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After reviewing the last revised version of your manuscript, I see that the main comments suggested by the reviewers have been included, while the suggestions not considered are justified in detail. Therefore, I am satisfied with the current version and consider it ready for publication.
[# PeerJ Staff Note - this decision was reviewed and approved by Richard Schuster, a PeerJ Section Editor covering this Section #]
After reviewing this revised version of your manuscript, I see that the main comments suggested by the reviewers have been included. However, there are still some details that need to be clarified before having a final version that can be published.
L64 & L67: the first sentence begins with “Alpha diversity” but the following sentence begins with “B-diversity”
I will default to the editor’s decision about which format they prefer, but I would suggest being consistent between the two sentences.
L177: Should “survival specimens” say “surviving specimens”?
L208-210: this small paragraph can be combined with the previous
L221-226: This is a very long sentence, I would suggest splitting this up
L247-251: Erythrolamprus typhlus shows only 1 individual in Figure 3A and Table 1 but is not included in this list
L248: Corallus hortulana here but Corallus hortulanus in Figure 3A and Table 1
L267: I think it is warranted to provide a citation at the end of this sentence, even if it is personal observation or unpublished data
L332: I would suggest changing “Together, these factors contribute to reduced…” to “Together, these factors likely contributed to reduced…”
L380: the word “and” between the two species names should not be italicized
L388-390: I think this is a strong statement given the relatively short duration of the sampling and would suggest replacing “can significantly” with “might”
L148: I would suggest also adding the annual temperature range in addition to the mean
L210: Would median values be more meaningful? Or are mean and median values not that different between the wet and dry seasons?
Addressed in other sections of this and the prior review
Overall, I am pleased with the improvements made in this version of the manuscript. The objectives in this version reflect the experimental design, duration, and scope of the project. Substantial improvements have been made in regard to the level of detail in the Methods section, and address prior confusion I had when reading subsequent sections. However, I still contend the level of detail in all figure and table captions is insufficient to stand alone and should be addressed before final acceptance. I believe this manuscript provides a crucial baseline for the diversity and temporal dynamics of snakes in the region, adds valuable information to our knowledge of snake communities in Brazil and beyond, and would be of interest to the readers of PeerJ.
After reviewing this revised version of your manuscript, I see that the main comments suggested by the reviewers have been included. However, there are still several background details that need to be clarified. Therefore, I personally reviewed each of the points raised, however, after reading the manuscript, I realize that most of these modifications require more detail.
It is important to consider the comments of reviewer 2, especially regarding objectives 2 and 3, regarding the factors affecting the temporal dynamics of the community and the biotic mechanisms that influence the stability or instability of the study community. With the methods used, it is difficult to examine the factors affecting the community, and consequently, the discussion is merely speculative.
Within the experimental design, the interruption of sampling due to the global pandemic is still unclear, as some animals were recorded between November 2020 and December 2022. Therefore, this point needs to be clarified.
More information on the methods used is needed, particularly on the criteria and characteristics of the trap locations.
Also within the methods, it is still unclear how sample coverage is used to assess the completeness of the inventory; therefore, it is necessary to include an analysis of sample coverage for each season to validate comparisons of both species richness and turnover.
In Table 1, the two potential new species are indicated with the number "1"; however, it would be better to replace this with a asterisk "*" to avoid confusion with the other numbers in the table.
**PeerJ Staff Note:** Please note that this revision has only been reviewed by the Academic Editor at this point. Once you have addressed their comments, it might still need to be sent out for peer review.
Thank you very much for your manuscript titled “On the composition and temporal dynamics of a snake community at the Cerrado-Amazonia ecotone” that you sent to PeerJ.
This study presents very valuable and relevant information on the snake richness and community structure of a snake community in a Brazilian transition zone, also analyzing the temporal dynamics of the snake community.
As you will see below, comments from referee 1 suggest a minor revision while reviewer 2 has serious observations and suggests rejecting the manuscript. Given this, I would like to see a major revision dealing with the comments. Their comments should provide a clear idea for you to review, hopefully improving the clarity and rigor of the presentation of your work.
Reviewer 1 has several editorial suggestions to improve the presentation and understanding of the manuscript.
