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Nothing further. Thanks for the comprehensive final editing.
[# PeerJ Staff Note - this decision was reviewed and approved by Dezene Huber, a PeerJ Section Editor covering this Section #]
Thank you for carrying comprehensive revisions to the manuscript. The reviewers and I are mainly happy with the new text, but the study would still benefit from some further revisions (see reviews). Would it be possible to insert the main two or main four leopard prey species into the abstract? Also, the Discussion would read better if the wider literature was more thoroughly integrated with the existing text (especially for a journal with a broad readership). I look forward to seeing the next version.
[# PeerJ Staff Note: It is PeerJ policy that additional references suggested during the peer-review process should only be included if the authors are in agreement that they are relevant and useful #]
I think the paper has improved a lot in terms of both clarify and language.
They added more citations from diverse regions. I still encourage them to use the following citations which appears to be in line with their research:
Mohammadi, A., Lunnon, C., Moll, R. J., Tan, C. K. W., Hobeali, K., Behnoud, P., ... & Farhadinia, M. S. (2021). Contrasting responses of large carnivores to land use management across an Asian montane landscape in Iran. Biodiversity and Conservation, 30(13), 4023-4037.
Snider, M. H., Athreya, V. R., Balme, G. A., Bidner, L. R., Farhadinia, M. S., Fattebert, J., ... & Kays, R. (2021). Home range variation in leopards living across the human density gradient. Journal of Mammalogy, 102(4), 1138-1148.
Soofi, M., Qashqaei, A. T., Mousavi, M., Hadipour, E., Filla, M., Kiabi, B. H., ... & Waltert, M. (2022). Quantifying the relationship between prey density, livestock and illegal killing of leopards. Journal of Applied Ecology.
Lumetsberger, T., Ghoddousi, A., Appel, A., Khorozyan, I., Waltert, M., & Kiffner, C. (2017). Re‐evaluating models for estimating prey consumption by leopards. Journal of Zoology, 302(3), 201-210.
There are still a couple of minor issues such as : Line 97: Please remove IUCN Red List of Threatened Species as it is not a citation, just use the proper citation, or the name of the author they cite is Linnell. So I think some minor revisions are needed and after they checked the whole manuscript thoroughly then the paper should be good to be published.
I think now they do a better job in explaining their methodology.
no comment
There are some new readability issues as you have added a lot of new text, but these can be fixed by a careful read through, dividing up and rearranging long sentences, and checking grammar (e.g., lines 66-71, 503, 534-539, 606-607, please don’t start sentences with “And” and such). In line 179 you change detection probability to detection behaviour – are these two equal?
The rewording of the abstract, introduction and discussion has improved the context and has provided more links with other studies outside of South Africa, as well as addressing the knowledge gap. The introduction has a better structure and now includes more varied citations. However, it would be nice later to expand on the similarities/differences of existing papers (even those with other big cats) with your results about leopard prevalence in Piketberg, and overall implications in order to gain a global perspective, expanding around line 479. I also previously asked if there were any incentives/protection measures for facilitating leopards on transformed land in South Africa; please mention even if there aren’t any.
Thank you for clarifying the cannibalism in leopards. For the differences between livestock areas and non-livestock areas (Figures 5B and 5C), I appreciate that you have split the figures up for readability, but I’m still not convinced this is clear, as 5B and 5C look very similar, which may cause confusion - is there any other way you can show this difference other than these two graphs?
It may be useful to have a reminder of the names of the “main” prey species in the results section (e.g. those listed in introduction at line 140). Also, please clarify how you distinguished the presence/absence of disturbance in the supplementary table (was it people presence, rubbish, footpaths etc?) as it may help us to understand results such as porcupine in Piketberg being less likely to be detected near human habitation but more likely to be in areas of human disturbance (lines 430-433).
Separately, you mention that the leopard population has already been shown to remain stable during the decade before and during the years this study was performed in Cederberg – I think it would make sense to mention this in text and give some more background to the limitations. Seeing as you think your conclusions would still hold true, you could mention this population boom in Piketberg or hypothesise how the weather differences between the two years could influence community structure?
Thank you for including an ethics statement and additional information about human subjects; you could add this in-text for extra information about how you treated confidential data.
