reader a sense of the possible spatial biases in the data
Line 129: Were any other predictors considered? Possibly Sea Surface Height or measures of vorticity? Especially with the more oceanic, deep-diving species, it seems unlikely that surface-oriented predictors will have much value.
Line 138: I’m not clear how an 8 day composite was used to characterize the annual cycle of each variable? The mean, min and max values over the 16 year time period were calculated on 8 day composites? Also, why were annual means used instead of the values at the time of each sighting? That would seem to be more relevant and would potentially help incorporate temporal aspects to distribution like seasonality.
Lines 150 – 153: How would a principal components analysis determine which correlated predictor should be removed? It seems like the mean, minimum and maximum of the predictors will always be strongly correlated?
Lines 159 – 160: This sentence needs some additional work as I’m not quite sure what is being said.
Line 167: What is ‘the block as data portioning’? Is this using cross validation methods? The sample size is awfully small to be holding out some of it during model development.
Lines 168 – 170: What output was chosen? Logistic? Cloglog?
Lines 173 – 179: Performance measures ideally need independent data for comparison. Was this used or are the measures testing the model performance on the same data used to formulate the model?
Lines 181 – 183: This sentence is confusing. Predictors were deemed not significant when the cumulative percent contribution of 50% was reached? Consider re-wording for clarity
Lines 191 – 193: The reader needs to know what this sampling bias is. At a minimum there should be a figure showing the location of all sightings and some additional context here would be useful (all species were observed during one expedition/in one area/etc)
Line 195: The methods state there were five environmental predictors, but here there are up to 6?
Line 211: This is minimum temperature right?
Line 218: Minimum temperature?
Lines 285 – 288: This study identifies environmental covariates that are correlated with sightings. This is not to be confused with a causative relationship as implied by this statement. We do not know if the predictors ‘influence the distribution of cetaceans’ only that values within a certain range are associated with sightings.
Lines 302 – 304: So why was no attempt made to account for seasonal changes in dynamic predictors?
Lines 333 – 337: How was this identified? Visually? Was there a numerical way of adding the habitat suitability scores across all species? It is important to state that these areas are high suitability for a large number of the species modelled. Just mentioning ‘high suitable regions’ could be talking about just one species. There should also be a section in the Results describing these areas of common high suitability across species as I would think this is the most interesting part of the paper.
Table 2 line 5: I do not see ‘n’ anywhere in the table. Is this perhaps ‘Sum’?
Table 2: ‘Species’ is missing an ‘s’. How is there such a high OR for Dwarf sperm whales when the AUC is so high?
Figure 4: It looks like vessel track lines can be seen in panel C (in the north, northwest section on the shelf) and can be seen faintly in panel A and B. What could cause that since the predictor variables were all remotely derived (not ship-based)?


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: HABITAT SUITABILITY OF CETACEANS IN THE GULF OF MEXICO USING AN ECOLOGICAL NICHE MODELING APPROACH
Review round: 1
Reviewer: 3

Output:
Basic reporting: The article has the expected professional structure, with proper tables and figures, and sufficient references and background material. The raw data are provided, in the form of an Excel file containing the sightings used to fit the models. From this, the analysis could probably be reconstructed by obtaining covariates from the documented sources and fitting the models using the methodology described. The writing is generally good, aside from some minor wording issues (see below).

I find the Results section, where the species are each reported, to not be very interesting. Essentially these species subsections are just mechanical summaries of Table 2, the maps presented in Figures 1-4, and the response curves in Supplementary Information S2. Personally, I don’t find this dry narrative from lines 200-280 to be very helpful, because I can see all that information just by examining the plots and Table 2. But I recognize that it may be traditional to include such text in the Results section, so it is ok with me if you leave it in the paper. However, if you needed additional space, e.g. to expand the Discussion section, you could cut out lines 200-280, or further compress them. Also, you could draw polygons of high and moderate suitability on your maps, if you felt that communicating that information better would benefit your readers.

The paper would be improved by changing some words and correcting some minor grammar mistakes, enumerated below. However, it was easy to follow everything despite these minor issues.

Line 22: For “projecting” I suggest “the projection of” or “prediction of”.
Line 24: “module” should be “model”.
Line 28: You could probably remove the word “predictors”.
Line 29: “the most constant environmental predictors” sounds like they had the least variation. I suggest “the most frequently selected predictors”.
Line 33: Instead of “We identified in the northern GoM,” I suggest “In the northern GoM, we identified”.
Line 34: “high-suitable” should be “highly-suitable”.
Line 35: Throughout the manuscript, I suggest the term “moderately-suitable” rather than “medium-suitable”.
Lines 44-45: Because the word “species’” is plural, the word “response” should probably also be plural.
Line 51: “their distribution is” should probably be “their distributions are”.
Line 71: The common name for S. clymene is Clymene dolphin, with the C capitalized. Please capitalize the C of “Clymene dolphin” throughout the manuscript.
Line 80: “distribution” should probably be “distributions”.
Lines 82-83: The sentence starting with “Moreover” is not a complete sentence.
Line 84: “Presence-only” should not be capitalized. Also on line 361.
Lines 107-108: “GoM being the most of them” should be “GoM, most of them being”.
Line 119: Remove extra period.
Line 122: “spThing” should be “spThin”.
Line 127: “each thinned datasets” should be “each thinned dataset”.
Line 131: “on the cetacean’s distribution” should be “cetacean distributions”.
Line 132: “both the static” should be “both static”.
Line 134: I suggest “forms” instead of “metrics”.
Line 140: “include” should be “included”.
Line 141: Delete “were considered”; it is redundant.
Line 141: What does “grades” mean? I am not familiar with that unit.
Line 151: “need to” should be “needed to” or “should”.
Lines 152-153: I suggest deleting “therefore, only independent predictors were used”. Although collinearity is often mitigated using the technique you mentioned, and I don’t think you need to change your analysis, I’m not sure that the test of p >= 0.70 was sufficient to claim the predictors were “independent”. Therefore, I suggest you just delete that phrase.
Line 157: I suggest “from” should be “in”.
Line 160: “predictors” should be “predictor”.
Line 166: “selecting” should be “selected”.
Line 167: I do not understand “We applied the block as data partitioning”. Could you make this clearer, please?
Line 169: “and it was expressed” should be “which was expressed”.
Line 189: “0.75, according” should be “0.75; according”.
Lines 285-288: I do not understand what this sentence is trying to say. I suspect it is saying that although the two predictors do broadly influence the distributions of cetaceans in a direct way (e.g. through thermoregulatory constraints), they exert more influence in an indirect way by directly influencing the distribution of prey. Is that the right idea? Could you please rephrase the sentence to be clearer?
Line 303: The word “hypothesizing” does not make sense here. Who or what is doing the hypothesizing? In that sentence, the seasonal abundance changes are doing the hypothesizing. Please fix this.
Line 306: The word “Gulf” is capitalized here, but throughout most of the rest of the manuscript it is not. Please use consistent capitalization. (I do think “Gulf” is better than “gulf”, but either is ok.)
Line 308: “strategies, in turn, linked” should probably be “strategies, which are, in turn, linked”.
Line 313: What is “assed”? Please replace with the correct word.
Line 330: “use preferably” should be “preferentially use”.
Line 330: Remove the comma.
Line 355: I suggest “information” should be “knowledge” and “distribution” should be “distributions”.
Line 355: I suggest “to obtain” be changed to “obtaining”.
Line 357: I suggest this sentence be rephrased “As a result, robust knowledge of cetacean species distributions is sparse for several regions of the oceans, …”
Line 358: “because it allows to obtain” should be “because it facilitates development of”.
Line 363: Delete “prospectively;”. Also, I don’t understand what “ecological sound-based mitigation strategies” are. In particular, “sound-based” is odd.
Line 364: I believe “Those” should be “Thus”.
Experimental design: The article is within the aims and scope of the journal. The research question is well defined and the paper states how the research fills a knowledge gap (but see below). The investigation appears rigorous, and the methods appropriately selected, described, and executed well (but see below). Presence-only models were fitted for which there was strong potential for uneven sampling to bias the predictions, but the authors applied an appropriate mitigation to this common problem. To boost sighting counts and expand the range of sampling of model covariates, the analysis appropriately included sightings from outside the focal area but within the same ecoregions. Overall, the manuscript inspires confidence in the results. However, I have several concerns that should be addressed, numbered below.