Reviewer 2 identified several problems in the study that compromise its robustness and scope. This relates primarily to the formulation and failure to meet two specific objectives, as well as to the study design, which is lacking in detail or unclear in several aspects, including data analysis and interpretation of results.
Please note that we consider these revisions to be important and your revised manuscript will likely need to be revised again.
**PeerJ Staff Note:** Please ensure that all review, editorial, and staff comments are addressed in a response letter and that any edits or clarifications mentioned in the letter are also inserted into the revised manuscript where appropriate.
L15: I would suggest changing “for biodiversity conservation in the Anthropocene” to “for conservation of biodiversity during the Anthropocene”
L16-17: I would suggest changing “the largest forest-savannah transition zone globally” to “the largest forest-savannah transition zone in the world”
L17: I would suggest starting the sentence with “We also…”
L18: I would suggest removing “the” before community structure
L19: I would suggest changing to “The community had a balanced mix…”
L25: I don’t feel strongly one way or the other about snake community vs assemblage, but I suggest being consistent
L25: I would suggest rephrasing to “The snake assemblage was active throughout all seasons”
L26-27: I would suggest rephrasing to “high appearance rates during wetter periods and a high disappearance rate of species during the dry season”
L27: I would suggest changing “exhibits” to “exhibited”
L33-35: The sentence of two potential new species should be moved up to the results portion of the abstract and I would suggest rephrasing as “We also identified two potential new species, emphasizing the urgent need for further …”
L36: I would suggest rephrasing as “herpetofaunal diversity” or “diversity of herpetofauna”
L48: I would suggest changing “due to” to “because of”
L49: I would suggest starting sentence with “Such temporal shifts”
L52-53: I would advise against beginning both sentences with the transitional words
L58: In-text citations should be in chronological order
L60: I would suggest changing “in the Anthropocene” to “during the Anthropocene”
L69: I would suggest formatting as “- and -diversity”
L71-72: In-text citations should be in chronological order
L73-74: I would suggest formatting as “-diversity”
L77: I would suggest changing “while” to “whereas”
L85: I would suggest rephrasing to “…because they are powerful predators”
L86: I would suggest changing “food specialization” to “dietary specialization”
L87: I would suggest changing “while” to “whereas”
L90: I would suggest changing “Due to” to “Because of”
L93: In-text citations should be in chronological order
L94: I would suggest rephrasing to “several studies concerning snake communities…”
L95: I would suggest changing “in drier months” to “during drier months”
L95-96: In-text citations should be in chronological order
L99: I would suggest rephrasing to “…high turnover rates explained by -diversity”
L100: I would suggest reversing the order of “more influenced”
L101: I would suggest formatting as “-diversity”
L102: I would suggest rephrasing to “…activity patterns of snakes are positively influenced…”
L103: I would suggest changing “probably due to the interactions” to “likely because of interactions”
L104: I would suggest moving the portion after the final comma to be in the parentheses, such that it reads “… with biotic and abiotic variables (e.g., prey availability and latitude; Jesus et al. 2023)
L105: I would suggest rephrasing to “Herein, we examine factors influencing…”
L106: I would suggest changing “close to” to “near”
L106: I find the ending of the sentence “regarding species composition and seasonal turnover” to be awkward and suggest rephrasing it in such a way that retains the original intent
L108: I would suggest changing “In the rainy season” to “During the rainy season”
L110: I would suggest changing “which are part of many snakes’ diets” to “many of which are preyed upon by snakes”
L116: In-text citations should be in chronological order
L117-118: I find the sentence to be a bit clunky, and would suggest breaking the thought into two sentences that retain the original intent and prevent readers from becoming confused
L120: In-text citations should be in chronological order
L120: Because every objective begins with “to” I would suggest changing “Therefore, our objectives are:” to “Therefore, our objectives are to:”
L121: I would suggest changing “describe the snake species composition in a locality” to “describe the composition of snake species in a locality”
L122-123: I would suggest removing “compared to the dry season”
L123: I would suggest changing “due to” to “because of”
L129: In-text citations should be in chronological order
L130: I would suggest formatting as “- and -diversity”
L131: I would suggest changing “Due to the high degree of conversion of natural areas by anthropic actions” to “Because of the high degree of land conversion for anthropogenic needs”
L133: In-text citations should be in chronological order
