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Thanks to the reviewers who have made great suggestions. And thanks to the co-authors who did a good job of revisions. This MS is now ready for publication in PeerJ.
# PeerJ Staff Note - this decision was reviewed and approved by Ann Hedrick, a PeerJ Section Editor covering this Section #
The authors have addressed earlier concerns regarding figure presentation/captions, raw data, and requests for additional supplementary data. The paper remains well organized, written, and relevant.
The authors have improved the clarity and repeatability of the experimental methods. I appreciated their detailed response and clarification regarding sampling effort and between-patch comparisons (and the associated revisions to the manuscript) regarding sampling effort. At this time I am satisfied with their rationale for the analytical approaches taken.
No comment (see previous section).
Other minor comments/concerns have been satisfactorily addressed by the authors in the manuscript and/or in their reply to reviewer. I have no concerns with the manuscript as presented.
Thank you to the referees for reviewing this MS. Dr. Ernst has made substantial and important comments and recommendations both in her written review and in an annotated version of the MS. Following revisions and a response/rebuttal by the authors, I will ask Dr. Ernst for a second review.
Very well done
Super
A good look at an important sw Amazon system
Glad to see this finally finished. This manuscript is well written with all the essential elements covered; in addition, it is well illustrated and graphed. There was not even little things to nit-pick upon, except two suggestions: I would call the Guadua bamboo "tall" rather than "large," as at their field site most culms are rarely larger than 2.5" DBH. A second thing is that botanical names require authors and at least the first mention of the species should carry the author(s) name.
Please note: I have provided detailed comments and suggestions in the manuscript, attached as an annotated pdf file. The statements below highlight my overall impressions and some of the key issues that should be addressed prior to publication.
This paper evaluates differences in beetle communities between bamboo-dominated and terra firma forest patches in Amazonia, and in doing so provides data on a poorly understood insect fauna in an ecologically important habitat type. The article is mostly clearly/concisely written, although some sections of the discussion could be re-organized or removed for clarity and flow. The introduction provides adequate background information/literature and clearly states the study objective and hypotheses.
Figures are generally good, but I have some suggestions. For example, Figure 1 should show the location of each study site/forest patch. Figure 4, in addition of being of poor quality, does not add to the reader’s understanding of the experimental design – it should be removed. Figure 11 is similarly not useful. Some of the captions should contain additional information. Some of the tables can be combined.
Importantly, the supplementary information, as presented, does not constitute “raw data”. If more detailed data are not already being provided/made available elsewhere, I have made suggestions in the text for correcting this. I also suggest a second supplemental table be included to provide detailed information about each of the forest patches examined in the study. The authors should also make sure that any code used to conduct the analyses is included (if applicable).
This is an original primary research study within the scope of the journal. The research question and the knowledge gap it intends to fill have been defined clearly. The experimental design and collection methods are sound and rigorous, though some additional information (particularly pertaining to the sites) is required for clarity and replicability. I also had some minor questions regarding terra firma patch sizes/continuity, and possible edge effects from trap placements.
Although the analytical methods the authors used to evaluate differences between forest types and seasonal difference are sound, there is one significant issue with how the raw data were handled prior to the analyses. The authors state that the two forest patches in each pair receive equal numbers of traps, but that patches of different sizes received different numbers of traps – this means the sampling effort is not consistent between patches of the same forest type. A patch with 1 trap will almost certainly have “fewer” species than a patch with 10 traps, simply because one trap will collect fewer individuals than 10.
Patch-level species richness estimates using raw data, and any measure of community structure that uses raw abundance, are therefore not meaningful. The authors briefly address the sample effort in the context of the species accumulation curves, and I agree that when comparing “total species in bamboo” vs “total species in terra firma”, then the effort is the same (but note that I suggest the accumulation curves be replaced by individual-level rarefaction curves). Otherwise, I suggest that patch-level richness be expressed as rarefied species richness, and that any abundance data that are not pooled at the level of forest type be standardized by sampling effort (i.e. # individuals/# traps) before conducting any analyses.
These changes may generate very different results from what is currently presented, and could necessitate a major revision of the figures, results and discussion sections.
Assuming for a moment that the results remain largely the same even after the sample effort issue is addressed, the discussion is, for the most part, a reasonable assessment of the findings, although there are some sections that are poorly structured, or too speculative in their current form (they lack supportive information or justification). The authors’ conclusions relate to the original research question and are placed in a broader conservation context.
Please see the annotations in the attached pdf file for detailed comments and suggestions. My recommendation is “Major Revisions”. The study design and execution is fundamentally fine and the authors have amassed an important data set, but given the issues with the analysis mentioned above, and the lack of adequate raw data, it require a significant overhaul before it can be considered for publication. Given the potential for major changes in the results, I would need to re-evaluate the revision.
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