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This manuscript could have been accepted weeks ago had the authors followed basic reproducibility standards. The code file should be a .R file, not a .R.txt file.
[# PeerJ Staff Note - this decision was reviewed and approved by Dezene Huber, a PeerJ Section Editor covering this Section #]
You included a reference to a DOI. Please:
1) Link the website directly: https://zenodo.org/record/7074506#.YzdOanbMKUl
2) Please rename the code file extension to .R
3) Clearly indicate in the code where the data files are located, using the same file names.
This is the third time I ask and I will ask no more. I will not accept this manuscript until a link to the Zenodo repository is provided in the main text.
Please leave the link of the GitHub repo in the main text of the manuscript and merge tables 2-5 into ~2 main tables.
Figs 2-5 seem repetitive, please select the most relevant ones and leave the rest as supplementary material. Perhaps you could also bring some of the supplementary tables containing the ordination stats into the main text. Finally,
please include a valid link to your GitHub repository.
The revised manuscript has been improved but I would still like to see the RDA/CCA analyses in the main body of the manuscript rather than as supplementary material. As I mentioned previously, I believe this is a much more informative analysis than the purely descriptive NMDS. RDA is certainly not restricted to Euclidean distances, since you are able to run distance-based RDAs, so I would like to see a clear justification for using CCA instead of db-RDA. Also, you could show separate plots for constrained (RDA) and unconstrained (PCA) axes, something that will aid your discussion. Finally, I appreciate the clean and annotated R code, please leave them in an open-access repository of your choosing.
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The revision of the methods and discussion have improved the clarity of the manuscript. I only have a few minor suggestions:
Line 94: what are the height categories from determining low-stature vs. moderate-stature heights?
Line 202: the number of aerial photographs and range of dates used for each site should be mentioned in the main text rather than only the supplemental material.
I do not see Table S1 in the supplementary material.
I have now received two reviews for your manuscript. While they are both positive they raise a number of important issues that need to be thoroughly addressed. In addition, I suggest you run a Redundancy analysis (RDA) instead of a merely descriptive NMDS, to identify drivers of change in community composition and address some of the raised issues. There is an excellent tutorial here: https://www.davidzeleny.net/anadat-r/doku.php/en:rda_cca
[# PeerJ Staff Note: Please ensure that all review and editorial comments are addressed in a response letter and any edits or clarifications mentioned in the letter are also inserted into the revised manuscript where appropriate. #]
Appropriate and professional. There were a few minor typos/misspellings that may necessitate some editorial review.
As written, the methodology for assigning fire exposure category is unclear. While authors consulted historical photos and conducted interviews, information regarding the quantity and timeline of these sources has not been presented. I would suggest expanding on this to clarify how many visuals were obtained, over what timeframe, what could be interpreted from these and whether it concurs with anecdotal reports. A table or figure may help
In addition, more information on the transects is needed for the reader to understand how similar they are in terms of topography (i.e., elevation, slope, aspect, etc.), as this can also significantly influence vegetative communities.
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In regards to the plant species observed, it would be useful to note if any of these are protected, rare, invasive/exotic, etc. as fire regime can affect this.
Strydom et al. examined differences in species diversity and woody plant architecture in areas of the Cape Floristic Region categorized as low, moderate, or high fire exposure. The authors found differences in species cover and growth form among the fire exposure categories, where tall forest species tended to grow in areas of low fire exposure and short fire-adapted shrub species dominated in areas of high fire exposure. This work builds off of previous work from the authors assessing the architecture of dune species before and after fire.
Overall, the manuscript is well-written and easy to follow. The authors did a nice job citing the literature and providing background information on the study region and discussing previous knowledge. The figures are clear and the supplemental material is easy to navigate.
The methods seem fair and data are analyzed appropriately.
There are a few places that need clarification:
Line 224. Do all of these woody species have distinct canopies? If some of these shrubs are clonal, is it difficult to determine the boundaries of an individual during measurements of canopy length and width?
Lines 242-243. Clarify whether the assigned species architectural guild varied among fire exposure categories. For a single species was one guild assigned for all fire frequencies? Or could the assigned guild for a species vary across fire frequencies? This seems important based on the discussion on line 434. How much phenotypic plasticity did you see within species in this study? Were those species dominant across fire categories?
Did you measure all species in the transects or just woody species? I am curious on how the understory changes with different canopy covers in relation to fire exposure.
There were many shared species among the fire exposure categories. I am interested in how the dominance of species shifted among the fire categories. The reader can tease this apart in Table 1, but rank abundance curves may be useful for further quantifying changes in dominant species. The ‘codyn’ package in R has some useful functions for assessing differences in species dominance across sites.
The authors conclusions are supported by the data. I have a few suggestions for improvement of the discussion:
The differences in species diversity among fire exposure categories deserves further discussion. It is interesting that the moderate fire exposure had the lowest species diversity. This is surprising, since in other grassland and savanna systems intermediate fire tends to increase species diversity relative to frequently burned or unburned areas. What is limiting diversity in the areas with moderate fire frequency? What is promoting diversity in areas with low and high fire frequency?
I agree that fire frequency is likely a major driver of species composition and architecture, but could some of the differences in species abundances be explained by differences in topography that result in differences in soil moisture or other edaphic factors? Are there ephemeral streams at the base of the swales that promote the establishment and growth of riparian species? For example, on line 393 the authors discuss competition limiting thicket expansion into the fynbos. Could this also be due to differences in water use requirements among species? Does the drier dune crest meet the physiological requirements of thicket species? I think it is important to discuss your results in the context of different resource availabilities across the fire exposure gradient.
While interesting, the discussion on evolutionary responses of thicket species to fire exposure feels out of place. I’m not sure how this section adds to the take-home message. The paragraph on line 470 is repetitive with the earlier discussion on fire-adapted traits. The idea that hedge forming shrubs are associated with younger lineages could be briefly mentioned earlier in the discussion without as much background information on evolutionary drivers.
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