1. Lines 69-77 of the Introduction review what is known of cetacean species distributions in the Gulf of Mexico, but two very relevant papers are missing. (Disclaimer: I am the lead author on one, and second author on the other.) Roberts et al. (2016, in Scientific Reports) produced density surface models for all species sighted by U.S. NOAA surveys of the Gulf of Mexico from 1992-2009. The spatial extent of these models was roughly the U.S. EEZ, comprising the northern ~40% of the Gulf, as mentioned on line 57 of the present paper. Then, Mannocci et al. (2017, in Conservation Biology) produced density surface models for most of the entire Gulf of Mexico and much of the western North Atlantic. Thus, the present paper is not correct when it states in lines 77-79: “However, so far, there are no accurate predictions of the distribution of cetaceans (i.e., spatially explicit maps) on a broader spatial scale spanning the entire GoM.” This statement should be revised to account for the fact that Mannocci et al. did provide such predictions, and the paper should mention (e.g. at line 77) both the Roberts and Mannocci models as prior attempts to model cetaceans in the GOM.

However, I do not believe the existence of Roberts’s and Mannocci’s prior results takes away from the value of the present paper, which may be distinguished from them in several ways. First, obviously, Roberts’s predictions only covered U.S. waters. Second, both of those papers involved density surface models, which give absolute density—the number of individuals per unit area—corrected for sampling effort. This is often very relevant for management applications, which often involve avoiding harm to animals where they currently reside. It might be argued that a density surface model depicts a realized niche, while a habitat suitability model developed from presence-only data, as in the paper under review, depicts a fundamental niche. However, this kind of thing has been heavily debated in the literature by theoretical ecologists, so if you endeavor to make this distinction in your paper, I suggest you carefully prepare proper citations. Finally, the present paper was able to utilize sightings not available for the Roberts and Mannocci analyses. Those analyses required line transect surveys compatible with distance sampling methodology (Buckland et al. 2001), while the present paper only required sightings compatible with presence-only modeling. That allowed the present paper to utilize additional data, particularly in Mexican waters of Gulf of Mexico, where Roberts and Mannocci did not have any data, and parts of the Caribbean.

This last difference is an important distinction. It makes the approach of the present paper potentially more suitable for modeling the southern half of the Gulf of Mexico. However, if you decide to discuss this, please be careful to review the advantages and disadvantages of both approaches. On the one hand, density surface models such as those by Roberts and Mannocci incorporate survey effort and therefore are much less likely to be biased than presence-only models. However, because no data suitable for that method was available for the southern Gulf, the models must be spatial extrapolated there, which is a risky procedure (for a review, see Yates et al. 2018, in Trends in Ecology and Evolution). On the other hand, the presence-only model under review here was able to incorporate data from the southern Gulf, so the degree of spatial extrapolation is greatly lessened. However, because presence-only models do not make use of effort data, risk is high that predictions may be inaccurate unless sampling bias is carefully addressed (see Fiedler et al. 2019, Frontiers in Marine Science, for a specific example concerning cetaceans). Finally, the two approaches model different things—absolute density (individuals per unit area) and habitat suitability (a unitless measure)—which are not equivalent.

Finally, the introductory sentence of the Discussion (line 283: “To our knowledge, this study constitutes the first approximation of the potential distribution of 12 resident cetaceans of the GoM.”) should be removed or altered, in light of the prior work of Mannocci et al.

2. Please include as supplementary information one map for each species showing the sightings enumerated in Table 1. Please show both the “total records” and the “used records”, with the used records layered on top and appearing with a different color or symbol, similar to Figure 1 of Aiello-Lammens et al. (2015) (but please use colors that provide more contrast than purple and red, which are hard to differentiate). This will allow readers to examine the spatial distributions of sightings and see the effect of the thinning procedure. This is very important, as thinning was the method used to mitigate sampling bias in this presence-only model.

3. Unfortunately, I discovered an error in one of the input datasets that affects two of the models. The analysis aggregated sightings from multiple datasets, as is often done with presence-only models. These included datasets from OBIS-SEAMAP, a bioinformatics repository for marine mammal sightings. One of the datasets, known as PIROP Northwest Atlantic 1965-1992 (http://seamap.env.duke.edu/dataset/280) and referred to as Hyrenbach et al. 2012 in the supplementary spreadsheet of sightings, had been processed incorrectly by OBIS-SEAMAP and accidentally switched species IDs for sightings of pantropical spotted dolphin (Stenella attenuata), of which very few were actually sighted, with Atlantic spotted dolphin (Stenella frontalis), for which many were sighted. I attached a PDF to this review showing the problem. This resulted in many sightings of S. attenuata appearing over the continental shelf of the eastern U.S. These should have been S. frontalis. I suspect this influenced the S. attenuata habitat suitability model to predict high suitability across much of the shelf of the northern Gulf of Mexico, even though almost no S. attenuata were ever sighted there (and those that were sighted were always close to the shelf break). This problem probably influenced the S. frontalis model as well, but those results do not appear to be as problematic, in my opinion.

Because of this problem, the pantropical spotted dolphin and Atlantic spotted dolphin models should either be fixed or be removed from the analysis. To fix them, you could either remove the Hyrenbach et al. (2012) dataset and refit the two models, or you could redownload this dataset from OBIS-SEAMAP, replace your current copy, and refit the models. The OBIS-SEAMAP data manager, Ei Fujioka (efujioka@duke.edu) has already fixed this problem after I reported it to him. He apologizes for this mistake. If you have any questions, you are welcome to contact him and myself (jason.roberts@duke.edu). The Results for these species should be updated accordingly, and Discussion at lines 315-323 adjusted as necessary.

4. I am unclear about whether all the predictors listed in Table 2 were actually used to make the final predictions. Lines 181-183 state “we identified the environmental predictors that best explain the data, we established a 50% threshold of the cumulative percent contribution (Supplemental Data S2).” Does this mean that you discarded less important predictors and based the final predictions on a model that included only the most important ones (that summed to >= 50%)? Or did you retain all the predictors shown in Table 2, but just use the 50% criterion to determine which predictors to discuss in the Results and to show in Supplemental Data S2? If it is the latter, which is suggested by lines 194-195, I think you should: 1) Adjust Supplemental Data S2 to include plots of all predictors. 2) Delete the sentences at lines 179-183. You do not need to explicitly state that this 50% criterion is what you used to decide which predictors to discuss. You do not need to change the text of the Results, in which you discuss only the predictors contributing >= 50%. It is ok to omit the less important predictors from your narration without mentioning why.

