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: HOW BEAVERS AFFECT RIVERINE AQUATIC MACROINVERTEBRATES: A REVIEW
Review round: 2
Reviewer: 2

Output:
Basic reporting: The paper has been improved, focusing on the key messages of the paper.
Experimental design: The title and abstract are much better. Paper objectives are better, and  integrating strong perspectives following the results obtained.
Validity of the findings: Paper objectives are better, and  integrating strong perspectives following the results obtained.
Additional comments: Most of the suggestions made have been taken on board by the authors. I support its publication in its current form.


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

Input:
Title: THE INFLUENCING FACTORS FOR DISTRIBUTION PATTERNS OF RESIDENT AND MIGRANT BIRD SPECIES RICHNESS ALONG ELEVATIONAL GRADIENTS
Review round: 1
Reviewer: 1

Output:
Basic reporting: This manuscript describes resident and migrant bird species richness distribution patterns along altitudinal gradients in South Korea, it is generally well written and easy to read, the results are consistent with many previous studies, and I enjoyed reading it. In the manuscript, however, there are some important weaknesses that need to be addressed.
Experimental design: Methods are not clear. The authors state that they used the same methods and data as in their previous study, but this is very inconvenient for readers. Without checking the previous article, we can’t understand the experiment design. “Materials & Methods” needs to be rewriten and be clearer.
For example, lines 67-69, what is the motivation for excluding the subalpine forest data, what does “minimize the differences in bird communities among forest types” mean? If the study aims to understand the resident and migrant bird species richness distribution patterns at different elevations, why does community matter, or why this community matters that much?
Lines 63-69, how were these plots distributed at different elevations? How did the authors conduct the point counts? Were the sample efforts the same at different elevations?
Lines 79-81, how did the authors measure spring temperature (any specific time to measure or downloaded data from somewhere?), vegetation coverage, and habitat diversity? Please explain more about habitat diversity and how did the authors measure horizontal habitat heterogeneity?
Figure 4, please make it clear what are the values represent (-0.69, 0.33, 0.75, 0.26...)
In the discussion, lines 179-181, the authors first mentioned about “15 habitat types”, is it horizontal habitat heterogeneity? If it is, please provide the details in the methods.
Validity of the findings: In this study, habitat diversity has a significant effect on the resident species richness but not on migrant species richness. Rather than seeing a summary of this result (habitat as a whole), I would like to see which habitat(s) contributed more in the model, and understand well how habitats affect the two types of species richness.
Additional comments: Overall, I would like to see a more detailed and independent manuscript of this study. I hope my comments are 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: THE INFLUENCING FACTORS FOR DISTRIBUTION PATTERNS OF RESIDENT AND MIGRANT BIRD SPECIES RICHNESS ALONG ELEVATIONAL GRADIENTS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The language needs to be checked (see eg the first two sentences of the abstract), the references to the literature are often approximate if not wrong, and the papers refer to mechanisms whereas it is based on correlations and only one year of data.
Experimental design: The data (already analysed in other papers) are derived from a snapshot study (one year, 15 min point counts). This will lead to high uncertainty in estimates of species richness - detectability among other sources of biases should be assessed.
Validity of the findings: The models used (structural equation models) do not bring any new information as used. The authors need to frame their questions so that the models can in fact help answering them. Right now, there is very little added value compared to previous papers published on the same data by the same authors.
Additional comments: Latitude and altitude (or rather elevation – see Körner 2007) are not variables that can affect directly species – the effects is through their associations with e.g. temperature, photoperiod, precipitation etc. This paper attempts to disentangle these effects using a survey done in in one year (2015) and already analysed in other papers by the same first author (Kim et al. 2018, 2019, 2021). As such this I a very limited dataset, particularly for migrant species that can fluctuate much between years. The difference with previous papers is the use of structural equation models (Figure 1) – but see my comment below. The paper also claims to investigate mechanisms (eg the title), but the paper only investigates correlations based on very indirect measurements (habitat diversity etc).
You write that “Herrera (1978) discovered that the number of migrant passerine birds increased with increasing latitude in Europe.” – this is wrong, Herrera investigated the proportion of migrant species, this is not the same thing (there are far fewer bird species in northern, subarctic Europe than in southern Europe). And Herrera contrasted the results obtained in Europe to those obtained in North America by MacArthur. You need to carefully assess the way you refer to the literature, it is often at best approximate.
Species richness should be estimated using one of the many methods adapted to your survey methods, to account for differences in detectability among species and habitats. As far as I could understand, there was only one point count of 15 min, so I would expect a rather large uncertainty in species richness estimates. There is a large literature on this – see Yoccoz et al. 2001 for some examples, and more recent books by e.g. M. Kéry for different modelling approaches.
You use a SEM (structural equation model), but it does not bring any new information as you could have obtained exactly the same results by fitting multiple regression models with resident/migrant species richness as a response variable and either mean spring temperature or coverage and habitat diversity as predictors, and comparing how well these models predict species richness (but this was already done in Kim et al. 2018 as far as I could judge). What could be interesting is to ask if for example temperature may have a direct effect on richness when the indirect effect on habitat variables are taken into account (investigating such direct/indirect effects is one of the main reason to use SEM or graphical models, see eg Grace et al. 2014). In other words, are the effects you estimate in models a and c completely accounted for by the effects you estimate in model b and d? Given that the models b and d do not fit, it is probably not the case. Note also that it is redundant to have elevation in all models as the coefficients by construction will be the same. Note also that you can investigate direct/indirect effects of elevation using the same tools.
You show nonlinear effects on Figure 5, but your models are all linear, right? You need to be consistent.
Check the language – for example the first sentence does not make sense with “latitudinal and altitudinal resident and migrant” – I guess you mean the latitudinal and altitudinal patterns... And the second sentence is more or less a copy and paste of the first, etc.

Nigel G. Yoccoz

Refs
Grace, J. B., Adler, P. B., Harpole, W. S., Borer, E. T., & Seabloom, E. W. (2014). Causal networks clarify productivity-richness interrelations, bivariate plots do not. Functional Ecology, 28(4), 787-798. doi:10.1111/1365-2435.12269
Kim, J.-Y., Lee, S., Shin, M.-S., Lee, C.-H., Seo, C., & Eo, S. H. (2018). Altitudinal patterns in breeding bird species richness and density in relation to climate, habitat heterogeneity, and migration influence in a temperate montane forest (South Korea). PeerJ, 6, e4857. doi:10.7717/peerj.4857
Kim, J.-Y., Seo, C., Hong, S., Lee, S., & Eo, S. H. (2019). Altitudinal range-size distribution of breeding birds and environmental factors for the determination of species richness: An empirical test of altitudinal Rapoport’s rule and non-directional rescue effect on a local scale. Plos One, 14(1), e0203511. doi:10.1371/journal.pone.0203511
Kim, J.-Y., Shin, M.-S., Seo, C., Eo, S. H., & Hong, S. (2021). Testing the causal mechanism of the peninsular effect in passerine birds from South Korea. Plos One, 16(1), e0245958. doi:10.1371/journal.pone.0245958
Körner, C. (2007). The use of ‘altitude’ in ecological research. Trends in Ecology and Evolution, 21, 569-574.
Yoccoz, N. G., Nichols, J. D., & Boulinier, T. (2001). Monitoring of biological diversity in space and time. Trends in Ecology and Evolution, 16(8), 446-453.


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

Input:
Title: THE INFLUENCING FACTORS FOR DISTRIBUTION PATTERNS OF RESIDENT AND MIGRANT BIRD SPECIES RICHNESS ALONG ELEVATIONAL GRADIENTS
Review round: 2
Reviewer: 1

Output:
Basic reporting: I reviewed the earlier version of this manuscript and I find this revised version a considerable improvement. I appreciate the authors’ efforts to make this version more understandable. Methods of data analyses have changed and as a consequence some results have changed as well. For example, habitat diversity is not significant with pSEM, but the other main results remain the same.

However, from reading this version, I have the feeling of the authors being somewhat careless with the writing. There are many typos throughout the manuscript, and some sentences are repeated and redundant. As a minor suggestion, I suggest the authors to consistenly use either altitude or elevation in text and figures. Overall, although this manuscript has improved with the revision, it still requires a careful read and some corrections.
Experimental design: The method of vertical coverage measurement remains unclear, how did the authors measure the coverage? If the plot size is 50 m radius and all of them with two layers coverage measurement, it is a lot of work, I guess ArcGIS doesn’t provided vertical coverage.
Validity of the findings: In this version, a new hypothesis has been put forward -- interspecific competition. Although the idea has merit, I would be very conservative talking about interspecific competition in this study. First, I don’t see any direct evidence of competitions between residents and migrants, as they mentioned in the Introduction lines 30-32, the distribution pattern of residents and migrants could just be due to their habitat or food preferences. Maybe there is competition, but please provide the evidence for it. For example: how much overlap on diet, habitat preferences, etc...? This information can be found from Birds of the world: https://birdsoftheworld.org/bow/home. This could provide some useful information about potential “interspecific competition”, but this is a suggestion that the authors could consider.