L134: I would suggest changing “deserves special attention in understanding” to “allows a unique opportunity to understand”
L135: I would suggest changing “due to” to “because of”
L136: I would suggest changing “anthropic” to “anthropogenic”
L138: I would suggest changing “We conducted the study in” to “We surveyed in”
L140: I would suggest changing “The vegetation found at the park” to “The vegetation within the park”
L150: I would suggest changing “Our sampling occurred from” to “We sampled from”
L151: I would suggest changing “Due to” to “Because of”
L153-154: The two paragraphs can be combined
L154: I would suggest changing “To capture snakes, we used” to “We captured snakes using”
L155: I am assuming the top of the bucket was flush with the ground’s surface. If so, I would state so
L157: I would change “For the temporal dynamics” to “To assess temporal dynamics”
L157: The phrase “each month yearly” might be confusing for some. I would suggest replacing “yearly” with “during all sampling years”
L158-159: I would suggest changing “In addition, we actively searched” to “We also actively searched”
L169: I would suggest changing “All the activities were processed under” to “All activities were conducted under”
L175: I am not sure what “(same approach)” is referring to, please make it clearer or remove
L182-183: I would suggest combining the sentence as “…package (Hsieh et al. 2020), which estimates biodiversity…”
L189: I would suggest changing “allowing an understanding of the relationship” to “providing an opportunity to understand the relationship”
L190: I would suggest changing “To make the map” to “To produce the site map”
L193: I would suggest removing “the” in the phrase “analyzed the capture history”
L194-196: I would suggest rephrasing to “For our temporal analysis, we represented capture history of each snake species as a binary variable (0 or 1)”
L199: I would suggest changing “Additionally, we assessed” to “We also assessed”
L206: In-text citations should be in chronological order
L208: In-text citations should be in chronological order
L219: I would suggest rephrasing to “Species accumulation curves indicated a tendency for stabilization”
L220: I would suggest rephrasing the beginning of the sentence as “The family Dipsadidae contained the highest richness…”
L220-222: I would suggest using the “spp.” or “sp.” abbreviations for each of the species abundances per family
L235-236: I would suggest changing “of the dry season” and “of the wet season” to “during the dry season” and “during the wet season”
L238: I would suggest changing “in the wet seasons” to “during the wet seasons”
L239: I would suggest changing “where the community experienced” to “when the community experienced”
L240: I would suggest removing “a” from the phrase “characterized by a significant species loss” or changing it to “characterized by a rate of significant species loss”
L241: I would suggest changing “wholly sampled due to the” to “fully sampled because of the”
L241: I would suggest beginning a new paragraph with “Stability metrics…”
L247: I would suggest changing “suggesting” to “indicating”
L253: I am not sure if ecologically unstable is the best descriptor, perhaps heterogenous?
L253: I would suggest changing “due to” to “because of”
L256-257: I would suggest rephrasing to “We also added 23 species to prior lists”
L257: I would suggest changing to “…the combined data were”
L259-260: In-text citations should be in chronological order
L262-266: there is a lot to digest in these lines, perhaps listing the species names alone and pointing readers to an appendix would reduce the clutter
L268: I would suggest changing “may be linked” to “might be linked”
L271: Might be more consistent to say “warmer/wetter periods” and “colder/drier phases”
L272: In-text citations should be in chronological order
L274: I would suggest changing “due to” to “because of”
L280: I would suggest adding “likely” between “ecotone” and “reflect”
L282: I would suggest rephrasing to “Our analysis of temporal dynamics”
L283: I would suggest replacing “intimate” with “seeming”
L284-285: I would suggest changing “due to” to “because of”
L287: In-text citations should be in chronological order
L288: I would suggest rephrasing to “with wetter periods marked by more species appearing”
L290: I would suggest removing “The” at the beginning of the sentence
L291: I would suggest rephrasing “diversification of snake diets” to “diversification of prey resources available to snakes”
L294-295: In-text citations should be in chronological order
L295-296: I would suggest rephrasing “most species in this study prey mainly on amphibians and lizards” to “most species in this study disproportionately prey upon amphibians and lizards”
L304: I would suggest rephrasing as “… (e.g., Drymarchon corais, Boa constrictor), whereas others are…”
L312: I would suggest changing “suggests” to “indicates”
L316: I would suggest changing “due to” to “because of”
L324: I would suggest changing “This dominance” to “Such dominance of a few species”
L333: Depending on how the editor feels, I would advise against beginning the new sentence by abbreviating the genus
