Environmental Heterogeneity Affecting Community Assembly Patterns and Phylogenetic Diversity of Three Forest Communities at Mt. Huangshan, China
, Shuifei Chen 2, Rong Zhao 1, Yueyao Feng 1, Yao Li 1, Hui Ding 2 and Yanming Fang 1,*Round 1
Reviewer 1 Report
The manuscript examines how environmental variables (space, climate, and topography) are related to phylogenetic diversity and structure in a small-scale approach of plant community in an altitudinal gradient at Mt. Huangshan, China. The authors studied 176 plant species from communities at three different altitudinal zones: 400-600 m; 700-800 m; and 800-900 m. They found how important the role of deterministic biotic interactions is in driving phylogenetic patterns. As a whole, I consider the study well written and very clear. The topic is interesting and relevant to the audience of the journal.
More detailed suggestions are below. I hope the authors find the comments useful and that improve the manuscript.
Title
I would like to suggest that the title would be more specific. As it is defined, is very general and unattractive.
Introduction
L.42-48: This sentence needs review. The text is confused when it comes to niche theory and phylogenetic niche theory.
L.59: “Many researchers have used….”. You need to provide more than 1 study reference because you said many researchers....
L.68: “Faith’s PD …”. You must define and add a reference.
L.78-79: It would be interesting to explain a little better how phylogenetic structure is related to precipitation.
L.81: “…factors controlling community diversity patterns”. Where?
Material and Methods
All scientific names of species must be in italic format.
Figure 1: The figure resolution is not good. You need to describe in the caption what each illustration on the figure represents. I suggest putting a) b) c).... and explaining each one in more detail. Adding photos of vegetation to each plot would also be nice. You must indicate that the contour lines refer to the altitude above the sea.
L.202: “anoverdispersed”. Needs correction.
L.206: “Species richness was measured as the number of species in a quadrat”. So you're considering alpha diversity in each quadrant. But for beta diversity, what is your sample unit? quadrats? or communities? It must be explained.
L.210-211: “… evaluates deeper relationships…”. What are these deeper relationships? Are these relationships closest to the base of the phylogenetic tree? Clarify, please.
Equations:
n means what? Is the total number of species? You have to clarify here.
L.213: What is the K1/k2 community? Is plot 1/community 1? Need to clarify and use the same name throughout the manuscript.
L.229: It is important to explain why there are 32 vectors. What do they represent?
L.232: “19 bioclimatic factors”. It would be good to point them out somewhere… supplementary material….
L.240: Was the SES calculated with ‘picante’ too?
L.241-243: Did you do some preview transformation on these data? This is very important.
Results
L.260; 264: I suggest captions in the supplementary figures.
L.272: “…zones”. Maybe change by altitude rather than zones and use the same name throughout the manuscript.
L.296: How stronger? How were the results of these correlations compared to affirm that they are stronger? Please explain.
L.299: Who are these variables? I suggest that you add a table in the supplementary material to indicate what these 19 bioclimatic variables are.
L.302: “…differed slightly from those of forward selection”. How does it differ? Be more specific.
Table 2: The table is a little difficult to understand. Perhaps placing a separation between one factor and another could help. You also need to better indicate what each letter and abbreviation means.
L.313: “elevation”. Did you mean altitude? We can confuse it with the elevation of topographic variables. I suggest keeping altitude.
L.315-316: review and clarify. Layers? Communities? Why not altitudes?
Figure 3.: Please, put the meaning of SES.PD.
L.341: What are the three layers? Communities? Why not use altitude?
L.373: and for D'nn?
L.375: “65%”. Please correct.
Discussion
Perhaps it would be interesting to start the first paragraph of your discussion with a review of the main objectives and then go into the details...
L.401: “K2P distance”. You need to explain what this means.
L.405: “…that total plants have overdispering phylogenetic structures…”. On line 202 you say that if the NIT or NRI are negative this would be indicative of overdispersion...
L.433: “with soil and micro-habitat advantages”. Could you please be more specific?
L.453-454: I missed a little discussion about how these environmental filters work by selecting certain traits so that this group of species can survive in these harshest environments.
Author Response
Dear Professors,
We are really appreciative of the support provided by you and your journal, and also sincerely appreciate the reviewers. According to your suggestions and the reviewers’ comments, we revised the manuscript. We hope that the revised manuscript should be up to meet the standard of your esteemed journal. Now we re-submit the manuscript to your journal.
All concerns that should be considered were addressed in the revision one by one as follows, please examine. Please see the attachment. The black words are the reviewers’ comments and the red words are the responses from the authors.
Author Response File: 
Author Response.pdf
Reviewer 2 Report
The title of the paper could be more descriptive, it is a bit vague and doesn’t clearly describe what the paper is about.
There are some issues with the methodology that need clarification/justification. I am not sure why these three plots were chosen. They cannot easily be compared because as far as I can tell whilst the three plots are located in the same scenic area, the plots have different altitudes, are in different locations, are different sizes, have different vegetation compositions and vary considerably in the number of quadrats samples taken in each plot (I=256,II=25,III=25). I cannot tell how closely these plots are located from the information given. There isn’t a lot of detail given about the three plots, no history or details of current and past management/use which could affect the plant community composition. The plots appear to be at very different altitudes, the range for each varies with no overlap in altitude. They are clearly distinct, but despite this are referred to as being part of a transition in lines 410-411. It also lacks an adequate discussion and justification for why these particular methods were used for the phylogenetic analysis. You mention niche and neutral processes but not historic. Only woody species are included but there is no justification why this is the case, if the interest is conservation is claimed then why only look at woody species. What is the rationale for separating trees and shrubs in the data presentation and how was this determined, by height, by single stem or both? Needs defining as some trees can be shrubs and vice versa. If I understand correctly the environmental variables used here were taken from World Bioclim, was there any ground truthing, how accurate was that data. It is also made clear that not all environmental variables were considered which I think is a problem.
The focus of this paper is really on the phylogenetic analysis and has little to do with conservation, and it is not clear why this is drawn into the discussion and conclusion. You can’t state as you have that these findings can solve the conservation problem of plant diversity. You should focus on your findings rather than overreaching and making big points about conservation which isn’t your focus.
Supplementary data:
S.1 I count only 34 entries on the pie chart, but there are 57 families, what is eles? This is very untidy
S.5 not total for NTI
Supplementary tables S1-S3
Table s.1: why is % success for rbcL shown as 100% in this table? Please check other % values also
In your climatic variables, you only have these listed as climate 1, climate 2 etc. what actually do these relate to are these the same as biol 1, 9, 10 and 15 mentioned in your manuscript?
Looking through these variables they seem to vary little, first four columns are exactly the same of the first 60 samples, I didn’t check other rows or columns but this needs explanation.
Comments for author File: Comments.pdf
Author Response
Dear Professors,
We are really appreciative of the support provided by you and your journal, and also sincerely appreciate the reviewers. According to your suggestions and the reviewers’ comments, we revised the manuscript. We hope that the revised manuscript should be up to meet the standard of your esteemed journal. Now we re-submit the manuscript to your journal.
All concerns that should be considered were addressed in the revision one by one as follows, please examine. Please see the attachment. The black words are the reviewers’ comments and the red words are the responses from the authors.
Author Response File: Author Response.pdf