Thank you for revising your discussion section, it is easier to read now and has a better flow. There are some parts that are not particularly clear however, as some results are phrased in a way that seems as if they have the same relationship strength. The hyrax/caracal link is still a little confusing at first as to how hyrax avoid caracal but caracal choose areas with higher hyrax activity (lines 518 to 523), so may need further rephrasing on some conclusions.
Thank you for submitting this study to PeerJ. I regret that I am unable to accept the manuscript for publication, at least in its present form. However, I am prepared to consider a new version that carefully takes into account the suggested edits. The reviewers liked many aspects of your study but also highlighted some important parts for revision. These need to be addressed in detail in the new version. Such a revised manuscript may be reviewed again and there is no guarantee of acceptance. Please pay close attention to the Methods section of the paper, and be very clear about the ethical approval for the research, e.g. "The authors must provide an ethics statement as part of their Methods section". Does the permit cover the ethics of the research? Please provide additional information.
See this PeerJ link for additional guidance: https://peerj.com/about/policies-and-procedures/#animal-research
When you revise the study, please prepare a detailed explanation of how you have dealt with all of the reviewers' as well as my own comments.
[# 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. #]
This paper provides important insights into leopard ecology and its prey in Africa using diversity indices and occupancy modeling. Even though the paper has been written great, it still can be improved in terms of grammatical flaws. In general, this paper lacks a flow in its introduction. Perhaps the main flaw is that they built multiple occupancy models for different prey species without incorporating each species' unique ecology into their models. Moreover, authors should provide more citations from other leopard populations both in Africa and also even Asia as of right now to me it is a local-scale study that suits local journals.
I will point out my specific comments about the whole manuscript in detail below (Additional comments section).
- I’m confused about why occupancy models were created for all the species? Does data availability govern your choices or …? Please explain.
I think their findings are valid, my only concern is the occupancy models as I mentioned earlier.
I appreciate that authors uploaded all of their data and r codes.
Their conclusions are not well-stated and backed up by their data, and analyses.
Abstract:
In general, please restructure your abstract, and instead of starting with leopards from the very beginning, talk about the bigger picture. You should provide 1-3 lines of context for the readers.
Introduction
-Your introduction in its current form is suitable for a local journal or a cat specialist journal as you talked about leopards and Western Cape a lot. What you have to do is to talk about the bigger picture and ecology, this way you can absorb more readers from diverse backgrounds.
Line 56: I would suggest restructuring the opening as in its current form its not ideal for the first sentence of the first paragraph.
Line 67: It is too early to start talking about leopards
Line 52-55: It is too early to be that specific and talk about your study species in such a general sentence. You don’t need to talk about all four of your study species ecology instead talk about the processes (habitat suitability, anthropogenic impacts, why these species matter, …) in your introduction.
Methods:
Line 175-176: What do you mean by that, you should either cite a paper that you followed or just explain it here.
Line 176-179: There is no need for this information, you can talk about it in the discussion but not here.
Line 179-181: Please mention the home range size as well.
Line 191: For the covariates table in your supplementary, please add the citation for each of them that justifies its relevance to species ecology.
Line 225: I don’t think taxonomy would be a great equivalent for species composition, its basically a field of science dealing with naming species, but us as ecologists use species composition simply for knowing the number of species, so please remove that.
Line 290: Please correct the sign before QAIC (I assume its delta)
Results:
Line 296: You mean 10114? Please remove the space.
Line 297: Please remove the space between numbers.
Discussion
Right now you only cite papers mainly from that area or some general citations about leopards (not as diverse as it should be).
You should also discuss some papers from other parts of the world on different subspecies of leopards: Indian leopard, Persian leopard, African leopard in other countries, etc.
Also on top of that, you should see the big picture and compare your results even with different ecosystems with big cats (Jaguars in South America, Tigers in Southeast Asia, Cougar in North America?).
Figure 1: The towns/villages sign in figure 2 is confusing, it is even outside of the study area boundary, so what are you trying to show?
Figure 4: The quality on these graphs is so low and the axes are hard to read, I don’t know if the journal is going to be ok with it as well, so if possible, increase the quality on these.
The basic reporting is professional and readable throughout. The structure of the article conforms to acceptable format and the camera trap data is converted into excel files; both the excel data and R code can be opened. Clarity can be improved in some places by using simpler phrasing if there is an alternative available (e.g., extirpation vs local extinction) or dividing up longer sentences for ease of reading (e.g., lines 85 to 90). There are some areas where text can be improved for understanding, but these are detailed below.