5. In the Supplementary Information S2, figures S9 and S11, the chlorophyll covariate is a flat line with slope of 0. This suggests that no matter what chlorophyll value occurred, the predicted value is the same. Is that indeed what is happening here? If so, please remove these terms from the model (because they had no influence on the predicted value) or provide some justification for keeping them in the model. Alternatively, these might be piecewise functions in which the predicted value is 0 outside of the flat line currently shown in the figures. If this is true, then please adjust the figures to show red lines at y=0 to indicate that the predicted value is 0 in those ranges.
Validity of the findings: Aside from the issues I noted in the “Experimental Design” section of my review, I believe the analysis is reasonable. The underlying data have been provided and were treated in a statistically sound way. Except for the two spotted dolphins I noted, I believe the results yield plausible habitat suitability maps. The Discussion section contains appropriate and interesting interpretations of the findings, with supporting citations. The Conclusions are well stated, with appropriate caveats.
Additional comments: Although I have written extensive comments, they are relatively easy to address and do not require any of the analysis to be changed, except for the two spotted dolphins. Because of that, I am recommending a “Major Revision” to the editor, because those results should be reviewed once they have been changed. I congratulate the authors on producing what I believe to be plausible habitat suitability predictions using a presence-only approach, which can be tricky to accomplish, given the potential for uneven sampling to bias the results. I hope that my comments have been helpful.


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

Input:
Title: HABITAT SUITABILITY OF CETACEANS IN THE GULF OF MEXICO USING AN ECOLOGICAL NICHE MODELING APPROACH
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors have addressed most of the comments.  I just have a few minor suggestions below, which I hope could help further improve the clarity of the paper.

-	(1)  For Response # 2, since you have some absence data (i.e., presence-absence data available for the north of the GoM, where cetacean surveys are carried out systematically), I would suggest trying another presence-absence modeling approach on the north of the GoM subset and comparing its performance with MaxEnt on the entire presence-only dataset.  The comparison could be included in the supplemental material, and can be used to demonstrate if MaxEnt is still a better option when both presence and absence data are available.

-	(2)  For Response # 6, Line 181 (clear version), “Omission rates greater that the expected value of 0.1” to “Omission rates greater than the expected value of 0.1”.

-	(3)  For Response # 8, I still think it would be worthwhile to acknowledge in the Discussion section the potential influence of biotic interactions on cetaceans’ distributions in the study area based on literature.  Sometimes physicochemical conditions may be an indirect reflection of biotic interactions, falsely suggesting a direct dependence on abiotic factors where in fact a biologically mediated dependence might be the case.  The value of incorporating biotic interactions in improving the performance of habitat suitability models has been mentioned in quite a few studies and reviews (e.g., Van der Putten et al. 2010, Wang and Jackson 2014, Godsoe et al. 2015, Yates et al. 2018).  Jointly modeling target species with their competitors, predators or facilitators has also been used as an option to achieve higher reliability and transferability of habitat suitability models (e.g., Zurell et al. 2009, Maguire et al. 2016).

References
Godsoe, W. et al. (2015) Information on biotic interactions improves transferability of distribution models. American Naturalist 185:281–290.
Maguire, K.C. et al. (2016) Controlled comparison of species and community-level models across novel climates and communities. Proceedings of the Royal Society B: Biological Sciences 283:20152817.
Van der Putten, W.H. et al. (2010) Predicting species distribution and abundance responses to climate change: why it is essential to include biotic interactions across trophic levels. Philosophical Transactions of the Royal Society B: Biological Sciences 365:2025–2034.
Wang, L. and Jackson, D.A. (2014) Shaping up model transferability and generality of species distribution modeling for predicting invasions: implications from a study on Bythotrephes longimanus. Biological Invasions 16:2079–2103.
Yates, K.L. et al. (2018) Outstanding challenges in the transferability of ecological models. Trends in Ecology and Evolution 33:790–802.
Zurell, D. et al. (2009) Static species distribution models in dynamically changing systems: how good can predictions really be? Ecography 32:733–744.


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: HABITAT SUITABILITY OF CETACEANS IN THE GULF OF MEXICO USING AN ECOLOGICAL NICHE MODELING APPROACH
Review round: 2
Reviewer: 2

Output:
Basic reporting: The basic reporting is generally good although there are still a number of minor grammatical issues that could be resolved (for example Lines 65, 108, 180, 255, 265-266)
Experimental design: No comment, everything seems reasonable
Validity of the findings: Everything seems to be in order. I would suggest the authors consider adding a sentence or two to discuss why the suitability region in Figure 5 is so much larger in the northern Gulf compared to the western or southern Gulf.
Additional comments: The authors did a good job addressing and responding to my comments on the previous draft. I only have a few additional minor comments:
Lines 24 – 25: Maybe use language like ‘suitable for high diversity’?
Lines 86 – 88: Awkward wording
Lines 188 – 191: This could be simplified to something like “ ‘Regions capable of supporting a high diversity of cetaceans (suitable regions) were defined as regions where the high suitability areas of at least seven species overlap.’
Line 211: The figures should be referred to parenthetically after descriptive statements (like the second sentence) so this first sentence of the paragraph should be deleted.
Lines 249 – 250: Except you just stated that there was over-fitting. So maybe tone this down/revise it slightly to say you attempted to account for bias using the spatial filtering but it may not have been completely successful?
Figure 5: Additional detail in the caption is needed to make the figure understandable on its own. How were the areas of high diversity identified?


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: HABITAT SUITABILITY OF CETACEANS IN THE GULF OF MEXICO USING AN ECOLOGICAL NICHE MODELING APPROACH
Review round: 2
Reviewer: 3

Output:
Basic reporting: In general, the manuscript has been substantially improved over the original submission. The authors largely addressed the points raised in my original review. The writing has also been improved and is largely free of grammatical errors. A few minor errors remain but they are not significant enough to block publication, and I'm not going to take the time to enumerate them here. However, if the editor does return the manuscript for additional revisions, I suggest the authors make one more pass through the text to check for proper English.
Experimental design: No comment
Validity of the findings: All habitat suitability maps now represent plausible results based on what has previously been reported in the literature. The model response curves appear to be generally consistent with what is known of the species for this region. The problem with the two spotted dolphin species I raised in my original review has been corrected.
Additional comments: I congratulate the authors on their improved manuscript and recommend it be accepted for publication.


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

Input:
Title: IMPACT OF WORK ENVIRONMENT PERCEPTIONS AND COMMUNICATION SATISFACTION ON THE INTENTION TO QUIT: AN EMPIRICAL ANALYSIS OF NURSES IN SAUDI ARABIA
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is interesting study which covered very important topic that still in hot discussion in Saudi nursing community and healthcare in general. The paper were well written, however, there some parts need revisions for clarity and flow of writing. The manuscript were very well structured and figures were clear. The results were connected to the research objectives.
Experimental design: The study have been investigated very important issues in Saudi Arabia. The research hypotheses were well stated. There was clear explanation to the ethical approval and how the data was collected. Methods were explained clearly, however, some areas need justifications.
Validity of the findings: Statistical tests need to be justified/or revised.
Additional comments: This is very interesting study which discussed the attrition of nursing workforce in Saudi Arabia. I have made some comments and hopefully they benefit the enhancement of the manuscript:
In the abstract:
''In addition, we aimed to explore the mediator effect of communication satisfaction on the association..''
I think ''explore'' is not the right word here maybe investigate or examine.
Please write the SPSS version in the abstract as well.