Lines 214-216, I just see the distribution pattern but not “proportion of migrants and residents” in the results.

Lines 163-168, I am confused by the discussion, the authors say that altitudinal patterns of species richness have shown a mid-peak but not for residents and migrants. The following sentence says “both resident and migrant species richness repeated the fluctuation and then showed a decreasing pattern in each direction, starting at 700 m”. This is a bit self-contradictory to me. In figure 2, we can actually see a “soft” mid-peak around 700 m, but the authors call it “mid-point”, is it actually the same? By the way, in figure 2, “(a)” is missing.
Additional comments: This experiment was well designed in general as at least two papers have been published from it, and I like the attitude of authors wanting to maximize the value of the data. But I must say I was expecting to see more values from this study and some deeper thinking about the findings of the study. As it is now, the study is still limited in terms of the depth of the research questions addressed.


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

Input:
Title: THE INFLUENCING FACTORS FOR DISTRIBUTION PATTERNS OF RESIDENT AND MIGRANT BIRD SPECIES RICHNESS ALONG ELEVATIONAL GRADIENTS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The language is still poor in many places (unclear sentences, typos etc).
Experimental design: the analyses do not account for year-to-year variation or detectability.
The statistical model is poorly justified and some components are arguably wrong.
Validity of the findings: Given the limited scope of the data and the poor justification for the statistical model, the findings are unlikely to be robust.
Additional comments: I am sorry to write that this revision must have been done a bit too quickly and does not answer my main concerns.
-	replacing mechanisms by causes does not make it better when the point is that you are looking at correlations based on a small dataset and you cannot assess causes based on this. You may say that your statistical model is helpful in making predictions in a given context (and since you have only one year of data the validity of such predictions is hard to assess). Going from a SEM to assessing causes require both more data and evidence that the structure of the model may reflect the actual causal mechanisms. For example altitude (you should use elevation – see Körner’s various papers) has indeed a causal relationship with temperature (the physical basis is well-known), but the causal relationship with vegetation (different from the effect of temperature as your figure seems to imply) is far from being clear – and seems even wrong (ie spring temperature is related to vegetation).
-	You have now more or less copied and paste the description of the survey methods from Kim et al. (2018). But regarding the uncertainty in the description of bird communities, you only write “Therefore, our one-year dataset might possess an uncertainty that year-to-year variations were not verified in the present study.”. Besides the fact that the sentence does not really make sense, the problem is that this year-to-year variation exists (not that it might exist) and that it is known to be large in most bird communities. Moreover, standardization of methods helps in reducing variation, but it does not suppress it or remove biases due for example to different species detectabilities. I have participated myself to field campaigns monitoring bird communities and the variation from day to day can be large, even if the counts are made at the same time, with the same weather etc. Just design your study so that you can account for it (e.g. by having repeated counts). There is now a very large literature on bird communities based on occupancy models showing that even with highly standardized data, detectability is an important issue.

There are still many typos that reflect that the revision was done too quickly – eg in the abstract:
l. 27: higher overstoy vegetation
l. 28: birds, , higher overstory
In the changes made l. 82-83 of the word document:
“are poplated by coniferous shrubs. Because, standardized sampling effort per vegetation types are an importnat part of altitudinal studies”
etc.


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

Input:
Title: THE INFLUENCING FACTORS FOR DISTRIBUTION PATTERNS OF RESIDENT AND MIGRANT BIRD SPECIES RICHNESS ALONG ELEVATIONAL GRADIENTS
Review round: 3
Reviewer: 1

Output:
Basic reporting: Some sentences are still unclear or have a meaning different from what is intended, for exemple:
End of abstract “demonstrated that mean spring temperature and overstory vegetation coverage were more explanatory than other variables”. What do you mean? A variable is explanatory or not, do you mean that they explain more of the variation in species richness? As all non-native English speaker, we struggle with the language, but it should not prevent aiming at clear sentences.
l.61: “however, limited studies have discussed examined altitudinal patterns…”. I guess you do not mean that the studies were limited (that is lacking rigor or coverage), but that there were a limited number of studies.
You have removed causes from the title and abstract, but you still refer to causal relationships in the text, e.g. l 133 ff (or Table S1 and S2):
«Our conceptual model models examined the causal relationships among mean spring temperature, vertical habitat heterogeneity, or and horizontal habitat heterogeneity: 1) altitude would directly affect mean spring temperature, vertical habitat heterogeneity, and horizontal habitat heterogeneity”
Altitude may have a causal effect on temperature but is unlikely as such to have a causal effect on heterogeneity (i.e. as you explicitly mention temperature, do you mean it would be through another mechanism, ie atmospheric pressure, precipitation, forest use?? See Körner 2007). You are exploring correlations (that could be partial etc – as in the original papers by Wright), but don’t call them causal when there is no causal mechanism underlying them and well supported by available data.
Note also that the differences between significant and non-significant regression parameters (ie your tables S1 vs S2) are not due to using a SEM but comparing multiple regressions to univariate linear regressions.
Check the language for example L 163: “Migrant species richness was decreased with mean spring temperature and increased with overstory vegetation coverage”. Something like “Higher mean spring temperature and overstory vegetation coverage increased migrant species richness”. Check the whole results paragraph.
In Tables S1/S2, no explanation is given of what is in the tables (beta, critical value, standard estimate)
The paper by Körner about using elevation rather than altitude is McVicar and Körner (2013). Many people still use altitude and not elevation but I agree that elevation is probably the right word to use.
Körner, C. 2007. The use of ‘altitude’ in ecological research. Trends in Ecology & Evolution 22:569-574.
McVicar, T. R., and C. Körner. 2013. On the use of elevation, altitude, and height in the ecological and climatological literature. Oecologia 171:335-337.
Experimental design: See previous comments - the authors now acknowledge that for example one year is a limited study, but with a rather strange sentence "Therefore, our one-year dataset might possess some  uncertainties  as year-to-year variations were not verified in the present study". You cannot "verify" year to year variations.
Validity of the findings: There is confusion regarding the differences between the simple linear regressions and the multiple regressions underlying the results of pSEM. Also the causal language needs to be removed .
Additional comments: No additional comments


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

Input:
Title: THE INFLUENCING FACTORS FOR DISTRIBUTION PATTERNS OF RESIDENT AND MIGRANT BIRD SPECIES RICHNESS ALONG ELEVATIONAL GRADIENTS
Review round: 3
Reviewer: 2

Output:
Basic reporting: Although I found this work interesting, I feel there are still a few areas that need clarity whether because of English language improvement or because just a clearer explanation is needed.

Parts of the introduction could be improved by specifying the nature of the relationships (that is the results) of the multitude of studies mentioned so that it’s not just a list. For example:
L52 how do temperature gradients influence distribution of resident and migrant spp?… the next sentence immediately transitions into a different factor completely so that nothing is learned about the relationship/actual result.

L58 “…as the food resources make them unsuitable for resident species” Why? As is, this sentence is confusing.

L69… Confusing sentence, suggested improvement “However, the hypotheses tested, which include the attraction hypothesis that states ???? and wide-ranging bird groups, were not applicable to bird species distribution along the altitudinal gradient.”

L79 modify what is in parenthesis to: “understory and overstory vegetation coverage*. Otherwise, it is confusing why coverage would represent vertical heterogeneity when it is inherently a 2-dimensional variable.

L80 add “…(habitat diversity) using linear regression and piecewise structural equation models.” To specify the methods used.

L80. You state that your conceptual model is shown in Fig1. THIS IS INCORRECT. As is, the conceptual figure is currently Figure 2. I suggest you move your conceptual figure to indeed be figure 1, so it corresponds with the text. I was a bit surprised to encounter this type of careless error at this stage in the review process.
Experimental design: I am surprised that the authors did not include a map of the study area showing the plots (experimental design) so that readers better understand this aspect (and also appreciate the amount of field work that seems to have gone into this study). This is especially because you already have GPS coordinates.

L85 replace ‘performed’ with ‘undertaken’ and add ‘located within Jirisan National Park…”
L88 end of that sentence should read “which include ridges populated by coniferous shrubs”
L115 delete “(richness)” because richness always refers to number of species not to different habitat types.
L119 It is very strange to include roads as a habitat type. Perhaps add land use/habitat types to refer to the subcategories.
L135 Make the : into a period to end the sentence. I suggest starting the next sentence with “We hypothesized the following: 1) altitude….”
Validity of the findings: L176 “we are still unsure why altitudinal patterns…” This is not sufficient. Can you offer explanations based on your analysis of that study and the literature.
L178 did you intend to finish the sentence clarifying that the absence of the mid-peak in this study? If so, modify to “…did not show a mid-peak in this study.”
L180 This sentence could be clarified by modifying as follows: These results demonstrated that neither resident species nor migrant species singularly affected the mid-peak pattern, and the mid-region which had the highest species richness could adequately accommodated both resident and migrant species.
L218 – 221 You state the main result of the linear regression models independently from the pSEM. Add a sentence that consolidates these results, given you state in L217 that the results of the two modeling approaches “were considerably different”.
L221 that states “the pSEM analyses showed that temperature had a considerable effect on dist of resident species, and the effects of other variables were negligible.” Seems to be incomplete compared to your last sentence of the conclusion L236 that states “However, the results of pSEM analyses, …showed that mean spring temperature and overstory vegetation were more explanatory than other variables.” So is overstory vegetation as an influential factor missing in L221?
Additional comments: In your abstract, your first words read a bit odd, I recommend you replace the word ‘or’ with ‘and’ to read “Latitudinal and altitudinal patterns….”