You give good background information on leopards and their prey in this region, and sufficient knowledge to understand potential human-animal conflict in South Africa. I would like to know further information on current conservation on private lands and how much is known about leopards on these farmlands that isn’t about conflict? Are there any incentives (e.g., tourism, grants) for farmers to facilitate leopard occupancy, or are there any current measures of protection on private land? If there aren’t any, please say so. It would also be interesting to know if there are any other comparisons of apex predators between conservation land and farmland elsewhere in the world, and how this study relates to them and this knowledge gap. Are most existing leopard studies in South Africa performed in protected areas, and this is the first to examine them outside?
Figure 1 names the green area on the map as CapeNature Reserves - could you please clarify that the Cederberg areas listed in text (lines 153-154) are known collectively as the CapeNature Reserves? If not, please clarify what the CapeNature Reserves are to those unfamiliar with South Africa.
There are a few areas where it is unclear whether leopards are being included with the result numbers and it could affect the readability of the text; could you please clarify throughout when you are talking about all medium-to-large terrestrial mammals or just prey species? For example, the phrasing in-text (lines 308-310) about Table S2 and the numbers you draw from it are a little confusing; you mention “Thirty potential natural prey species were photographed across the two regions”, but Table S2 has 30 entries including leopard. My apologies if you are including leopards preying on each other, but maybe you could mention this or change the phrasing to “Thirty terrestrial mammals…” to avoid confusion?
On line 357 could you please expand or rephrase “leopards were less likely to be detected … in areas utilised for grazing (Table 1; Figure 4G & H)”, as I first interpreted it as “leopards are less likely to be detected in areas with livestock”, which suggests a difference between the figures 4G and 4H for all the vegetation types. If there is a difference, can you please draw attention to it or use a different figure, as at first glance there is none? If “areas utilised for grazing” does not equal “livestock”, please also clarify this.
Overall, the submission is self-contained and coherent; I think that the ideas and study design is great, you’ve measured a lot of environmental and anthropogenic factors, and looked at each species in depth. Your aims are clear, to determine if there was any difference in leopard and prey populations between the two areas, and the factors that affected animal distribution.
I believe this is an original primary research article within the aims and scope of PeerJ. I find the study interesting and meaningful, but I would like a little more information on how your research fits with the knowledge gap about apex predators outside of conservation areas (as discussed above, e.g., are there any existing studies similar and what did they find), and if yours is the first in this knowledge gap please identify and say this.
Investigation is to a high technical standard, methods and information on site selection/factors are detailed. For more information, could you please say if there was/was not any notable large differences between the two sampling years that are not listed, e.g., weather, population boom, that could have affected differences in rate?
In the methods or results, could you please clarify that you are counting the water mongoose spoor (as observed in the initial survey but not in the camera traps) in the richness estimates, as I needed some time to figure out why the numbers on line 309 are different to the richness estimates for Piketberg and not for Cederberg.
It may be helpful to have more information on the predominant livestock in this region (e.g., are they cattle?) and if possible, the distribution of the different types of the 55 farms. It is probably not possible, but did you look at any differences in occupancy between different types of farm land use, e.g., fruit vs crop?
My main concern with the methods section is that there is no ethical statement. Even observational studies require further information about ethical approval, and since you are dealing with camera traps, this may require human ethics too. Please provide an ethics statement as part of your methods section detailing full information as to approval, granting organisation, reference number and if you followed guidelines for ethical standards during this study. As you are using camera trap footage, I would also like to know whether you sought human ethics approval, as cameras can also capture images of humans throughout, and I would also like to know how you approached this data when analysing (please see Sharma et al. (2020) Conservation and people: Towards an ethical code of conduct for the use of camera traps in wildlife research. https://doi.org/10.1002/2688-8319.12033) for more information.
This study is not implied to be replicated or derivative of existing work, and apart from not being able to record livestock, I believe the authors did a good job of recording species and extrapolating information from the camera trap records. The number of species, abundance and factors affecting mammal occupancy are largely explained well and in detail. Sometimes I was a little confused about how you phrase or conclude relationships between prey and predator distribution, as some parts in the discussion are phrased in a causative, directional way. This could be improved by re-phrasing some parts on which animals “avoid” each other (for example, the relationship between hyrax and caracal), and explaining how it is not due to other confounding factors. Overall, conclusions are well-linked to the original research aims.
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