Introduction:
Very well written, defining all the concepts that related to the current research.
''It is a behavioral tendency—or the cognitive expression associated to the behavioral decision—of an individual toward quitting his or her employment. Specifically, employees᾿ intentions to quit often arises because of the physical end results of task allocations within the firm.'' please provide reference here.

''Long working hours comprise one of the challenges encountered by personnel within in the Saudi health system. Additionally, the lack of appropriate training opportunities for nurses to advance their careers and of opportunities to work independently is another important challenge. Depressive and complicated work circumstances are further causes that lead nurses to leave their existing jobs in health institutions in Saudi Arabia.'' they maybe very common facts about the current situation in Saudi Arabia related to the nursing workforce, but please add references to support your claims.

Literature review:
The literature review needs revision to enhance the flow of the writing. Please revise each paragraph and ensure it is consistent with its topic sentence. Some of the paragraphs have general topic sentences which are not relevant to the entire paragraphs.

It will be good adding Saudi studies that covered the current topic for example related to work satisfaction in Saudi Arabia. Same apply to work environment and attrition of nurses in Saudi Arabia. Was there any recent statistic in Saudi about the current attrition rate?

The literature review does not indicate the significance of the study. Why this study was very important to address? What was the gap in knowledge?

Methods:
Given that it was not clear from the literature review why this study was conducted using descriptive, correlational design, it would be good adding a sentence in the research design justifying the choice of the current used design.
I expect this to be reinforced as last paragraph in the review section.
sample and population: Valid and active, were some of the nurses who work in that hospital either part time or full time nurses did not have valid and active licenses? Please revise this sentence.
Please justify why 40 hours per week and why two years of experience. Is there a reason relevant to the current research?
It was good mentioning each used scale with information related to its validation. Just one minor comment, please reorder the information about them in the manuscript according to how they appeared in the study’s questionnaire and under the section about research instruments.
What is Helsinki declaration in the ethical approval? please explain it for the readers.
It was not clear why there was mixing between parametric and non parametric statistical tests. If the data were not normally distributed Spearman’s correlation test will be the good choice as you did to investigate the relationship between the variables. However, median and IQR will be the best to present these data instead of mean and SD.
Can you please explain PROCESS tool in the data analysis?

Results:

Revise the written numbers to match the tables. The majority of the participants were female 7(8.7%), please revise this written sentence.
Discussion and conclusion:
As the literature review please revise the flow of the writing under the discussion section.
It will be great connecting your findings to what was already found locally (in Saudi Arabia) and internationally. Then you can build on this knowledge by writing about what your study added to this knowledge. From the current writing it is not clear the strength of your study's results and what their contribution to the knowledge.

Not clear how these conclusion and recommendations were drawn from.  I suggested revising the discussion section to enable the readers to demonstrate the link between your discussion, recommendations and conclusion. Please revise the recommendations and conclusion part for clarity and maintain their alignment with the discussion of the results. As well. please revise the conclusion part in the abstract to make it stronger. The conclusion part looks very general and does not demonstrate the importance of the study's results.

Overall, it is really good study and will benefit the policy makers in Saudi Arabia to consider the factors that affect the attrition rate of nurses as stated in the manuscript. However, it needs revisions to demonstrate the strength of this study and clarify its addition to the current knowledge.


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: IMPACT OF WORK ENVIRONMENT PERCEPTIONS AND COMMUNICATION SATISFACTION ON THE INTENTION TO QUIT: AN EMPIRICAL ANALYSIS OF NURSES IN SAUDI ARABIA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The study analyzed the risk factors for intention to quit and found that  improving communication satisfaction and work environments for nurses could reduce their intentions to quit. However, this conclusion is too  strong that cannot be supported by current study design. this should be rephrased as an observational study can at best provide preliminary results. This conclusion can only be supported by RCT (different levels of communication satisfaction). for most of the times, modifying risk factor may not help to change the outcome.
Experimental design: 1. The conclusion cannot be supported by the study design.
2. The authors proposed a novel framework in figure 2. But I think this can be better represented in a structural equation modeling framework (Zhang Z. Structural equation modeling in the context of clinical research. Ann Transl Med. 2017;5(5):102. doi:10.21037/atm.2016.09.25); they currently employed  logistic regression model to address this model, which is inappropriate. This should be discussed and data be reanalyzed to see robustness of the current finding.
3. Within the causal inference framework, the authors can establish the acyclic directed graph; but current  analysis is not methodologically correct. for instance, work environment is a confounder based on figure 3; so the independent effect of work environment on intention to quit should be -0.226; however, there should be many other confounders , which the authors did not fully accounted for. thus, the independent effect of -0.226 is not valid.
Validity of the findings: 1. The current finding cannot be supported by the analysis/study design.
Additional comments: 1. The abstract cannot expess the main idea of the study; especially, the result section is poorly written without any useful information; you need data to support your conclusion in the abstract to make it stand alone.
2. intention to quit can be influenced by numerous other factors such as financial issues, work load and so on. How can you address these factors?


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: IMPACT OF WORK ENVIRONMENT PERCEPTIONS AND COMMUNICATION SATISFACTION ON THE INTENTION TO QUIT: AN EMPIRICAL ANALYSIS OF NURSES IN SAUDI ARABIA
Review round: 1
Reviewer: 3

Output:
Basic reporting: For a research article, there is no need for a separate section for "Literature Review" (page 9). Please incorporate this as part of the Introduction section.

Please distinguish clearly between theoretical framework and conceptual framework. You mentioned theoretical framework on page 8, along with Figure 1 and Figure 2. However, your Figure 2 appears to be the conceptual framework of the study.

Table 3 is confusing. You reported results of regression models. I can only see independent variable in the model(s). Where is the dependent or criterion variable?
Why did you conduct MLR with only 1 independent variable and 1 dependent variable?
What is the regression equation?
In MLR, researcher uses several independent/predictor variables to predict the outcome of a dependent/criterion variable. This is not reflected in this study.
Experimental design: The Methods section needs more elaboration, in particular, data analysis.

It is inadequate to just mention multiple regression analysis. For example, you must clearly identify the independent/predictor variables (IV) as well as the dependent/criterion variables (DV) used in the MLR. Did you conduct a step-wise/forward/backwards regression? etc.

I am also unclear why you brought in Spearman's Rank correlation. You can get a correlation matrix as part of the findings when you conduct MLR.
Furthermore, to conduct MLR, both the IV and DV must be continuous variables. Spearman's Rank correlation is for ordinal data.
Looking at your hypotheses and results, I would think you wanted to do a prediction study. Please make sure that the statistical tests used is correct and clearly described in data analysis.
Validity of the findings: The authors used three study instruments in this study, However, reliability and validity of the findings were not reported.
Additional comments: 1. Please improve on the Abstract. It does not accurately reflect the content of the manuscript, in particular, Results.
2. There is a need to distinguish between between theoretical framework and conceptual framework and use them appropriately.
3. Methodology of the study needs more elaboration, in particular, data analysis.
4. Results of the study need to be clearly reported. Please recheck Table 3.