Table 1 Include an additional column with the functions/equations of the models you used or at least the important coefficients. Alternatively, include the equation in your figure showing the ‘relationship between BIRD species richness and altitude.

Fig of the Conceptual Scheme – To avoid repetition with Fig 4 of the pSEM, I only see value in retaining this figure if you represent your hypotheses, ie. your expectations of positive or negative relationships, by adding a + or – sign on the arrows or showing arrows for positive expected relations in black and negative expected relationships in red (or grey).

Figure 3 Altitudinal patterns of resident and migrant spp richness. Overall, a nice figure, but can you explain the meaning of the dots in your figure text.

Figure 4, modify the last sentence of your figure text description to “Model-fit statistics (Fisher’s C and P-value) for the pSEM are given.” A note about the arrows, typically the magnitude of the standardized regression coefficient is represented by the thickness of the arrows. Can you adjust your arrow thickness to reflect this? If you will be using color in your figures, might as well make the negative relationships red or grey and the positive relationships black as is typically done for pSEMs.

Figure 5 Consider modifying figure text description to something like “Schematic representation of convergent response of two quadratic richness curves along altitude to help visualize the altitude with peak richness.” I also recommend distinguishing which curve is for resident bird species and which is for migrant bird species. This can be done by directly labeling, changing the line style or using color to distinguish the curves.


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

Input:
Title: THE INFLUENCING FACTORS FOR DISTRIBUTION PATTERNS OF RESIDENT AND MIGRANT BIRD SPECIES RICHNESS ALONG ELEVATIONAL GRADIENTS
Review round: 4
Reviewer: 1

Output:
Basic reporting: The authors have mostly answered my previous comments, and the language has been improved.
Experimental design: The authors refer to the limitations of the study, and the methods are sufficiently well described
Validity of the findings: The data are limited but can still contribute to a wider assessment of associations between elevation and bird communities
Additional comments: No additional comments


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

Input:
Title: THE INFLUENCING FACTORS FOR DISTRIBUTION PATTERNS OF RESIDENT AND MIGRANT BIRD SPECIES RICHNESS ALONG ELEVATIONAL GRADIENTS
Review round: 4
Reviewer: 2

Output:
Basic reporting: The manuscript is improved. But, I feel there are still a few areas that need clarity whether because of English language improvement or because just a clearer explanation is needed. It was unfortunate that the line numbers in the rebuttal did not match the lines in the new manuscript pdf. In the future, just accompany your explanation/justification with a copy of the modified sentence into the rebuttal letter directly.

L52 It is good to see implementation of the recommendation. For clarity, please modify your sentence to read: “Elevation-based temperature gradients are the most important factor that can influence the distribution of resident and migrant species by affecting bird fecundity and levels of parental care in breeding birds (Evans, Warren & Gaston, 2005; Elsen et al., 2021; Badyaev & Ghalambor, 2001)”

L71 elevatinal – correct your spelling

L73-76 suggested for clarity: ”However, this heterospecific attraction hypothesis and contribution of the group with the widest range were not applicable to bird species distribution along the elevational gradient, nor towards explaining the mid-peak pattern.”

L76 to 79 Having gone back to the original Kim et al 2018 paper, I now realize that difference between the previous study and this one. I think that you need to explicitly mention somewhere in the last two paragraphs of the introduction that Kim et al detected this mid-peak spp richness pattern as a function of elevation for migratory and resident birds grouped together overall. In this paper, it seems like you all are now dividing that data into two groups: the resident spp and the migratory spp to “gain a more thorough understanding of what might explain the pattern”.
Experimental design: I still feel a simplified version of your original map, or at least tell the reader “for a map refer to Kim et al 2018. Having in this m.s. directly could help orient the readers to the experimental design of this work (and just generally to help orient readers without having to go digging).
Validity of the findings: L182 fix word order from ‘quadratic negative relationship’ to ‘negative quadratic relationship. Do the same for the positive one.

L186 I think this first paragraph of the discussion is really confusing. Since two of the authors are in both papers and the same dataset was used in both papers, it seems that you all should be best poised to resolve “why elevational patterns of spp richness were found to have a mid-peak in the previous study…” but not in the current one. I still think it is not sufficient to say ‘we are unsure why the difference…’.

L189 You state “According to our results, for two intersecting quadratic curves, which meet at the mid-point, the sum of the center regions was greater than the sum of the side regions” Doesn’t this result explain and support the mid-peak pattern identified in Kim et al 2018, where the grouped data resulted in the hump? It seems to me like this indicates some support of that mid-peak pattern (and your figure 5 explains the logic of why this is so). So I remain confused to why you keep saying that the results of the previous study and this one are contradictory.
Additional comments: Figure 3 You have still not stated what the meaning of the dots in your figure text. Do these signify significance? If so, at what p value, etc.


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: PHYLOGEOGRAPHY OF AMYGDALUS MONGOLICA IN RELATION TO QUATERNARY CLIMATIC ARIDIFICATION AND OSCILLATIONS IN NORTHWESTERN CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The English language should be improved to ensure that an international audience can clearly understand the text. Here some examples where the language could be improved:
L16 – that is occurred | that occurs
L29 – have experienced | to have experienced
L46 – mosaic fragment | fragmented mosaics? Mosaic fragmented landscapes?
L61 - ... occurs from | … that occurs from …
L64 – concentrate | concentrates or is concentrated
Experimental design: , I found their manuscript lacks more robust analyses to support some statements. Thus, to better support their results about the restricted gene flow between western and eastern groups I would recommend the implementation of demographic analyses that explicitly test it. Several approaches could be used to draw demographic models. For instance, an approximated likelihood framework could be used to evaluate thousands of distinct models. A relatively recent tool is PHRAPL (https://phrapl.github.io/). Here are two papers that used it to infer demographic models:
Oliveira et al. 2018. Phylogeography of Muller's termite frog suggests the vicariant role of the Central Brazilian Plateau. Journal of Biogeography. 10.1111/jbi.13427
Everson et al. 2020. Speciation and gene flow in two sympatric small mammals from Madagascar, Microgale fotsifotsy and M. soricoides (Mammalia: Tenrecidae). Molecular Ecology. 10.1111/mec.15433
A second alternative is implementing an Approximate Bayesian Computation (ABC) approach. DIYABC (http://www1.montpellier.inra.fr/CBGP/diyabc/) and PipeMaster (https://github.com/gehara/PipeMaster) are just two tools off the top of my head that are relatively easy to understand and to be used, with good tutorials available. Here are two papers that used them:
Garg et al. 2020. Last Glacial Maximum led to community-wide population expansion in a montane songbird radiation in highland Papua New Guinea. BMC Evolutionary Biology. 10.1186/s12862-020-01646-z
Thom et al. 2020. Climatic dynamics and topography control genetic variation in Atlantic Forest montane birds. Molecular Phylogenetics and Evolution. 10.1016/j.ympev.2020.106812
And, of course, the authors could implement their own ABC approach using the ‘abc’ package, from R (the vignette: https://cran.r-project.org/web/packages/abc/vignettes/abcvignette.pdf)
Another exciting path in model-based phylogeography is machine learning, although I am not sure if so few loci are right for this kind of analyses. The authors could be inspired by these papers:
Flagel et al. 2019. The unreasonable effectiveness of convolutional neural networks in population genetic inference. Molecular Biology and Evolution. 10.1093/molbev/msy224
da Fonseca. 2020. Phylogeographic model selection using convolutional neural networks. Molecular Ecology Resources. 10.1111/1755-0998.13427
The author also discuss that the environmental heterogeneity promotes differentiation between the two groups. The authors should also implement some analyses to support this statement. I recommend the generalized linear mixed modelling (GLMM) approach to test whether population genetic structure is driven by the environment or other variables. Refer to these papers for some examples:
Dantas-Queiroz et al., 2021. Underlying microevolutionary processes parallel macroevolutionary patterns in ancient neotropical mountains. Journal of Biogeography. 10.1111/jbi.14154
Lexer et al., 2014. Genomics of the divergence continuum in an African plant biodiversity hotspot, I: drivers of population divergence in Restio capensis (Restionaceae). Molecular Ecology. 10.1111/mec.12870
Validity of the findings: Zhang et al. investigate the phylogeography of Amygdalus mongolica, a shrub species from the northwestern China, a region with multiple fragmented environments. The selected species has the potential to shed light on how the last glacial and interglacial climatic fluctuations shaped the demographic patterns of species that occur on this region. As their main result, the authors found that the current phylogeographic structure of A. mongolica is mainly derived from the allopatric divergence of isolated lineages due to expansion of arid environments over the Pleistocene, yielding potential local adaptive differentiation between the fragmented groups.
The authors use genetic markers from plastidial and nuclear genomes, but also implement spatial analyses in their methods. Although the use of so few loci today is seen with skepticism, they were capable of extract relevant information from their limited dataset.
However, I found their manuscript lacks more robust analyses to support some statements. Thus, to better support their results about the restricted gene flow between western and eastern groups I would recommend the implementation of demographic analyses that explicitly test it.
Additional comments: Minor issues:
•	The Introduction is quite small, lacking a more robust rationale of the background of the manuscript. Can you provide more details about the studied region? More evolutionary studies developed throughout these mountains? What are the geological, palynological data that support the view that those mountains weren't covered by an ice sheet over the lgm?
•	L15-16 – Amygdalus mongolica, a relict and … | Amygdalus mongolica is a relict and …
•	L45 – have caused drier climates … | Led to a drier climate, yielding a mosaic of fragmented landscapes
•	L46 – to the shrink … | to the shrink of what?
•	L46-49 – excessive use of ‘fragment’. Also, this sentence is quite confused. fragmented landscape drove fragment distribution restricting gene flow between fragmentations?
•	L66-67 – a Tertiary Miocene relic plant of the Ancient Mediterranean … | Can you provide a reference for this statement?
•	L90 – Remove “According to this study”
•	L100-101 – which containing an abundance of genetic variation… | Can you provide a reference for this statement?
•	L122 – defined groups | which groups?
•	L115 and L125 – please, cite R accordingly.
•	L224 – mainly distribute | are mainly distributed
•	L237 - I wouldn't say that 0.65 is a high posterior value, as stated in your figure 4. Can you inform why did you choose such threshold?
•	L249 – And | Besides
•	L249 - Bayesian skyline plot (BSP) result was also consistent with species expansion (Fig. 6). | Was it? The panels of figure 6 do not show any postglacial expansion, except maybe for the overall analysis using ndna
•	L331-345 - The conservation approach, although important, seems to be a little disconnected from the 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: PHYLOGEOGRAPHY OF AMYGDALUS MONGOLICA IN RELATION TO QUATERNARY CLIMATIC ARIDIFICATION AND OSCILLATIONS IN NORTHWESTERN CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is in general understandable, however some sections are not clear. The Introduction has the right amount of information, while Results need a more detailed explanation. Some Figures have good quality, however, figures 3 and 7 need to be reformatted and/or are not properly described.

