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Thank you for the relevant modifications done on the manuscript.
[# PeerJ Staff Note - this decision was reviewed and approved by Dezene Huber, a PeerJ Section Editor covering this Section #]
Thank you for the work you have done to respond to all the referees' comments. I think you have done a good job to improve your paper in light of these comments.
I have only some minor remaining corrections/changes that I would like you to do:
Hereafter line numbers refer to the word file with tracked changes.
- Line 143, remove the comma after "precipitation"
- Line 243. Write alpha instead of alfa
- Line 358, replace "an at the region" by "and the region"
- Line 388, Write a sentence to make it clear that beta_cc does not take abundance into account, while Hill numbers do.
- Throughout the paper, refer to the D indices as "Hill numbers" or simply "diversity measures" rather than as "True diversity measures"
I have now received the comments raised by two reviewers on your manuscript. They have made thorough evaluations. I ask you to consider all comments to revise your manuscript and respond to each of them.
**PeerJ Staff Note:** Please ensure that all review, editorial, and staff comments are addressed in a response letter and that any edits or clarifications mentioned in the letter are also inserted into the revised manuscript where appropriate.
In this study, the authors report on the diversity of hummingbirds and flowering plant communities in central Mexico, at different scales of organization, namely: alfa, beta and gamma diversity. Their goal is to describe the structure of these communities across four types of habitats and to find the main environmental factors influencing the composition of plants and bird communities. To achieve this the authors performed field samples over an entire year at 20 (500m length) transects (5 per each type of the 4 habitats studied, if I got it right). From this data true diversity indexes were calculated at different spatial scales such as alpha, beta and gamma. Then the changes in species composition is related with environmental variables. In general there are more plants than hummingbirds at the four habitats studied, and few species in both trophic groups are dominant in several habitats. Turnover of species is the main driver of dissimilarity in species composition across habitats for both trophic groups, excep perhaps in the case of plants when comparing oak and juniper forests where nestedness has a large contribution. These patterns of species composition are mainly driven by variation in climatic variables, precipitation if I understood correctly.
I think the study is well designed with a generous sampling effort, enough to describe plants and hummingbird communities, and sound analytical methods used to describe taxonomic diversity at different spatial scales, although I did not fully understood the Mantel test, but maybe is just me.
I find two main points of concern. 1) I feel that authors, at many points throughout the ms, tend to overstretch the scope of their results and conclusions. The first sentence of the introduction is a good example. First, you don’t need to use that amount of jargon, then the study doesn’t really quantify interactions in order to “unravel” the complex interaction webs formed between plants and hummingbirds. I recommend authors stick to their results and avoid making conclusions on themes not really addressed here. I honestly believe that a more concise text would make this a much more valuable contribution. 2) I see the discussion disconnected from the expectations laid out in the introduction, e.g. does your results conform with your expectations and with what others have found before? How does these results fit in the literature?. I found hardly any mention about the expectations in the discussion. 3) I found interesting that authors are studying habitats that form gradients of humidity and temperature in the same landscape, from that perspective one would expect to see a great turnover of species (plants and hummingbirds) along these environmental gradients. The results reported here confirm that expectation? Could you elaborate more on why turnover of plants is higher than hummingbirds? Is it because higher mobility in hbs that allow them to occupy different habitats and under this scenario of high turnover which conservation strategy should maximize biodiversity conservation. These a re just some thoughts that I think were almost completely missed.
Minor points
The results reporting section could turn very hard to read, this is mainly because of the use of acronyms. For instance, FP stands for flowering species but there is also PF which stands for Pinus forests, right? This together with the other acronyms makes it very hard to follow. Maybe just refer to hummingbirds and plants, and also you could name oak forests, pine forests and so on.
275-290 To illustrate the heterogenous abundance of the referred flowering plants and hummingbirds it might be better to use a figure instead of describing this with a complicated text (the combination of acronyms, scientific names and percentages is not so friendly to follow), maybe a couple of barplots would do the job.
Paragraph 291-297, maybe should go first in this sections?
How the distance among the study sites could have influences beta diversity patterns? Is this accounted for somehow? Also the lowest dissimilarity of hummingbirds assemblages as compared to plants might be due to a critical difference between the two groups, hbs have a much higher mobility than plants that may allow them to exploit different habitats
121 assembly? Instead of assemblage
129 maybe start a different paragraph.. i.e. “The main goal of our research… “
139 was humidity included in the analyses or this refers to precipitation ? resource availability refers to environmental variables as well?
142-143 drop off sentence
145 why delicate?
156 from other areas studied?
161 totaling 80?
226 why the subscript B_3 for turnover? Maybe use the conventions nestedness and turnover
351 Could you be more specific here? Which environmental variables?, or is this the PC 1 or PC2. In that case it would be good to know the variables that contributed more to the respective PC, I think I read before it was rainfall related variables?
363 You don’t need to repeat the results with this detail at this point
365-366 I think this might be an over stretching statement, I do not see how authors measure ecosystem stability to support this argument or pollination dynamics?
370-371 the concept of keystone species is really not appropriate to these plants, I thnink, more precisely could be dominant or key resources
391-392 What does cascading effects mean?
402 not needed jargon
Table 3 could be a figure?
No research question clearly stated. the field study design seems appropriate for the purpose of the study which was to describe diversity patterns across habitats.
Overall the discussion is disconnected from the expectations laid in the intro.
The second paragraph of the conclusions section does not really refer to the results obtained from this study. I find this one of the weakest points of the ms
no comments
It’s a good paper, and it is easy to read in professional English. The academic tone is maintained throughout the paper. There is just one spelling mistake in Line 288, and some phrases are not clear in Line 156.
However, there are some clarifications and corrections.
The first phrase is evident in the abstract (lines 19-20). Ecological and environmental factors are not clarified (Line 20). The results should start by mentioning diversity, not abundance (Line 32).
The introduction is well-written and provides useful references. I just recommend a useful reference on a dry forest plant-hummingbird network (Martinez-Garcia et al. 2020. Tropical Conservation Science) for Line 109.
Table 1 should be formatted to stay below the title, and the legend of the figures where the habitat types are mentioned should have the same order as they appear in the figures.
The icon for plants in Figures 4 and 5 should be replaced because people with limited sighting ability could confuse it with a bird.
The hypotheses are well stated. However, the statements at the end of the introduction should be either merged with the conclusion or deleted (Lines 142-145).
The study design is well done, but as mentioned before, in Line 156, where the locations sites are described, the words “areas” and “urban” seem missing descriptors.
The bird and plant assessments are accurate; however, in their description of sample completeness, rarefaction is not mentioned if that method is used (Line 184).
The True diversity measures are explained in detail; just a redundancy in an equation could be avoided (Line 219), and the citation of the vegan package is missing (Line 242). I recommend adding a paragraph quoting previous research on how these diversity measures were used for birds or plants (Line 243).
The results are well stated; however, the quotations of figures 2 (line 266), 3 (line 283), 4 (line 321), and 5 (line 341) do not start with subsection A but B. I recommend modifying the text or the figure in each case to keep a sequence.
The results of what I assume are a rarefaction are mentioned (line 291), but a supplemental figure showing the asymptote is needed.
The discussion is good, but there are long sections that read like a treaty with no reference to the results. The tables and figures must be quoted to back up all affirmations regarding the results (line 361).
No comment
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