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: IMPACT OF WORK ENVIRONMENT PERCEPTIONS AND COMMUNICATION SATISFACTION ON THE INTENTION TO QUIT: AN EMPIRICAL ANALYSIS OF NURSES IN SAUDI ARABIA
Review round: 2
Reviewer: 1

Output:
Basic reporting: Thank you to the authors for addressing my feedback as (reviewer 1). Thanks for editing the paper. I have reviewed the new changes, and I am happy with the paper in the latest version to be accepted. I still think this study is valuable and worth publication. Hopefully, the readers will consider the findings to help nurses to continue in the profession.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: no comment


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

Input:
Title: IMPACT OF WORK ENVIRONMENT PERCEPTIONS AND COMMUNICATION SATISFACTION ON THE INTENTION TO QUIT: AN EMPIRICAL ANALYSIS OF NURSES IN SAUDI ARABIA
Review round: 2
Reviewer: 2

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


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: IMPACT OF WORK ENVIRONMENT PERCEPTIONS AND COMMUNICATION SATISFACTION ON THE INTENTION TO QUIT: AN EMPIRICAL ANALYSIS OF NURSES IN SAUDI ARABIA
Review round: 2
Reviewer: 3

Output:
Basic reporting: There were numerous grammatical errors in the manuscript. Editing to correct the errors is necessary.

Sufficient background of the study was provided.

There were six tables and four figures - far too many for a manuscript. Please consider to reduce the number of tables. Note: In the previous manuscript, there were three tables but it has increased to six in this revised manuscript.
Experimental design: In the previous manuscript, the dependent variable(s) was/were not identified. The author used MLR as the statistical method to analyse the data.
However, in the revised manuscript, there were two independent / predictor variables (work environment, communication satisfaction) and two dependent / criterion variables (communication satisfaction, intention to quit). I also noticed that you were using communication satisfaction as both an independent variable (see Table 5 & Table 6) and a dependent variable (see Table 3).
Please note these two points:
(i) MLR is used for predicting the value of one dependent variable from the values of two or more independent variables
(ii) a variable cannot be both an independent variable and a dependent variable at the same time

Furthermore, in the revised manuscript, you were conducting some simple linear regressions, where there was only one independent variable and one dependent variable (see Tables 3, 4 & 5).
Validity of the findings: When the statistical methods used were questionable, validity of the findings would be affected.
Additional comments: I find this revised manuscript just as confusing, in particular data analysis and results. Please relook at the statistical methods used to anlalyse your data. Be very careful when MLR could be used.

Reduce the number of tables used.

The manuscript needs English editing.


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: SURVEILLANCE OF TUBERCULOSIS AND TREATMENT OUTCOMES FOLLOWING SCREENING AND THERAPY INTERVENTIONS AMONG MARRIAGE-MIGRANTS AND LABOR-MIGRANTS FROM HIGH TB ENDEMIC COUNTRIES IN TAIWAN
Review round: 1
Reviewer: 1

Output:
Basic reporting: This statistical analyses and results presentation remain not reach the basic standard for a scientific manuscript, so I am not able to verify the validity of this study. I highly recommend the author to find a statistical consultant and go through the analytic plans and the result tables carefully.
Experimental design: NA
Validity of the findings: See basic report
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: SURVEILLANCE OF TUBERCULOSIS AND TREATMENT OUTCOMES FOLLOWING SCREENING AND THERAPY INTERVENTIONS AMONG MARRIAGE-MIGRANTS AND LABOR-MIGRANTS FROM HIGH TB ENDEMIC COUNTRIES IN TAIWAN
Review round: 1
Reviewer: 2

Output:
Basic reporting: Dear Academic editor,

Thank you for inviting me to review this manuscript “Surveillance of tuberculosis and treatment outcomes following screening and therapy interventions among marriage migrants and labor migrants from high TB endemic countries in Taiwan (#47696)”.

I have comments and questions for the authors to improve their manuscript.

Review comments

Major comments
1.	The justification for comparing only treatment outcomes of marriage migrants and labour migrants from TB high endemic countries should explained. Why the authors did not compare the treatment outcome with Taiwanese population data?
2.	The study did not use the same assessment criteria to assess TB trends. They used 1-2 rounds of post-entry TB screening for marriage migrants and 4 rounds of Post-entry TB screening. The authors should justify this.
Minor comments
Abstract
The authors used labor migrant as different comparison groups, how do the authors know marital status of labour migrants?
 Is this post-entry ?
… “with 61% bacteria-positive and 31% smear-positive cases..” what is the difference between smear-positive and bacteria-positive? Smear-positives are also bacteria positive even if they are culture positive.

“TB cure/treatment completion” use either treatment completion or cure rate. Cure rate and completion are different.

In statistics and analysis section

…..“The TB incidence (per 100,000 population) was calculated as the number of newly detected 114 labor migrants with TB during the study period (2012-2015) divided by the population per year”…...
Is the population (denominator) the total population of Taiwan or total labour migrant population? This needs to be clear for the readers

Line # 125-126. The authors estimated the treatment outcomes by considering transferred out cases and treatment completion rate only. For international comparison why the authors did not estimated the lost-to-follow up cases?
Lines # 151, 168, . postentry…is this post-entry? if so ,correct this throughout the manuscript

Why the authors presented both Pearson’s correlation and linear association?

Why the authors did not categorize TB cases as bacteriological confirmed and smear-or bacteriologically negative cases?

Discussion

General comments; no need of presenting the results here in the discussion.  All the statistics were already presented in the results section

Line # 246. ….after 2014 vs. before 2013 being less transfer out.. isn’t this less transferred out? not clear

The authors used only ss- and ss+ cases in the discussion of treatment outcomes. What about bacteriologically confirmed cases; culture positive cases. The authors could consider merging either ss+ and culture positive cases together or include bacteriologically confirmed cases in the discussion.

Limitation
“The proportions of migrants with TB who had reactivation or transmission cases were not defined by the lab”. This statement is confusing and not clear.

Table 1. In clinical characteristics, the authors analysed and reported B+ and SS+ separately. The authors need to make clear whether SS+ cases were included in the B+ cases.
Table 2. Under CXR; “Abnormal w/o cavitation” and “Abnormal w/ cavitation, should be written in full.

Under sputum culture. CC+, and CC- should be made clear for the readers new for the field
Experimental design: Original primary research within Aims and Scope of the journal.
Research question well defined, relevant & meaningful. It is stated how research fills an identified knowledge gap.
Yes

The submission should clearly define the research question, which must be relevant and meaningful. The knowledge gap being investigated should be identified, and statements should be made as to how the study contributes to filling that gap.
Rigorous investigation performed to a high technical & ethical standard.
Yes

The investigation must have been conducted rigorously and to a high technical standard. The research must have been conducted in conformity with the prevailing ethical standards in the field.
Methods described with sufficient detail & information to replicate.

Yes, with minor revision

Methods should be described with sufficient information to be reproducible by another investigator.
Validity of the findings: Conclusions are well stated, linked to original research question & limited to supporting results.

With modification
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: REPRODUCIBLE, PORTABLE, AND EFFICIENT ANCIENT GENOME RECONSTRUCTION WITH NF-CORE/EAGER
Review round: 1
Reviewer: 1

Output:
Basic reporting: The writing was very good, clear and well explained, it was a really pleasant reading. The references were well chosen and representative of the aDNA field, the introduction and background appropriate and the authors clearly show how nf-core/eager fits and contributes to the development of the aDNA field. The manuscript provides an extensive description of all features included in the software and their purpose and the figures and tables are relevant and good supports of the written content in the article (two minor comments below). The manuscript format is appropriate.