Most of the software references are wrong.

Genbank accession numbers do not correspond to the studied species, this should be updated in NCBI or explained in the manuscript.
Experimental design: Research questions are well defined and relevant. The proposed analyses are in accordance with the objectives. The number of markers, the sample number, the analyses in general fulfill the PeerJ standards. Methods are well described and seems to be reproducible.

Overall, analyses are adequate, however some suggestions are listed below.
Validity of the findings: The findings and their interpretation are more or less well presented. However, some results need to be explained. For example, there is no mention in Results about gene flow, and the genetic landscape figure is not described.

The conclusions are connected to the objectives, and apparently supported by the results.

I believe that this work has relevant results. However, the manuscript needs some work, and some parts are overstated and should be reconsidered. For example, in line 246: "postglacial range expansion had been demonstrated in the total populations" while this is in contradiction with the previous results, please avoid the use of this kind of expressions.

Nevertheless, I consider that this work is an important contribution to the management of an endangered species. The proposal of protection areas gives the manuscript practical recommendations.
Additional comments: Consider to change the order of Results. First present the distribution of the haplotypes and then the genetic structure.

Aside to Barrier, consider to use the SAMOVA progam (http://cmpg.unibe.ch/software/samova2/) to statistically identify the number of genetic clusters.

The gene flow estimates were not presented in Results. Also, for the estimation of gene flow use a more robust method like migrate-n (https://peterbeerli.com/migrate/).

The authors state (Lines 212-214): "The genetic landscape shape interpolation surface plots of cpDNA and nDNA sequences indicated significant genetic divergence
occurred between the Western and Eastern regions of A. mongolica (Fig. 7)" What "significant genetic divergence" means? Based on that figure how did you get to this conclusion?

Change the order of the Figures as Fig. 7 is presented before Fig. 4.

Which tree-visualization software did you use?

How heterozygous sites for nuclear genes were verified and codified?

Please present the maps potential distribution based on MaxEnt as supplemental material.

Specific comments

Line 109. Check the ClustalX reference. You can see this paper to corroborate software's year and version: Chenna, R., Sugawara, H., Koike, T., Lopez, R., Gibson, T. J., Higgins, D. G., & Thompson, J. D. (2003). Multiple sequence alignment with the Clustal series of programs. Nucleic acids research, 31(13), 3497-3500.

Line 114. This reference is for Arlequin not for DNAsp, please correct.

Line 118. This reference is for TCS not for HAPLONST. HAPLONST site (http://www.pierroton.inra.fr/genetics/ labo/Software/index.html)

Line 120. The correct reference is "Slatkin, M. (1985). Gene flow in natural populations. Annual review of ecology and systematics, 16(1), 393-430."

Line 121. There should be specified in methods how the groups were defined for AMOVA. Actually, this should be done also for gene flow an the ht and hs

Line 123. The reference for Network is missing.

Line 125.  The reference is wrong.

Line 139. The reference for MEGA X is wrong, please check the software manual.

Lines 140, 144, 166. These references are wrong.

Line 154. I believe that this paragraph should be in line 157.

Line 171. Missing reference.

Line 207. Use lower case for HT and HS as described in methods.

Please include in the text the confidence intervals for divergence estimates.

Lines 244-250. This results are contradictory, and this should be addressed in Discussion. Check if the Skyline plots are plotted from present to past (that is the default), if so, these behavior suggests a population size contraction. Also, the values of the estimates of the effective sizes along their intervals as well as the time of the population size change should be reported.

Figure 1c and 1d. The polygons represent Delunay triangulations? Please especify.

Figure 3. Although 3D components are visually appealing, their interpretation may be ambiguous due to the rotation of the axis. Please use just two components, and use more plots if more than two components are needed to be plotted.

Figure 4. Add the scale bar and specify the units.

Figure 7. It is not clear how the z-axis should be interpreted. It is scaled? It appears to have negative values as it shows "peaks" and "valleys". This does not make sense as all values should have the same sign.


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: PHYLOGEOGRAPHY OF AMYGDALUS MONGOLICA IN RELATION TO QUATERNARY CLIMATIC ARIDIFICATION AND OSCILLATIONS IN NORTHWESTERN CHINA
Review round: 2
Reviewer: 1

Output:
Basic reporting: In general, the manuscript is understandable; however, the English still needs some polishing. See comments for examples.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: The present version of the manuscript shows notable improvement, and most of the comments were properly assessed. However, there are some points about the demographic analyses that still need clarifying.

Line 289:
"But postglacial range expansion had been demonstrated for the overall populations and two groups by the unimodal mismatch distribution"
I'm not sure if the range expansion is demonstrated. Please, tune down this kind of categorical statement, use "indicated" or "suggested."

In line 293, the authors state:
"However, only the Bayesian skyline plot (BSP) result of overall populations of nDNA was consistent with species expansion."

These results should be presented and interpreted as they are: the three tests for the cDNA displayed an effective size contraction, while the nDNA showed a slight size change by group, and the overall analysis displayed a contraction followed by small population growth.
At this point, it is needed to consider: What is the demographic signal expected in the glacial scenario?  If my interpretation is correct, there should be a population contraction caused by the non-favorable conditions followed by a recent range expansion; however, only the contraction signal may be recovered if the expansion is very recent. Thus, the BSP results are somewhat in agreement with the authors' premise. Nevertheless, there are some questions left: Why are discrepancies between the markers? Maybe these are the consequence of differences in the markers' intrinsic effective size (haploid plastid vs. nuclear) and/or in mutation rate? Consider these points to be addressed in the Discussion.

Some specific comments:

Please, in Figure 1, include a mini-map showing the location of the area of study on a broader scale.

The legend of Figure 4 has a duplicated sentence.

Line 45. Consider splitting the sentence  "plant growth. For example,".
Line 74. remove "the" in "...2015), the altitude more than ...".
Line 75. remove the comma in "..Plateau), ".
Line 76. Remove "And" and "which".
Line 77. Add "by" "..in valleys, and by the Helan..".
Line 105. Consider rephrasing as "..sites are the same as our team's previous study..".
Line 106. Replace "including 3" with "including three".  Remove "..are presented in Table 1." an just use "(Table 1)".
Line 137. Correct the format of the parenthesis in "(GST, NST)".
Line 138. Remove "using Permut 2.0".
Lines 106,105,165,218,219,232. Check the spaces before and after parenthesis.
Line 172. Replace "burn in" for "burnin" or "burn-in".
Lines 174-183. Maybe you should state at the beginning of the sentence that all these tests were implemented with Arlequin.
Line 293. Add "the"  before "Bayesian".


