zenrabbit
commented
4 years ago Recommendation by the Subject Editor (Dr. Johannes Penner): XXX XXX Major Revison XXX
Dear Mr. Zuliani,
I fully agree with reviewer 1 that the manuscript needs a major overhaul. Please consider especially that review very carefully and how the excellent recommendations can be incorporated and manscript be improved substantially.
Looking forward to your revision Johannes Penner
Reviewer(s)' Comments to Author: Reviewer: 1
Comments to the Author In this manuscript the authors describe a study of the impacts of changing shrub cover on vertebrates and invertebrates using camera traps. This is certainly an interesting manuscript which is appropriate for Wildlife Biology. However I found the manuscript very frustrating to read, largely because it looks like it is has been hurriedly put together without proofreading. There are a large number of inconsistencies, the Methods need more information and refinement, and in my view, a great deal of critical literature has been omitted.
A central issue I had with this manuscript is that it is essentially about shrubs, shrub density and shrub cover, but there is no literature on what I would have expected to have seen; a discussion of shrub encroachment, thickening, savanization, or whatever you like to call it. There are many papers on the effects of increasing shrub dominance on biota, both vertebrates and invertebrates, but these have not been accessed by the authors. I would have expected the more senior authors to have pick this up before submission. Further, there is a preponderance of literature, mainly from North America, which is disappointing, on facilitation, density dependency and associated ecological processes. Even a cursory glance of the encroachment literature (e.g. Jing et al 2020) or the many papers from the western US by Archer, Bestelmeyer and the many colleagues will reveal abundant literature on the impacts of changing shrub cover/density on organisms.
This leads me to the next issue, which is that it wasn’t until I got to the Results and the tables of linear models and their coefficients, that I realised that the authors were using camera traps to capture the activity of invertebrates. When the authors talk about local animal community at the end of the Introduction, I would have expected to see some prediction about what might happen with invertebrates, or at least mention the fact that invertebrates were an important focus of the study.
I’m also not convinced about the structure of the Introduction. The Introduction starts off with a discussion of positive interactions between plants and animals, the role of facilitation and positive interactions, but most of the references supporting this come from plant-plant examples. The manuscript considers the relationship between plants and animals. I was expecting therefore to see an Introduction with a clear progression that included four principal topics (paragraphs): a general discussion of plant-animal interactions with some examples, a discussion of the phenomenon that the authors are studying (increases in shrub density/cover), something about the authors’ study system (the target shrubs, why they are encroaching, why they are a problem, if they are a problem), and then a final paragraph that presents some hypotheses or predictions. Without this clear roadmap, and the final predictions, the manuscript languishes, and it wasn’t clear to me what the main take-home messages were.
It is also unclear why the authors couched their gradient in terms of shrub density, which tells us nothing about the extent to which these target shrubs occupied the landscape. It would seem more logical to describe the gradient in terms of shrub cover. After all, cover is related to potential habitat, protection of the soil surface and therefore niches for invertebrates, production of litter etc. I am yet to be convinced that density is a good attribute to use to describe such a gradient.
Please try not to use acronyms; they are a very poor way of writing and can only confuse the reader. Define residual dry matter at the beginning and call it something throughout (hereafter litter).
Methods
I found the methodology to be very confusing. There is just not enough information in this section for me to be able to be confident of the veracity of the particular field methods. Here are some examples:
How can there be 24 transects if there are 12 transects and three per plot?
The authors indicate that they sampled three shrubs and three open areas per plot except for sites containing less than three shrubs or no shrubs but there is no indication what the authors sampled in these latter situations
I would expect to see some discussion about the how the authors handled multiple repeats of the same animal. Perhaps it’s not an issue but at least you need to talk about it so that the audience is confident about what you did.
Statistical analyses
Did the authors use dry matter, temperature and shrub cover as covariates or as random effects; this is unclear, though they do say covariates. It is also unclear why shrub cover would be used as a covariate/random effect when I would assume that there would be a relationship between shrub cover and shrub density, but perhaps I’m wrong.
What multivariate analysis of composition did the authors use? Is this the same as PCoA or did you do another analysis?
There is nothing in the Methods about measuring evenness nor why you would be measuring it. Similarly there is no indication in the Methods how you assessed evenness. And what exactly did you do with sites that had fewer than three shrubs?
Why is there an analysis for residual dry matter in Table 1? Surely you are looking at the effects of shrub density on animals and using dry matter as a covariate/random effect
What is cover in Table 1? Is this plant cover or shrub cover?
It is unclear to me what density:microsite, density: phylum and micro-site: phylum are. I think I understand that they are interactions that it seems a weird way to present these analyses. Perhaps coefficient plots might be a better way of showing all of these things.
I found Figure 2 quite difficult to interpret. Might it not be better to have four panels as you have, but showing: open vertebrates, open invertebrates, shrub vertebrates, shrub invertebrates?
Similarly, not being an animal person, I don’t recognise a lot of the scientific names. It would be useful to denote whether they are vertebrates or invertebrates.
Results
I would tend to lead with a summary of the overall results (L240 – 243, L263 – 267), then go on to talk about the effects of increasing shrub density cover.
