General Comments:
I found this study hard to read because of the abundance of jargon. The introduction gave a very helpful introduction to the jargon, but failed to place the study in context and thus made it harder to care about the remainder of the study. The results and discussion sections read like long lists, filled with jargon, which again made it harder to care about the authors conclusions. In general, I think that this study needs to be majorly re-written. Particularly, the introduction should place more emphasis on where this study fits in, in the general context of community ecology and shallow reef fish ecology and what its findings mean in those contexts—moving the definitions and jargon-explaining to a table or a box. Then the results section should start with an overview paragraph that helps the reader anticipate the authors findings, then the rest should be given headers and short introductory sentences in plain English introducing what the findings in the respective paragraphs describe. The discussion section should focus on a few key findings and describe what those findings mean in plain English, describing the significance of the results to shallow-reef communities in Australia. Mentioning the significance of their results to other ecosystems, if relevant (at present the authors speak of their results as if they apply to general aquatic ecosystems which seems like quite a stretch, without proper justification). Reading between the lines, this study sounds like it has something interesting to say about shallow reef functional diversity and its relationship with environmental and human pressures, but the abundance of jargon makes that hard to discern.

Specific Comments
Abstract
- the sentences on line 7-12 are a bit unclear and overly jargon-y (making them hard to parse), suggest re-organizing to just say that ‘…pressures can affect community stability through direct and indirect (trait-mediated) impacts on average species stability and asynchrony in species’ fluctuations’
- average species stability (line 8) vs species average stability (line 11) vs species-averaged stability (line 17) <- choose one term and stick to it for the entirety of the manuscript
- your conclusion on lines 18-19 was not supported by the previous lines (you just said that enviro and human pressures indirectly affected asynchrony through facets of functional diversity)

Introduction
- I really appreciated the fact that this section introduced the concepts so well (e.g. lines 40-48 do a great job of introducing the jargon) but I think that the authors should have spent more time introducing the question that they were attempting to solve in the context of shallow reefs. e.g. Has this been looked at in shallow reef fish before? What have they found when they looked before? What is known about shallow reef fish compositions and how they are affected by environmental and human pressures? A strength of this study is the size of its dataset, but there is a whole multitude of literature on shallow reef fish communities that should be referenced here. Most of the content of this section would have been better introduced in a table containing definitions or a box introducing this concept, or majorly shortened. This section reads too much like a textbook introducing the concept of ecosystem stability in the context of species composition.
- line 50 - what are ‘selective impacts’? Please elaborate on this.

Results
- what is the STAR protocol? This is not defined in the Methods or in the Supplementary Material (as far as I can tell)
- It is not clear which methods were used to derive which results, please clarify what methods you used to generate each result listed here.

Discussion
- line 201-203 - Please provide context for this statement in the form of citations/references to other studies. Show us the evidence backing up this statement, do not just state it.
- same comment re: 219-220
- Line 217: reflect -> reflects
- Line 228-231: in what context do you anticipate that this will hold? Or not hold? This seems like a vast generalization with no caveats/bounding

I was reviewer 2 from the original revisions. I appreciate the work that you put in to adjust your manuscript based on the input of myself, the associate editor and the other reviewer. The manuscript reads much better now and I can appreciate more of the nuances and important aspects of the work.
General Comments:
- I thought that the comment from Reviewer 1 about structural complexity was interesting and worth adding in some wording to the study itself about the impact that the structural complexity of the habitat (or even just variation in habitat in general across the study sites or change in habitat over time) might have on the patterns that you are seeing. Also you mention that there is no dataset that covers the entire spatial extent of your dataset, but do you have any information about the benthic coverage of any of the sites at the time that these samples were collected? If so, would be interesting to investigate what role that might play in the patterns that you are observing.
Minor Comments:
Abstract
- Lines 13-15: human impacts is plural so it should be ‘through their negative’ and ‘were the main’
- The final sentence of the abstract mentions that ‘a comprehensive analysis […] is crucial’ – can you add one more final sentence to your abstract explaining how your findings in this study are crucial? i.e. does knowing what you know now change how you would manage temperate vs tropical reefs? Or change our ability to predict the status of shallow Australian reefs into the future? Elaborating on this statement will help communicate to the reader the importance/relevance of these findings
Introduction
- Nice job, I find it much more compelling and understandable now.
Materials and Methods
- Lines 150-151: Could you add a bit more explanation to this point? My understanding is that you included sites which had at least 7 years of data between 2008-2021 and you filled in the remaining years for each so that every site had data from 2008-2021? If that is indeed the case, could you add some wording or make a graph describing the number of years that made up the gaps that you filled in? Because, to me, this method seems quite reasonable for a year or two but if you’re filling in longer gaps it gets a bit dicier (as illustrated in fig S6).
o I am also having trouble interpreting Fig S6 – I can understand the difference between the two columns but within a column, what does each plot represent? Because each plot looks to have 25 points. Are they different replicates of the same test, of the 100 that you simulated? Please clarify.
- Watch your grammar
o there were a couple of instances where you need to add an ‘s’ to the end of the word
 E.g. Line 171: followS, line 187: linkS, line 225: followS, line 303: regressionS
o Also in line 298-299: should it be ‘first we ran linear models’?
- Lines 306-310: What you describe in the two sentences on these lines sounds like justification for the method that you described in the lines above, which is a bit confusing. Consider re-ordering.
Results
- In the abstract, the authors mentioned “Our results indicate higher asynchrony in tropical reefs due to higher trait diversity and trait redundancy and higher species stability in temperate communities due to higher mean trophic level.”. I found this result really compelling. But I couldn’t find this result in the results section, could you make it more obvious where this result comes from? Also is this a linear or a non-linear trend, i.e. do you see a distinct difference between temperate vs tropical communities?
Discussion
- Lines 481-482: The sentence “These results also link to the increasing mean community body size with the year-to-year variability in sea temperature” – this sentence is hard to parse, do you mean that the mean community body size increased as SST increased or that the mean community body size increased as the variability in SST increased?
- The final paragraph is quite short, would be worth adding more about the importance/relevance/implications of the findings of this study. Especially if you can say something that specifically derives from your findings as opposed to the general importance of considering functional diversity/traits.