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: PHYLOGEOGRAPHY OF AMYGDALUS MONGOLICA IN RELATION TO QUATERNARY CLIMATIC ARIDIFICATION AND OSCILLATIONS IN NORTHWESTERN CHINA
Review round: 3
Reviewer: 1

Output:
Basic reporting: The authors addressed all the previous comments. Also, this version shows a notable improvement; however, there are some details that should be addressed. For example, spaces between words and parenthesis are frequently missed. Please see the suggestions for details.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Line 45. There is an incomplete reference, and the phrase should start with a capital letter.
Line 55. Consider changing "There is now" to "Currently, there is"
Line 66. Remove "of" and replace it for a coma.
Line 67. Add spaces before parenthesis in "forests(Zhang" and "slopes(Zhang"
Line 87. Add a space after "sorting;"
Line 106. Change "Individual plants sampled grew at" for "Individual plants were sampled at"
Line 121. There is a mistake in "Ma(Ma et al"
Line 124. The reference of PHASE software is missing in the text and in the References section. Please rephrase this sentence; it is not clear.
Lines 134-137. Were both programs used to estimate GST and NST? I believe that one was for the estimation and the other for the significance; please clarify.
Line 162. Change "Fig Tree" for "FigTree" and add the reference.
Line 164. Add a space before the parenthesis.
Line 178. Consider to change the phrase for "A non-significant value (p>0.05) of SSD and Hraf indicated .... "
Line 238. Add a space in "Clade1"
Line 268. The word "range" is split.
Lines 284, 291, 295, 296. The study  species is misspelled.
Line 294. Use capital letters for  "Miroc". Also, specify in Methods that this model was used.
Line 299. Add a space in "overallgenetic".
Line 302. Use capital letters for "Maxent".
Line 341-342. This phrase is not clear. Please rewirite.
Line 379. Use "warmer".
Line 388. Consider replacing with "...accompanied by low genetic variation, could...".
Line 397. Move "however" to the beginning.
Figure caption 6. There is an incomplete phrase in "the grouping of populations consistent".


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: PHYLOGEOGRAPHY OF AMYGDALUS MONGOLICA IN RELATION TO QUATERNARY CLIMATIC ARIDIFICATION AND OSCILLATIONS IN NORTHWESTERN CHINA
Review round: 4
Reviewer: 1

Output:
Basic reporting: No coments
Experimental design: No comentsNo coments
Validity of the findings: No coments
Additional comments: The authors responded satisfactorily to all my comments.  I suggest that it should be published as it is (note that some minor corrections are listed below).

Line 84. Duplicated comma
Line 133. The R package is mentioned using quotation marks ' ', however, in subsequent paragraphs the quotations marks are not used (for example l. 144,145), please use the same format.
Line 150. Change the capital letter in "Based"
Line 341-342. Change the capital letters on "Land use/Cover"


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: ACIDITY AND AVAILABILITY OF ALUMINUM, IRON AND MANGANESE AS FACTORS AFFECTING GERMINATION IN EUROPEAN ACIDIC DRY AND ALKALINE XEROTHERMIC GRASSLANDS
Review round: 1
Reviewer: 1

Output:
Basic reporting: I have improved the English in some areas but otherwise fine.

Excellent understanding and use of germination, speed of germination.

References and background are fine.

Very good professionalism throughout.

The manuscript was self-contained as you define it.
Experimental design: This was all good.
Validity of the findings: This is fine.
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: ACIDITY AND AVAILABILITY OF ALUMINUM, IRON AND MANGANESE AS FACTORS AFFECTING GERMINATION IN EUROPEAN ACIDIC DRY AND ALKALINE XEROTHERMIC GRASSLANDS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript entitled "Acidity and availability of aluminum, iron, and manganese as factors affecting germination in European acidic dry and alkaline xerothermic grasslands" study the germination ecology of 10 species from acidic dry grasslands and 10 species from alkaline xerothermic grasslands.

The paper is very interesting. English is written correctly.
Experimental design: The materials and methods section is written clearly and in detail.

The results are also explanatory and clearly written.
Validity of the findings: Conclusions are well stated, linked to the original research question & limited to supporting results.
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: ACIDITY AND AVAILABILITY OF ALUMINUM, IRON AND MANGANESE AS FACTORS AFFECTING GERMINATION IN EUROPEAN ACIDIC DRY AND ALKALINE XEROTHERMIC GRASSLANDS
Review round: 1
Reviewer: 3

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: The introduction has a review appropriate to the topic. The hypotheses are valid and the scientific questions are related to the hypotheses.
The materials and methods used were adequate. The selection of botanical material was judicious, preliminary tests aimed at reducing uncontrolled errors. The experimental design followed scientific rigor.

=>Table 1: On the first line some words are improperly broken.

The results were satisfactorily presented and discussed.
Several data were generated by the experiments and analyzed by parametric, non-parametric and multivariate statistical methods.
The research findings brought new knowledge about xerothermic germination in European grasslands.
The conclusions are supported by the research developed.

The article is recommended 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: SOIL CHARACTERISTIC CHANGES AND QUALITY EVALUATION OF DEGRADED DESERT STEPPE IN ARID WINDY SANDY AREAS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The quality of the research presented is limited by an inconsistent ability to communicate the main ideas of the paper. Further editing is required to ensure that the paper reads as intended and communicates appropriately the methodologies undertaken and the results identified. Current issues that need revision include:
The concept of the TDS is not adequately explored on its introduction in line 125, but a good summary is provided later in 256.
The confusion of the terms index, indicator and attribute which are used somewhat interchangeably within the methods to refer to a property of the soil that may be included in the TDS/MDS, which is particularly problematic at line 231. Effort should be made to use distinct terms to refer to a variable before and after calculating the membership values in the distribution function, with the use of the term index for the transformed values on different scales being particularly confusing.
The methods for PCA and the transformations involved are reiterated in section 3.5.1 of your results, 370-382. This can largely be removed, but much of it is clearer than your original description and you may wish to use much of the wording here in the methods.
You incorrectly refer to microbial counts increasing with land degradation in 319, should be decreased.

Beyond this, there are many examples of unclear or awkward sentences which confuse the point of the paper, including at lines: 57, 59, 76, 92, 202, 228, 283, 550, 563 and across more locations. The current phrasing makes comprehension difficult. I suggest you have a colleague who is proficient in English and familiar with the subject matter review your manuscript.
Experimental design: The experimental design seems sufficient for a study of this nature, however i would advise that care be taken in explaining how the substitution of space for time in your analysis addresses the practical constraints of sampling in line 174.
Validity of the findings: Your findings are relatively well addressed within the discussion of the paper, and i thank you for the inclusion of the data set analysed. However I feel the paper is lacking in its discussion of the variables identified as contributing towards the MDS for degradation assessment. You explore the relationship between many variables and degraded landscapes within section 4.3, but a stronger link to the specific MDS subset in the discussion and conclusions would benefit the paper.
Additional comments: Overall the paper is an interesting exploration of the impacts of grassland degradation on soil quality, with sound methodology. Fault lies primarily in the clarity of the writing, with further editing and revision of the language used required before the paper is suitable for acceptance.


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: SOIL CHARACTERISTIC CHANGES AND QUALITY EVALUATION OF DEGRADED DESERT STEPPE IN ARID WINDY SANDY AREAS
Review round: 1
Reviewer: 2

Output:
Basic reporting: This study keeps using repeated sentences in the manuscript. Please remove the duplicated findings in difference paragraphs. The whole manuscript is too long as well and makes the reader fail to grasp the key information.
I would like to suggest restructuring the manuscript as a lot of information was delivered in the Results section, but they were supposed to be in the Materials & Methods section, for example, the weight of each indicator (Wi).
The grey area in Figure 1 was not explained.
Table 4 seems unnecessary. It is enough to just keep the accumulated variance of 2 principal components.
Experimental design: no comment
Validity of the findings: It seems hard to get the key point due to the meaningless duplicated information.
I would like to suggest selecting some key findings to describe not saying all of them.
Additional comments: What is “characteristic root฀1” at Line 246
line 389-394 unnecessary to show such information
line 400-402 This information was duplicated. It was mentioned before but once again here


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: SOIL CHARACTERISTIC CHANGES AND QUALITY EVALUATION OF DEGRADED DESERT STEPPE IN ARID WINDY SANDY AREAS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The current version is much clearer than the first one, with sufficient data, analysis and comparisons based on literature references.
At line 86 it is better to add references for the methods you mentioned.
Experimental design: The experimental design is good especially involving soil biological properties for soil quality evaluation.
The research questions have been well discussed.
Validity of the findings: The findings of MDS, TDS and SQI are consistent with ground truth and with other studies.
Additional comments: The study is almost ready to be accepted except the following minor issues.
Line 73 Monitoring soil quality is necessary to assess parameter changes.... Please clarify what parameters?
Line 95 dot(.) should be comma (,)
Line 211 no need to say as cited
Line 301,302 and other places. Please reduce the digits of the those numbers to be 2.
Line 418 remove sharply.