The authors provide extensive supplementary data that allow to fully reproduce all presented results and provide all accession numbers for downloading the public data used in the manuscript.

Regarding the figures, my only comments are the following:
Figure 2: The general idea of the figure is clear, but there are some parts that I don’t understand. For instance, I don’t follow the logic of the library names on the left, and how they are pooled across the pipeline. Maybe these names could be more didactic to better understand why there are different merging points. (Writing question about the title: is it Schematic or Scheme?)

Figure 4: I understand that this image is an example of the many schemes that are generated through the pipelines, but maybe it would be nice to show on the side (e.g., Fig 4b), the real plot that would be obtained for this step, so the reader can understand what the schematic image is explaining.
Experimental design: The experimental design and benchmarking strategies chosen were appropriate to demonstrate the performance of the software, and followed a high technical standard. The motivations for developing this software and the gaps that is looking to fill are also well explained. The pipeline provides an efficient, standardized, reproducible way to run multiple software that are commonly used for processing aDNA data, and it incorporates some new features and optimizations that are currently missing in other similar options currently available (e.g., PALEOMIX or EAGER).

Methods are clearly described with all necessary information to replicate (and on top of this, the GitHub site has extensive extra documentation for every single step that can be run in this pipeline). The authors have really done a remarkable effort in making every aspect of the method clear, transparent and well documented, to facilitate a rapid adoption in the field.

My only minor comment on this is the following:
Lines 234-235: Wouldn’t it make sense for the Benchmarking step to also run it with all default parameters normally used in nf-core/eager. This would allow to see whether results are reproduced regardless of parameter optimization. It would be interested to know if same conclusions are reached even without any a-priori information.

I also have the following suggestion for future releases:
It would be great to incorporate an additional step for metagenomic analyses, to eliminate low-complexity sequences (e.g., with BBMask from the JGI BBTools). This will greatly reduce false positives in downstream Kraken2/MALT analyses.
Validity of the findings: The pipeline improves currently available alternatives, and provides a very useful resource for the ancient DNA field, that can continue growing in the future with new features. The authors provide a thorough explanation of every point that is advantageous in this pipeline, while acknowledging aspects that may be considered disadvantageous for some users, but well justifying why it was done this way. It is definitely a great asset for the field.

My only very minor comment on this is the following:
Regarding the exclusion of mapDamage2 from the aDNA evaluation and modification step, I believe that the rationale behind could be a bit more explained given than many researchers in the field continue to use it (e.g., “more performant successor method is now available”, more performant in terms of what? Is DamageProfiler better at every level? A more detailed explanation would help here). For instance, table 1 indicates that Damage Rescaling is partial in nf-core/eager, so how is this managed?
Additional comments: I liked the article and the pipeline a lot, and I believe that it will be a very useful resource for the ancient DNA field. Most importantly, it is built in such a way that will greatly facilitate a continuous growth in the future, by incorporating new features or even be taken by different labs as starting points for building customized solutions optimized for the lab needs.

One minor comment:
- Line 122 and 145: There are two different references for MultiVCFAnalyzer. Is this correct?


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: REPRODUCIBLE, PORTABLE, AND EFFICIENT ANCIENT GENOME RECONSTRUCTION WITH NF-CORE/EAGER
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is well written in professional English. Nothing further to add.
Experimental design: No analyses of primary data is presented in the study.
Validity of the findings: The paper presents a pipeline utilizing known bioinformatic software to perform basic ancient DNA data processing. The pipeline provides many major advantages to the field in terms of usability, scalability, and reproducibility.
Additional comments: Fellow Yates et al present in their manuscript a one-stop-shop analysis pipeline for initial raw ancient DNA (aDNA) sequencing data processing utilizing a wide range of established bioinformatic tools. It is the successor of eager1 (Peltzer et al 2016) and based on nextflow (an omics-dedicated pipeline language). The improvements include (non-exhaustive list) a proper parallisation, ability to merge different types of data per sample (SE/PE, UDG-treatment), command-line usage (but GUI still available) and a significant extension of the software repertoire. Here, most important probably the addition to perform metagenomic analysis. The software and its configuration files are easily portable, which is an important step towards improved reproducibility and can streamline community access to the backbone results of published manuscripts/data. It targets a user base of both versed or inexperienced aDNA scientists, with the latter often without much/any knowledge in programming. To make up for that gap, they provide extensive documentation incl. info-graphics that simplify the interpretation of graphs. That is an important contribution in itself, given that in particular newcomers to the field who use nf-core/eager are prone to fly blindly through the myriads of (default) parameters that have a tremendous impact on their data and its interpretation/troubleshooting.

I performed a simple test run using a SRA file containing a known ancient organism. Set up of the pipeline was easy on a naive HPC system (minor trouble shooting due to SE data). The different report html’s carry plenty of information including explanations for less experienced users. I might have missed it, but there was no table with alignment-based summary stats (%coverage, mean coverage, % 3’/5’ deamination,…), which I would consider a worthwhile addition.

Overall, while the aDNA field is still a niche (expanding though),  I have no doubt that nf-core/eager will take its place as a widely used software for the time being.

I have only a few comments that I recommend to address:
- The authors decided to include the unsupported GATK genotyper. Including an officially abandoned piece of software (especially one that has known biases) seems ill-advised and I suggest to remove it. A simple replacement could be samtools mpileup, which is scalable and together with bcftools generates VCF files for downstream filtering/analyses.
- I recommend to add a main text figure that provides an overview about all the supported bioinformatic tools and how they relate to one another (input/output) and towards what type of analyses/result they lead.

Disclaimer: This review is written by Felix Key. I have co-authored manuscripts with several of the authors stemming from my time at the MPI SHH (’16 - ’18). However, I have no asset of any kind in the nf-core/eager pipeline.


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: REPRODUCIBLE, PORTABLE, AND EFFICIENT ANCIENT GENOME RECONSTRUCTION WITH NF-CORE/EAGER
Review round: 1
Reviewer: 3

Output:
Basic reporting: This is a well written paper, with clear logical progression, and informative figures. The introduction provides adequate background about the unique characteristics of aDNA and cites relevant prior literature. The authors do a convincing job of identifying the need for an updated aDNA pipeline, and clearly outline the areas in which nf-core/eager improves and extends upon prior methods.
Experimental design: The authors have done an excellent job of incorporating current aDNA best-practices into the design and workflow of their computational pipeline. Whilst reasonable opinion might differ about specific choices of tooling and the configuration of some flags, nf-core/eager provides most users with an excellent foundation for processing their aDNA data.
Validity of the findings: The authors commitment to clear user documentation, computational reproducibility and implementation of modern software development practices are to be commended. As the authors correctly highlight, the literature is full of “insufficient 'prose' based reporting” of computational methods. Adoption of high-quality standardised pipelines like nf-core/eager are an important step towards improving the validity of finding across the broader aDNA literature.
Additional comments: Line 321: The link to the user documentation (https://nf-co.re/eager/docs) is incorrect
Line 374: Please provide an ftp link to the NCBI screening database
Line 380: The directory containing the demonstration and benchmarking environments is “content/supplement/”


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: GENOMIC CHARACTERIZATION AND PHYLOGENETIC ANALYSIS OF THE FIRST SARS-COV-2 VARIANTS INTRODUCED IN LEBANON
Review round: 1
Reviewer: 1

Output:
Basic reporting: L28 in the abstract "Presently, and reached almost 15 million cases." This sentence is incomplete and does not make sense.
L30 "it has so far managed the initial SARS-CoV-2 wave", this line needs to be restructured to "it has so far managed to cope with the initial SARS-Cov-2 wave".
Experimental design: The study's main result is a phylogenetic analysis of the strains recovered from isolates obtained from Lebanese patients. There is no mention in the methods section how the short sequenced reads are assembled into whole viral genome sequences to infer a phylogeny. The only detail given was the use of BWA MEM aligner which only aligns sequenced reads to a reference.