There is a lot happening in these results, and it would be good to try to streamline them a bit more. You could say something like “Increasing shrub density was associated with increases in x, y, z but declines in a, b, c (Fig. #)”
Composition cannot increase (L 244), it can only change,
I have problems with statements that say X predicted Y otherwise we get into potential issues of causality. I would rather see statements such as (L257) “Both animal abundance and evenness were highly positively(?) correlated with increasing shrub cover”
Discussion
It is nonsensical to say that we would establish a shrub density gradient to increase the abundance of local vertebrates (L279-281). I think what you are alluding to is that the presence of shrub density gradient might lead to increases in X, Y, Z,
I know this might seem pedantic, but burrows cannot suggest anything (L 291). You could say that ‘The presence of burrows beneath shrubs suggests that this species…………..’ Similarly, you can appreciate the help or assistance you have received from BLM (L 361)
I can imagine that you have temporal data from your camera traps on animal activity during the day, but I did not see it in this manuscript. Therefore the statement in L304 – 306 is not supported by the results of your study.
References
A couple of things about the references. A large number of references certainly shows scholarship, but a good journal generally restricts the number of references to 50 or fewer. I would like to see more international literature and some attention to missing literature on the impacts of encroachment or shrub increase on animal communities.
Minor points
L 90: shrubs and shrub density. Why talk about both? Surely you can’t have shrub density unless you have shrubs. L 109: spp. or sp. are not a italicised L 117: californica L 126: numbers less than 10 spelt out in full, except for units of time L 127: were recorded L 136: what is a walk-through survey? Do you mean time-based sampling, optical reconnaissance sampling or what? I suggest that you refer to and cite an appropriate text or monitoring manual (e.g. Elzinga et al.). L 156: data are plural…..” All camera trap data were recorded….” L 175: phyla. I would not be calling invertebrates and vertebrates phyla, they are all animals and therefore are in the animal phylum. L 179: spelling of poisson L 246: residual dry matter is a proxy for vegetation effects……… I think this is what you mean. Relative dry matter is not capitalised, it’s no different to biomass L 250: Invertebrate species richness and evenness increased ……….. L 251: local? What do you mean by this? Is this the same as residual dry matter L 335 and elsewhere: Refugia is a better word to use here
I think that there is a potentially really interesting story here, but it needs some reorganisation, attention to detail, and serious review by the more experienced co-authors before it is resubmitted to any journal. Good luck with your revisions
David Eldridge August 25, 2020
Reviewer: 2
Comments to the Author You have conducted a study combining trap cameras and transect surveys with measures of shrub density and correlated factors. You obtained a wealth of data which you have analyzed with appropriate statistical methods. The results show interesting interactions that are likely to inform restoration objectives and methods in drylands. Your figures in particular convey your results extremely well.
However, your paper suffers from a host of spelling and grammatical errors which detract from your results. I have transmitted a few hear but there are likely others I have missed. Prior to acceptance I would expect you to conduct a thorough reread and perhaps get an outside reader to copy edit for you.
I also suggest you consider citing one or more of these papers on the interaction of shrub density and vertebrates:
Germano, D. J. and C. R. Hungerford. 1981. Reptile population changes with manipulation of Sonoran desert shrub. Great Basin Naturalist 41:129-138.
Germano, D. J., C. R. Hungerford, and S. C. Martin. 1983. Response of selected wildlife to mesquite removal in desert grassland. Journal of Range Management 36:309-311.
Germano, D. J., and D. N. Lawhead. 1986. Species diversity and habitat complexity: Does vegetation organize vertebrate communities in the Great Basin? Great Basin Naturalist 46:711-720.
Here are some errors I found:
Line 92: This sentence runs on: “c. direct local 93 differences in microclimate between shrub and open microsites have indirect effects through 94 residual dry matter on the soil surface mediates shrub-animal associations.”
Line 114, typo, should be: and the min was 0 and max was 12
Line 117, the species epithet should not be capitalized.
Line 129, typo, should be: either suspended above ground or on a stake or embedded in the soil
Line 179, I believe “quasipoisson” was intended here
Figure 2: “Leopard lizard” should be represented as “Gambelia sila”
Line 272 & 273 “influence” should be singular
Line 289 “Observations…suggest (singlular)”
Line 312 I would say “shrubs may be fundamental”
Line 322 would be better stated as “where a large abundance of grasses were present under the canopy” Line 324: over interpreted, I would say: “avoidance of these specific areas may serve as a beneficial survival technique”
Table 1: Should be “Gambelia” and Great Basin Gopher Snake should be Pacific Gopher Snake
Line 720 The species epithet for Ephedra californica should not be capitalized
new map for fig 1 still needed - one with region, insert etc like I sent you for Nature Ecology and Evolution paper. combine fig 1 and 2 and map one sweet and clear map fig 3 - rename circle 'Shrub plot' to 'plot' please - ie you can have a plot without shrubs fig 3 still not there for me - needs be jazzed up more when you have time after you get thesis into library - solid shrub icons, relative sizing, little n and N like I asked for, show replication of plots either in words or via a much deeper figure, use a little cam trap icon, replace triangle with a little person icon etc.. list total number of days sampled in plot - ie make it so sweet fig 5 etc - make shrub line green, size = 2, and open line black or another color etc. cut null from stats tables, and revise to match journal style fig 6 in the version you sent is missing vert and invert???