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: DIFFERENTIATED HISTORICAL DEMOGRAPHY AND ECOLOGICAL NICHE FORMING PRESENT DISTRIBUTION AND GENETIC STRUCTURE IN COEXISTING TWO SALAMANDERS (AMPHIBIA, URODELA, HYNOBIIDAE) IN A SMALL ISLAND, JAPAN
Review round: 1
Reviewer: 1

Output:
Basic reporting: Overall, the manuscript is technically sound and with a good structure. The English language is confusing at times, with several grammatical errors throughout, so the authors need to thoroughly revise the main text.
The figures need some work also. The captions are not self-explanatory and thus make the figures hard to comprehend. For instance, figures 1-2 are incomprehensible to me. Also I would suggest authors to reference the location of the island in the one or more figures using a world/regional map.
The hypothesis being tested is sound (distribution/demographic fluctuations) but the results and analyses are weak and do not give support to this hypothesis.
Experimental design: The research question and methods are ok in general.
The ENMs and niche overlap tests are mostly well done and reported.
However, the genetic analyses are underwhelming and lack detail.
For instance, it is not clear what the sample size is. Line 117 states '48 specimens' but then '68 specimens' are reported in line 123. Also, the genetic landscape-shape interpolation analyses is not explained and thus these results are mostly obscure (see figure 1-2).
In general, the methods need more explanation so the reader can understand how different methods were used and how these are interpreted.
In addition, there are some interesting details on the study system that are only given in the discussion, such as the relationship of group B with another species (H. nebulosus). This is mentioned in line 328, but it would be great having all this background information beforehand. Reading through the text I actually thought of the two groups as sister lineages, just realizing that they are not at the very end.
Validity of the findings: The results of the ENMs are mostly fine, but the genetic analyses are very weak. As the manuscript stands, it reads almost entirely as an ecological niche paper. The genetic diversity analyses are very shallow and are not really contributing to testing the main hypothesis. As such, the manuscript is weak and the main findings do not support the main conclusions.
There is really no effort to integrate genetic diversity with ENMs and the estimation of the  basic statistics is not enough to address the question. Overall, as it stands the paper is basically a paper on ENMs and it feels that the population genetics section was a late add on to the manuscript. The ENMs are well explained and conducted but the genetic diversity methods are only briefly explained.
This is exemplified by the fact that something related to population genetics is only mentioned twice in the discussion, and only tangentially (lines 305-306, 369-371). The rest is a discussion of the results of ENMs.
The title mentions genetic structure, but  there is really no analyses addressing this. Honestly, the landscape-shape interpolation, although interesting, does not provide anything  to the conclusions/discussion.
I would suggest authors think of other type of analyses that can be more powerful to uncover the history of demographic fluctuations and genetic structure. I can think of STRUCTURE-like analyses, mismatch distributions, ABC analyses or simple regressions of genetic diversity vs. ENM stability. This can prove more interesting to uncover interesting patterns (and possibly timing of events). These are just thoughts, and I am not recommending any of these analyses before authors check if their genetic data is sufficient.
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: DIFFERENTIATED HISTORICAL DEMOGRAPHY AND ECOLOGICAL NICHE FORMING PRESENT DISTRIBUTION AND GENETIC STRUCTURE IN COEXISTING TWO SALAMANDERS (AMPHIBIA, URODELA, HYNOBIIDAE) IN A SMALL ISLAND, JAPAN
Review round: 1
Reviewer: 2

Output:
Basic reporting: Please see my general comments.
Experimental design: Please see my general comments.
Validity of the findings: Please see my general comments.
Additional comments: This is a very interesting manuscript about the niche and range differentiation of two salamanders on Tsushima Island, an island with an interesting geological and geographical history.

I think that the first two paragraphs of the introduction need some re-writing. Ideally, an introduction should start from broader concepts and then narrow down to the specific questions that the authors try to answer, via step-by-step logic transition. The introduction in this manuscript touched on many concepts that are important, but the logic transition is inadequate, leaving the concepts disconnected from one another. This makes it difficult for readers to follow.

I strongly recommend that the authors improve the quality of writing in this manuscript. English is my second language, and I think my academic English level is somewhat representative of an average reader of this paper, as most readers of scientific papers are not from English-speaking countries. In several places, I failed to follow what the authors tried to express. Below I have given a detailed account of the parts of writing that confused me.

I would like to see more discussion on how biotic factors such as competition may have also contributed to the present distribution pattern of the two groups. You mentioned that both salamanders have been found at some localities, but is there any sign of competition between the two species (e.g., competition for resources such as prey items)?

Specific comments:
Line 17-18
Suggest changing “affected considerably on the shaping distributional pattern and population genetic” to “considerably shaped the distribution and population genetic structure of organisms”
Line 21
Suggest changing “pattern” to “distribution”
Line 23
Suggest changing “the population genetics and ecological niche modelling approach” to “population genetic and ecological niche modelling approaches”
Line 16
Should probably be an “of” followed by “similarity”?
Line 29
Change “to occur” to “to have occurred”
Line 29-31
Suggest changing to “The highest suitability was predicted for Group A in southern Tsushima Island”.
Line 36
Should be “nonequivalence”
Line 45-46
Suggest changing “is central research of ecologists to understand” to “is central to the understanding of”
Line 105
“in the contribution” sounds a bit strange. “in this study” is probably better
Line 106
What hypothesis? “Hypothesis” means something very specific in biology. If you have one, state what it is. If you do not have one, the use of “hypothesis” is confusing.
Line 108
Do you plan to introduce both the objectives and the methods used? Then it is better to make the three “objectives” consistent. Currently, the first “objective” is strictly an objective, while the second “objective” is actually a method and the third contains both an objective and the corresponding method.
Line 126
Rather than a table, a figure showing the localities where samples were collected will be much more intuitive for the readers to grasp this information. In my opinion, Table 1 is better suited for the supplementary material.
Line 128
“Totally” should probably be changed to “In total”.
Line 144-145
“we randomly selected points within 100 meters, with ten replicates from others” seems too vague for me to understand that you actually did.
Line 183
“showed to” should be “is shown to”
Line 213
Need to specify which version of R was used.
Line 215-217
I find this sentence very confusing. The way this sentence is structured makes it sound like the goal of the test is to create a “null distribution”, and this is achieved by comparing the ENM of A to a randomly generated ENM. It is beyond me how you can create a null distribution by comparing two things. Furthermore, in ecology, the goal of a test is very often the opposite of what you said, that is, to compare the observed data against the null. Do you mean that “the test compared an ENM of Group against a null distribution generated from random points selected within the geographic range of Group B”?
Line 226-227
What is the null hypothesis? Is it niche conservatism? Please specify.
Line 228-230
I do not understand this sentence because of the grammar errors… Is it “… that uses kernel density to estimate the environmental distribution of species and the distribution of available environment to quantify niche overlap in a two-dimensional environmental space.”
Line 244-246
What is the biological meaning of the negative value? I think most readers including me will appreciate it if you remind them of this.
Line 256
“almost” should be “most of”
Line 326
“that shrinking” should be “the shrinking”
Line 338
What kind of gradient is this? It is too vague for me to understand. Can you elaborate?
Line 340
Should be “is broader”.
Line 342
“tolerant”, not “tolerance”.
Line 350
This seems to hint at competition avoidance in Group B. How can this be concluded from you ENMs? I am not convinced.
Line 352-353
I do not think you can be so certain about this, although it may be a reasonable guess. This uncertainty needs to be reflected in your writing using words such as “may” or “suggest”.
Line 356
“distribution of”
Line 362-363
What gradient? Temperature, precipitation, or something else? Please be specific.
Line 370
I do not understand the use of “resemble” here. Please be more specific.
Line 374
What do you mean by “a tendency for Group B”? Again, please be specific.
Line 381
“nonequivalence”
Line 386-387
This confuses me. What exactly are the null and alternative hypotheses for the background tests?
Line 396
“to compare” should be “comparing”
Line 401
“must be” is too certain a tone here. I do not think you can be this sure (we almost never can in biology).
Line 416
“correlated”, not “correlation”
Line 433-434
Suggest changing “the distinctively selecting the set of available conditions for each species” to “that each species selects a different set of available conditions”
Line 436
“selection”, not “selections”


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: DIFFERENTIATED HISTORICAL DEMOGRAPHY AND ECOLOGICAL NICHE FORMING PRESENT DISTRIBUTION AND GENETIC STRUCTURE IN COEXISTING TWO SALAMANDERS (AMPHIBIA, URODELA, HYNOBIIDAE) IN A SMALL ISLAND, JAPAN
Review round: 1
Reviewer: 3

Output:
Basic reporting: I read the paper titled “Differentiated historical demography and ecological niche forming present distribution and genetic structure in coexisting two salamanders (Amphibia, Urodela, Hynobiidae) in a small island, Japan”

It deals with a very interesting topic although mainly herpetological.  The paper studied the ecological niche of two sympatric salamander gropus/species (one still to be described taxonomically I f I have well understood) providing new data on their population dynamics using genetic information.
The results underline how the two groups/species although sympatric have different distinct areas of high genetic difference and
I found particularly interesting the part dealing with the paleo-climate reconstructions that showed different fluctuations and different ranges compared to the current distribution as the results on the ecological niche of the two groups.

The paper is an important contribution for understanding coexistence mechanism of similar groups/lineages/species in small territories.