What are the justifications for using IQTree as a phylogeny inference? have the authors tried also bayesian methods (such as MrBayes?)? There are many studies benchmarking tree construction software which often show superior quality of RAxML over IQTree.

If the main results of this study are to be based on the inferred phylogeny it is to my opinion some comparisons between different inference tools to be performed.

The long branches in the reported tree is a bit concerning, have the authors tried using different reference viral genomes to map the different strains to?

Was there any particular reason to use SNP-sites? did the authors try using GATK-3?

The methods are missing details on how variants were called to be SNPs, what thresholds were used? and what was done for quality control other than filtering out low quality reads? was sequencing depth taken into account?
Validity of the findings: The findings discussed were consistent with the demonstrated results.
Additional comments: Overall the study offers some insights on how the the novel coronavirus was introduced and spread in Lebanon, the manuscript should warrant publication upon 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: GENOMIC CHARACTERIZATION AND PHYLOGENETIC ANALYSIS OF THE FIRST SARS-COV-2 VARIANTS INTRODUCED IN LEBANON
Review round: 1
Reviewer: 2

Output:
Basic reporting: Line 40: No comma is needed after “which”

Line 53: “myaglia” needs to be written as “myalgia”

Line 66: Lebanese needs to change to Lebanese individuals

Line 74: The date range might be better if written as 21 Feb 2020- 15 March 2020

Line 75:  In “with at”, “at” is redundant

Line 197: Before: “China CDC”; After: “Chinese Center for Disease Control and Prevention (China CDC):

Line 201: “the” in “or the in” is redundant

Line 231: Before: “predominate”; After: “predominant“

Line 240: Before: “entry 614G”; After: “entry of the 614G”
Experimental design: Before: “are also reflective of the situation in regions that lack genomic and epidemiological data, such as Iran.”

After: “are also reflective of the situation in regions that lack genomic and epidemiological data.”

Reason: There are already several studies by Iranian researchers with sequenced patient data.

What are the other applications of this work? If there's other applications, please add. For example, as a preventative measure, for vaccine design, or to show which countries were the first to have the outbreak (e.g. based on fewer mutations).
Validity of the findings: Line 213-220: It would be helpful to add information about the samples, and recent travel history. For instance, Wuhan 412981 (EPI_ISL_412981) was sequenced in Jan 18 2020 (no recent travel to Iran), EPI_ISL_408482 in Jan 19 2020 (no recent travel to Iran), and EPI_ISL_412965 in Feb 2 2020 (recent travel to Iran), in Figure 2, or as a separate table or figure. Also, an unrooted representation of the tree may show the relatedness of the nodes better.

It might be helpful to add Jalview alignments showing some or all of SNVs.
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: GENOMIC CHARACTERIZATION AND PHYLOGENETIC ANALYSIS OF THE FIRST SARS-COV-2 VARIANTS INTRODUCED IN LEBANON
Review round: 1
Reviewer: 3

Output:
Basic reporting: There are several places throughout the text with small language typos that may make it difficult for an international audience to understand. Some examples where the language could be improved include lines 29 and 31.
Experimental design: The work presented by Feghali et al in “Genomic characterization and phylogenetic analysis of the first SARS-CoV-2 variants introduced in Lebanon” is important, timely, and likely to be of interest to a wide audience. It addresses an important knowledge gap as there do not appear to be any similar studies investigating SARS-CoV-2 the area. The approaches are well suited to investigate the source of SARS-CoV-2 in Lebanon and the conclusions (that there were likely multiple introductions) are well-supported by the results. They were very thorough. The weaknesses of the manuscript, if any, can be resolved with some additional clarification and elaboration as outlined below.

Line 81- Do you mean qRT-PCR?
Line 84- I was under the impression that RdRp stood for RNA dependent RNA polymerase. Please confirm.
Lines 87- While the volume is helpful, it would be more meaningful to provide the concentration (if known). For example, 5ul of RNA extract could be 20ng of RNA or 200ng. Were the primers 5mM or 100mM?
Line 104- How was the consensus generated? Is that a feature in BWA-MEM?
Line 107- Can you please provide more information about how the 50 reference sequences were chosen. Did you choose the 50 most closely related sequences?
Line 109- Please include a table of metadata for all 50 reference sequences included in this study. The following data should be included if available: name, accession number, date of collection, location of origin, travel history.
Line 192- Do you mean M33F?
Line 213 and 231- The results of the Pangolin analysis are used to draw significant conclusions. Can you show those results? Even if you just add the lineage/clade to one of the other tables.
Validity of the findings: The conclusions of this paper are well supported by the results. However, there are a few places where additional elaboration is needed.

Lines 152-158- According to your figure, the bootstrap support for the clustering pattern seems to be well-supported. Can you please specify the values in the text or on the figure? Also, please reference figure 2 here.
Line 165- I am not sure what you mean by “S1 exhibited less genomic diversity than S2 and S8 when compared to each other”. Do you mean that S1 was less divergent from the other sequences that it clustered with?
Line 210- Why do you include that there are 2 main lineages if your sequences fall into 3 clades?
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: GENOMIC CHARACTERIZATION AND PHYLOGENETIC ANALYSIS OF THE FIRST SARS-COV-2 VARIANTS INTRODUCED IN LEBANON
Review round: 2
Reviewer: 1

Output:
Basic reporting: looks good!
Experimental design: looks good!
Validity of the findings: looks good!
Additional comments: the manuscript looks much refined after addressing reviewers 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: GENOMIC CHARACTERIZATION AND PHYLOGENETIC ANALYSIS OF THE FIRST SARS-COV-2 VARIANTS INTRODUCED IN LEBANON
Review round: 2
Reviewer: 2

Output:
Basic reporting: For supplementary figure 1, I suggest using a better quality format if possible. You can see the higher quality formats from here:
http://www.jalview.org/help/html/io/export.html
Experimental design: My previous comments have been addressed satisfactorily.
Validity of the findings: My previous comments have been addressed.
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: MYOFASCIAL RELEASE VERSUS MULLIGAN SUSTAINED NATURAL APOPHYSEAL GLIDES’ IMMEDIATE AND SHORT-TERM EFFECTS ON PAIN, FUNCTION, AND MOBILITY IN NON-SPECIFIC LOW BACK PAIN
Review round: 1
Reviewer: 1

Output:
Basic reporting: first of all, i would like to thank the authors for their efforts and interesting manuscript.
yet i have few general comment:
1- the English language used was acceptable, and clear, yet it need extra revision by a native English person.
2- the literature was sufficient and cover adequate knowledge about the topic.
3- figures presented are not in a good quality regarding the resolution. and need some modifications as i recommended in the attached annotated pdf file.
4- the tables missed some data, and i posted some comments on this issue.
5- the article structure is good, and my single comment here is about the lack of randomization. however, i posted few comment i believe they will increase the strengths of the article.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: No additional comments


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

Input:
Title: MYOFASCIAL RELEASE VERSUS MULLIGAN SUSTAINED NATURAL APOPHYSEAL GLIDES’ IMMEDIATE AND SHORT-TERM EFFECTS ON PAIN, FUNCTION, AND MOBILITY IN NON-SPECIFIC LOW BACK PAIN
Review round: 1
Reviewer: 2

Output:
Basic reporting: No
Experimental design: No
Validity of the findings: No
Additional comments: The findings of this study add on support to the existing literature. Future research could concentrate on different perspectives of the treatment and outcome measures.