Just a major and few minor issues should be addressed to improve the reading of the manuscript.

The main issue is that it is not very clear is the level of sympatry of the two groups and if there is introgression or not among them. Please in the paragraph dedicated to H. tsuensis, detail/describe these aspects.

Also the use of “species”, “groups” “lineages” for the two salamanders studied could be more consistent throughout the text.

Minor points:

Line 63 check if “foundation” is the correct word; I’m not sure of what it means in this context.

Lines 82 -83 the description of the island jumps here a bit unexpected. It could be great to develop a bit more tha narrative of the previous paragraph to increase the connection with the following one

Lunes 92-93 the same for the salamander; maybe it could be possible to state already in the paragraph before that the island is important because inhabited by a peculiar salamander but the species are not two?). In that way the paragraph on the salamander(s) does not fall unexpected for the reader.

Line 101: please clarify which study

Line 104: please maybe it is better to be consistent and use instead of species groups or lineages as made above.
Line 105 : which contribution?
Line 342 check if it should be word or words
Lines 404 -409 it could be possible to refer also to the paper of Ficetola et al., 2018 Differences between microhabitat and broad-scale patterns of niche evolution in terrestrial salamanders Sci. Rep., 10575
Lines 432-434 please rephrase as it I not very clear the meaning of this sentence there is something awkward in it.
Experimental design: The eperimental design was clear nad described in detail
Validity of the findings: Results seem consitent with the methods used
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: DIFFERENTIATED HISTORICAL DEMOGRAPHY AND ECOLOGICAL NICHE FORMING PRESENT DISTRIBUTION AND GENETIC STRUCTURE IN COEXISTING TWO SALAMANDERS (AMPHIBIA, URODELA, HYNOBIIDAE) IN A SMALL ISLAND, JAPAN
Review round: 2
Reviewer: 1

Output:
Basic reporting: The English is unclear at times.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This is my second time reviewing this paper and I think it has improved greatly.
The authors have done a good job at addressing my previous concerns. The methods are much clearer now and the introduction is more fluid.
I believe that the paper is worth publishing and has scientific merit, but also feel like it needs some additional work. The main take away point I'm left with is interesting, but in my opinion this has to be made more explicit, specially in the discussion.
To me this main point would be: the differential demographic/historical response of two mostly sympatric salamander species in a small oceanic island, and why this might be happening.
If authors agree with me that this is the main take-away message, perhaps highlight it in the discussion. This is somehow resumed in lines 434-435, but it is buried in the middle. Why not start here with the main point up front, and then give a more nuanced explanation using the evidence at hand (ENMs, niche tests, demography), and finally discuss possible reasons why this is happening (authors mention different times of colonization).
These are my suggestions to make the results really stand out.
In sum, I think this paper should be published and not much needs to be changed in terms of methods, but also feel that the main point remains somewhat hidden.

Some suggestion on figures: would it be possible to merge figures 2 and 3, so that the comparison between species is more straightforward?
Also, I feel that figure 6 is a bit redundant with figure 8.
Another suggestion for figure 8 to arrange maps differently: four panels on top for group A (left to right: LIG, LGM, HOLO, PRE) and four panels on bottom for group B (same as above). I believe that can help make the visual comparison easier.


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: DIFFERENTIATED HISTORICAL DEMOGRAPHY AND ECOLOGICAL NICHE FORMING PRESENT DISTRIBUTION AND GENETIC STRUCTURE IN COEXISTING TWO SALAMANDERS (AMPHIBIA, URODELA, HYNOBIIDAE) IN A SMALL ISLAND, JAPAN
Review round: 2
Reviewer: 2

Output:
Basic reporting: Please see my additional comments.
Experimental design: Please see my additional comments.
Validity of the findings: Please see my additional comments.
Additional comments: I did not think I needed to re-review it, as the changes I suggested in the last round of review were minor. Indeed, the authors made all the changes I would like to see.


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: GENETIC POLYMORPHISMS IN THE IFNL4, MXA, AND MXB GENES WERE ASSOCIATED WITH BIOCHEMICAL INDEX OF CHRONIC HBV PATIENTS FROM YUNNAN, CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: Clear
Experimental design: Well defined
Validity of the findings: All underlying data have been provided
Additional comments: HBV infection caused hepatitis B, which was the most popular viral hepatitis in China. Interferons and its downstream interferon-stimulated geneswas important in viral infection. The authors collected HBV patients and controls to genotype genetic polymorphisms in the IFNL4, MxA, and MxB gene. Their results suggested that SNPs in these genes were associated with HBV infection in Yunnan population. Moreover, the genetic variations also influenced biochemical indexesof HBV patients. Some suggestions as following:
1.	Some grammar errors could be changed, for example “All seven SNPs were tag SNP or functional SNP” should be changed to “All seven SNPs were tag SNPs or functional SNPs” in page 5.
2.	In Results section, the sub-title of “Rs17000900 was associated with HBsAg seroclearance of patients” should be changed to “Rs17000900 associated with HBsAg and biochemical indexes of patients”
3.	In abstract, the sentence “Above all, although the genetic polymorphisms were not ……”, which genes did these genetic polymorphisms belong to should be clearly described.


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: GENETIC POLYMORPHISMS IN THE IFNL4, MXA, AND MXB GENES WERE ASSOCIATED WITH BIOCHEMICAL INDEX OF CHRONIC HBV PATIENTS FROM YUNNAN, CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: See below
Experimental design: See below
Validity of the findings: See below
Additional comments: Thanks for inviting me to review the manuscript entitled" Genetic polymorphisms in the IFNL4, MxA, and MxB genes were associated with biochemical index of chronic HBV patients in Yunnan, China". I have already reviewed this article in another journal (Infection, Genetics and Evolution) and my decision was reject. My comments is below:

* The abstract should be rewritten in plausible form. The name of SNPs should be added in Abstract. ALT, AST, TBIL, DBIL, IBIL, and ALB have to be fully written when mentioned for the first time.
* Inclusion and exclusion criteria are missing and are better to be added.
* Case-control study: Inappropriate study design, Control group of no considered value.
* The number of samples is small.
* It is not sufficiently clear how these particular variants were chosen for study among the numerous variants that exist in these genes. Was it merely based on previous work by others or was there some hypothesis?
* It should be discussed how a non-coding variant that does not affect protein sequence of the gene product might mechanistically affect the course of infection and response to treatment.
* Which genotypes of HBV are common in Yunnan, China? Was there relationship between these SNPs and HBV genotypes and viral load?
* The discussion has been poorly written. I would like suggest that the authors revise it, especially when they compare their results with previous studies


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: GENETIC POLYMORPHISMS IN THE IFNL4, MXA, AND MXB GENES WERE ASSOCIATED WITH BIOCHEMICAL INDEX OF CHRONIC HBV PATIENTS FROM YUNNAN, CHINA
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors collected HBV patients and controls from Yunnan Province to analyze genetic variations frequency of the IFNL4, MxA, and MxB genes. Although no association was found between these SNPs and HBV infection, the biochemical indexes levels could be influenced by the genetic variations. Moreover, genotypes of SNPs were also associated with biochemical indexes in HBsAg-positive and -negative patients. These results could provide suggestions for therapy of HBV patients.
1. The sub-title of results should be simplified.
2. Did the study use the exact same analytical systems for HBV serology and RT-PCR?
3. How about duration of patient recruitment?
4. The “Material and methods” needs to be supplemented and improved.


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: GENETIC POLYMORPHISMS IN THE IFNL4, MXA, AND MXB GENES WERE ASSOCIATED WITH BIOCHEMICAL INDEX OF CHRONIC HBV PATIENTS FROM YUNNAN, CHINA
Review round: 1
Reviewer: 4

Output:
Basic reporting: The English language should be improved to ensure that an international audience can clearly understand your text. Some examples where the language could be improved are annotated in the pdf and include lines 16, 23, 41, 52, etc., There are also several grammatical errors in the manuscript as annotated in the pdf. The current phrasing makes comprehension difficult. I suggest you have a colleague who is proficient in English and familiar with the subject matter review your manuscript or contact a professional editing service.

The article needs some clarity and background information on certain things as pointed out in lines 19, 41, 56, 70, 82, 87, etc., It would also be great to have additional references to provide information to readers as pointed out in the pdf in lines 87 (reference for SnapShot method), 91 (LD), 114 (D'), etc.,

The authors conform to an acceptable format of 'standard sections' and the figures are relevant to the content of the article. However, to improve clarity of the figures, I would suggest increasing the font size of labels and uploading higher quality/resolution images. I appreciate the authors sharing raw data.
Experimental design: This research is within the Aims and Scope of the journal. Although Zheng et al., have conducted a rigorous investigation with a large study group size of 896, a clearly defined research question and knowledge gap (especially in the abstract) is missing. I suggest the authors consider stating them clearly.
Methods were described with sufficient information to be reproducible by another investigator.
Validity of the findings: I thank the authors for providing the data on which the conclusions are based, however, the conclusions need to be connected to the original question investigated. Defining the questions and gap knowledge would help make it clear.
Additional comments: The article requires significant revisions, which I feel are major enough that I would prefer to re-evaluate any revised version.


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

Input:
Title: GENETIC POLYMORPHISMS IN THE IFNL4, MXA, AND MXB GENES WERE ASSOCIATED WITH BIOCHEMICAL INDEX OF CHRONIC HBV PATIENTS FROM YUNNAN, CHINA
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
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: GENETIC POLYMORPHISMS IN THE IFNL4, MXA, AND MXB GENES WERE ASSOCIATED WITH BIOCHEMICAL INDEX OF CHRONIC HBV PATIENTS FROM YUNNAN, CHINA
Review round: 2
Reviewer: 2

Output:
Basic reporting: I thank the authors for their revisions.
The figures are still of poor quality and I cannot read the text.
Experimental design: No comments
Validity of the findings: no comments
Additional comments: no 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: QUANTITATIVE ANALYSIS OF VEGETATION RESTORATION AND POTENTIAL DRIVING FACTORS IN A TYPICAL SUBALPINE REGION OF THE EASTERN TIBET PLATEAU
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: The theme of this paper is "Quantitative analysis of vegetation restoration and potential drivers in typical subalpine areas of the eastern Tibetan Plateau", but most of the research in this paper focuses on the study of vegetation cover and environmental factors. However, vegetation restoration is a system project, which is influenced by many factors, among which human activities have a greater influence on vegetation, and the influence of human activities is not considered in the potential drivers of this paper, which is also inappropriate.
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: QUANTITATIVE ANALYSIS OF VEGETATION RESTORATION AND POTENTIAL DRIVING FACTORS IN A TYPICAL SUBALPINE REGION OF THE EASTERN TIBET PLATEAU
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1. You should give more details for the study area introduction, and let the reader know more about the area.
2. You should add the lat and lon in the figure 1, and let the reader know the specific location.
3. Have you estimate the VIF for those driving factors？ I think there are VIF to some extent.
4. In the section of conclusion, you give a lot of results description, but not conclusions.
5. In the section of discussion, you had better give some details for the limitation and uncertainty of this study.
6. There are many small errors, you should check the whole manuscript. For example, km2 in line 113.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: No 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: QUANTITATIVE ANALYSIS OF VEGETATION RESTORATION AND POTENTIAL DRIVING FACTORS IN A TYPICAL SUBALPINE REGION OF THE EASTERN TIBET PLATEAU
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors present a very important problem of vegetation recovery in subalpine areas. Generally, the manuscript seems to be within the scope of the PeerJ. In my opinion, the article is very interesting and does not require many corrections, but an improvement of the work is needed to give this paper its important value.
Point 1: Introduction (Line 91-99) could be described more precisely for the possible drivers of vegetation change across the Eastern Tibetan plateau, at least the Tibetan plateau, which may be more meaningful for you work.
Experimental design: Point 2: Data sources (Line 131-137): How to deal with the cloud influence about Landsat satellite images obtained from Google Earth Engine. How many images do you get for each pixel each year. It will be better to add a frequency map of images information obtained.

Point 3: Results (Line 294): Why do you make a separate section about FVC change on different micro-topography. I mean it could be include in the spatial variation characteristics of FVC change section. I propose to add a more detailed description about this objective or combine them.
Validity of the findings: Point 4: Which do you think is more important for vegetation change in your study area, natural or human factors? Some discussions about how to distinguish them could be added.
Additional comments: Point 5: There need some grammar check, such as line 415 comma.


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

Input:
Title: QUANTITATIVE ANALYSIS OF VEGETATION RESTORATION AND POTENTIAL DRIVING FACTORS IN A TYPICAL SUBALPINE REGION OF THE EASTERN TIBET PLATEAU
Review round: 2
Reviewer: 2

Output:
Basic reporting: Specific details:
1. The title format of each chapter in the manuscript needs to be modified based on the submission guidelines.
2. Inconsistent use of some terms. The descriptions of “slope(warm)” and “slope(cool)” are irregular. And in Line 303-304, the description becomes “sunny slope”. Please standardize academic terms.
3.Please simplify Figure 3. The information in Figure 3 is too much.
Experimental design: no comment
Validity of the findings: 4.In Line 257-260, how do the study come to this result? And what year of the data is used?
5. In Line 317-326, in addition to the concise and precise description of results, there should also be a brief analysis of this phenomenon.
Additional comments: This study analyzed the temporal and spatial characteristics of fractional vegetation cover (FVC) in a typical subalpine region based on linear regression and Hurst exponent. Furthermore, the driver factors of FVC were identified by Geographical Detector. The manuscript is well written, and the results can provide a scientific basis for future research. Some ideas deserve attention, but further revisions are surely needed.


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

Input:
Title: QUANTITATIVE ANALYSIS OF VEGETATION RESTORATION AND POTENTIAL DRIVING FACTORS IN A TYPICAL SUBALPINE REGION OF THE EASTERN TIBET PLATEAU
Review round: 2
Reviewer: 3

Output:
Basic reporting: I have completed the reviewed the manuscript peerj-68087  Title: Quantitative analysis of vegetation restoration and potential driving factors in a typical subalpine region of the Eastern Tibet Plateau.
    First of all, I affirm the positive response and improvement of the manuscript to the opinions of the two reviewers
I though this work can be given us a case-reference in understanding of vegetation restoration changes within typical watersheds in the subalpine region of the ETP and reveal important factors affecting vegetation restoration. The significance, relevance and timeliness of the topic was well done. However, this manuscript has some sections and expressions need to improve. For example, (a) quality and content of the research/review . Comments: Some details need to be improved.
(b) quality, brevity and clarity of presentation . Comments: Some parts need to improve.
(c) Innovation points, key links of research methods and uncertainty analysis of research results need further improvement.
Hence, on the basis of all my following comments, the publication of the manuscript in its present form is not recommended, and minor revision is requested.
Experimental design: First, It is recommended to provide a logically technical framework of your study how to be done, and a list of relevant information about the main data, and the analysis codes on GEE platform, which can be in the form of Appendix (i.e.,Supporting information).
Second, fractional vegetation cover (FVC) is the key word of this study, but important ecological background information such as vegetation composition and spatial pattern in the study area before and after vegetation restoration is not fully described in the manuscript, therefore, it is suggested to supplement relevant information from the perspective of phytocoenology.
Third, deciduous vegetation is involved in the research object, whether the influence of seasonal differences on FVC is considered.
Lastly, there are some the key research methods, especially the original ones of yourself, need to be explained clearly and their literature. eg, About human activities, Why did not you only choose distance from roads and distance from residents as explanatory variables for FVC changes？Why did not you consider soil nutrients, soil moisture, land use and other factors in higher spatial resolution？
In addition, there are many relative researches closely related to your research, it is recommended to make a search, read and reference the following literature.
【1】Fengkui Ma, Qun’ou Jiang, Lidan Xu, Kexin Lv, Guoliang Chang. 2021. Processes, potential, and duration of vegetation restoration under different modes in the eastern margin ecotone of Qinghai-Tibet Plateau. Ecological indicators, 132:108267, doi.org/10.1016/j.ecolind.2021.108267
【2】Xinping, Zhang , et al . 2017. Effects of land use/cover changes and urban forest configuration on urban heat islands in a loess hilly region: case study based on Yan’an city, China. International Journal of Environmental Research and Public Health, 14(8), 840. doi.org/10.3390/ijerph14080840.
Supporting information Section
【3】Zhang Xinping, Zhang Fang Fang, Wang Dexiang, et al. 2018. Effects of vegetation, terrain and soil layer depth on eight soil chemical properties and soil fertility based on hybrid methods at urban forest scale in a typical loess hilly region of China. PLoS ONE 13(10): e0205661. doi.org/10.1371/journal.pone.0205661
Validity of the findings: (1) Please explain why only vegetation coverage was selected as a measure of vegetation restoration effectiveness.
（2）The minimum non-heterogeneous spatial unit and its scale need be explained in detail.
（3）In the section of Limitations and uncertainties, the analysis and explanation in the current version of manuscript are not scientific enough, it is suggested to make a quantitative analysis of the uncertainty of the influence factors affecting FVC.
（4）In the conclusion part, the summary of the research results is weak, and Lack of recommendations for further research.
Additional comments: （1）English expressions:
I noticed that your English usage is slightly off and could benefit from editorial help of a fluent English speaker or editorial service.
（2）Novelty:  Unclealy,  please further clarify the innovation of your research.
（3）Finally, I suggest that the authors carefully examine the title of the article.


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

Input:
Title: QUANTITATIVE ANALYSIS OF VEGETATION RESTORATION AND POTENTIAL DRIVING FACTORS IN A TYPICAL SUBALPINE REGION OF THE EASTERN TIBET PLATEAU
Review round: 3
Reviewer: 1

Output:
Basic reporting: no comment
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: QUANTITATIVE ANALYSIS OF VEGETATION RESTORATION AND POTENTIAL DRIVING FACTORS IN A TYPICAL SUBALPINE REGION OF THE EASTERN TIBET PLATEAU
Review round: 3
Reviewer: 2

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