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: MYOFASCIAL RELEASE VERSUS MULLIGAN SUSTAINED NATURAL APOPHYSEAL GLIDES’ IMMEDIATE AND SHORT-TERM EFFECTS ON PAIN, FUNCTION, AND MOBILITY IN NON-SPECIFIC LOW BACK PAIN
Review round: 1
Reviewer: 3

Output:
Basic reporting: the articles fails to meet your standards in introduction and discussion. too long paragraphs as it were not concise and clear.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: your work is fine but needs rewriting to get into point and to justify your study without writing many mechanisms to explain your idea


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: MYOFASCIAL RELEASE VERSUS MULLIGAN SUSTAINED NATURAL APOPHYSEAL GLIDES’ IMMEDIATE AND SHORT-TERM EFFECTS ON PAIN, FUNCTION, AND MOBILITY IN NON-SPECIFIC LOW BACK PAIN
Review round: 2
Reviewer: 1

Output:
Basic reporting: good
Experimental design: good
Validity of the findings: good
Additional comments: i would like to thank the authors for their patience and work fro improving their manuscript.
my single comment here is regarding the footnotes of the tables, its still not written correctly. foot notes used to explain any abbreviation mentioned inside the table even if it was explained in the main text (the table is an idependant identity). so please add the explanation (full name ) for every letter or abbreviation in the table
examples:
SNAGs, sustained natural .....
VAS, visual analog scale
n, number


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: METABOLITE PROFILING OF ENDOPHYTIC STREPTOMYCES SPP. AND ITS ANTIPLASMODIAL POTENTIAL
Review round: 1
Reviewer: 1

Output:
Basic reporting: Generally, this paper is adequately sourced with appropriate references.
1. English language usage needs careful revision throughout
2. Legibility of figures must be improved. Figures, especially 4, 5, and 6, are blurry with small text that makes them illegible.
3. Supplementary table 1: as the compounds listed are only putative matches for ions and not confirmed, the M/Z values and retention times should be provided to allow these compounds to be identified. The type of analysis yielding this list should also be mentioned in the table caption.
4. supplemental metabolomics raw data Excel file: data need labels. Presumably these are ion abundances?
5. tables 1 and 2: unit needed for retention time, exact monoisotopic mass should be provided instead of molecular weight
Experimental design: This paper is a step toward the discovery of novel antimalarial compounds and excitingly reports extracts of bacterial cultures with antimalarial activity. Producing strains are identified as Streptomyces by DNA sequencing. Mass spectrometry of extracts is used to identify putative antimalarial compounds and metabolomics analysis is used, though the goal of this analysis is unclear.
1. The goal of the metabolomics analysis (ANOVA, PCA, OPLS-DA) is not clear. The authors should clearly explain what they mean by "prioritizing [the] most effective extract" (line 227). Are they prioritizing individual extracts based on uniqueness? Are they trying to correlate individual metabolites with observed activity? Presumably the ultimate goal will be identifying the individual compounds responsible for antimalarial activity in these extracts, but it's not clear how this metabolomics analysis advances that goal. Also, if the goal of metabolomics is dereplication rather than prioritization, this should be reflected in the title of the paper.
2. It's not clear why metabolites from day 14 and day 7 cultures of SUK 48 were chosen for dereplication (lines 241-255). A justification for prioritizing these extracts should be given. It's also not clear why these particular metabolites from these samples were chosen, nor how these ions were identified as [M + H]+ ions. These issues should be rectified.
3. Justification for analyzing these particular samples needs to be presented. Some form of sample collection or strain information should be supplied. If these are of interest because they are endophytic, what is the host plant?
4. The data in Figure 2 should be presented in a table rather than a bar graph. Also, A justification for evaluating each strain using a different series of time points should be provided. Unless there is a compelling reason, both should be evaluated using the same time course.
5. Line 222: method for quantifying generation times needs to be stated
6. Mass spectrometry data handling methods reference a "missing value" (line 176), but we don't know which group that was for which value is missing.
 7. Rephrase to clarify inoculation and culturing protocol lines 93-94: unclear whether there were multiple inoculations at different time points.
8. figure 6: how were these particular strains chosen for comparison? Was there a similarity cutoff? (Methods line 210-211). Other information given beyond genus and species should be defined.
Validity of the findings: 1. The identities of the putative compounds presented in tables 1 and 2 are not well supported by the data provided and the process by which these particular compounds were chosen as IDs for these M/Z values is not adequately explained. MS/MS data and analysis of isotopic patterns should be used for putative compound ID, not just M/Z values as done here. The fact that many of the compounds identified are from plants or Bryozoa rather than bacteria indicates that the IDs are probably incorrect. Further, it is unclear why multiple ions are given the same compound ID and same "tolerance" in tables 1 and 2 when they have different M/Z values.
2. The first paragraph of the discussion (lines 262-270) speculates on highly specific mechanisms to explain growth phase -dependent antibiotic observed in this study. No data presented in this paper supports any particular mechanism, so a more general discussion of production and the function of growth phase would be more appropriate.
3. The fact that both strains were identified as Streptomyces, and the significance of each belonging to a different clade should be discussed. (Lines 296-302)
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: METABOLITE PROFILING OF ENDOPHYTIC STREPTOMYCES SPP. AND ITS ANTIPLASMODIAL POTENTIAL
Review round: 1
Reviewer: 2

Output:
Basic reporting: Ahmad et al. reported anti-malarial activity of Streptomyces bacterial extract and attempted to isolate potent metabolites that might be associated with the drug-like activity. Authors approach to investigate anti-malarial properties of bacterial extract is intriguing. However, authors need to improve substantially the textual content, specifically English needed to be improved throughout the manuscript. Additionally, I have two other recommendations:

1) The resolution of figures 4 to 6 is very poor. It is very hard for reviewer to read the contents of the figures.

2) Please expand all the figure legends and explain the contents for readers.
Experimental design: How many independent biological replicates have been performed for generating bacterial growth curve and anti-plasmodial activity IC50 data ?  Authors should write the details in the experimental section.
Validity of the findings: 1) Line 223-224 Figure 2. Authors stated that anti-malarial potency of SUK 48 at day 14 is more as compared to day 7. However, in figure 2, both time points are close to zero. I suggest authors need re-plot the graph with correct Y-axis, which can demonstrate the observed small differences.

2) Line 223. Authors need to explain in methods or results section how they evaluated anti-plasmodial activity of the bacterial strains. Currently, what authors describe in section “In vitro antimalarial assay” line 99 is incomplete.

3) The asexual blood stages of 3D7 P. falciparum consists of rings, trophozoites and schizont. Authors need to describe at which stage of in vitro culture they incubated the bacterial extracts and for how long (duration of treatment). Does chloroquine treatment were carried out in similar conditions (similar stages and duration of exposure) ?

4) Are there any common metabolites between the extracts of SUK48 and SUK7?
Additional comments: No additional comments