L334: I would suggest lightening the language with “exhibited declines,” we know detection probabilities of snakes, even when trapping, is quite low and many individuals might have gone undetected
L334 & L336 : I would suggest changing “in the wet season” to “during the wet season”
L337: I would suggest changing “likely” to “potentially”
L342: I would suggest replacing “fauna” with either “community” or “assemblage”
L344: I can tell from Table 1 that one of the two potential new species is Apostolepis sp., but what was the other? I would suggest indicating both in the Table with some symbol, as well as a quick mention in the first paragraph of the results
Figure 2 legend has a “0” next to the orange circle; I’m not sure if that was intentional, but it and the symbol could be removed and I think readers could still understand the figure from the caption
Figure 3 caption could be rephrased to “Temporal dynamics of the snake community between …”
Figure 3 caption: I would suggest changing “Blue line: total turnover observe” to “Blue line: total observed turnover”
There is a typo in the Figure 4 caption for “Rank clock”
Table 1: I find the two habitat columns confusing; I would suggest combining into a single column or somehow adjusting the contents in each of the columns so there is no redundancy and the column headers are different. Additionally, I don’t see “SAB” defined (maybe semi-arboreal, which is defined as SA in the caption?), but it is used for the Oxybelis spp. and Spilotes sulphureus
Table 3: I would suggest adding “rate” to the column headers such that they read “Appearance rate” and “Disappearance rate”
Table 4: I see Loreau and Gross cited in the methods section, are these two different ways to estimate synchrony? If so, need to include that in the methods
In-text citations for three or fewer authors should have all author names listed and “et al.” reserved for 4 or more (e.g., L114, 182, 210, etc.)
In L151-153, the authors describe interrupting sampling because of the global pandemic, but mention animals recorded from November 2020 to December 2022. I am confused how these animals were recorded and how exactly they differed from prior sampling. I would suggest providing more details here.
L305-307: I suggest rephrasing the first half of the sentence; I don’t think the data presented provide enough evidence to justify the language “with many niches to explore.” There are too many axes of an n-dimensional niche hypervolume not assessed here to consider that might facilitate overlap (i.e., there might not actually be that many different niches, they might just be flexible enough to allow for overlap)
L308-317: I think the reasoning provided beginning in the second sentence makes sense, I don’t think the data presented justify the language regarding the lack of competition in the first sentence. Because there was no manipulation of the system, there cannot be evidence for or against the presence of current or past competition. I suggest acknowledging the fact that the study cannot identify or refute the presence of competition within the system, but patterns observed support the idea that other factors might play a larger role in shaping community structure. I also suggest “lightening” the language in subsequent sentence– i.e., in L312 & L314-315 changing “more likely” and “likely more” to “could be”
This manuscript concerning temporal dynamics of a snake community at the Cerrado-Amazonia ecotone in Brazil is well-written and provides crucial information on the diversity of snakes, a taxon that is often under studied and plays a significant role within tropical food webs. The authors report significant diversity within an ecotone that includes species from a wider range of habitats and even documented individuals from two potential new species of snakes.
I provide some editorial suggestions to consider and highlight some areas where more attention can be paid to journal formatting. I advise that more details should be added to figure and table captions such that they can stand alone. For example, the Figure 1 caption states “Geographical location of the study site” and then provides details about corresponding aspects of the site map, but without the accompanying manuscript text, I would not be able to understand what the study was or when it took place.
Overall, I applaud the authors’ ability to document such a range of not only snake taxa, but also such a diversity of life histories, some of which are incredibly cryptic and easily missed using less rigorous techniques. The data presented in this manuscript clearly fill a gap in knowledge regarding the snakes present within this ecotone and their temporal dynamics, which can not only improve future studies of herpetofauna in the region, but also highlight the need for conserving the biodiversity of this region. It was my pleasure to review this manuscript.
The manuscript On the composition and temporal dynamics of a snake community at the Cerrado-2 Amazonia ecotone proposes a general or main objective which is to examine the factors affecting the temporal dynamics of a snake community close to the Cerrado-Amazonia transition regarding species composition and seasonal turnover. To achieve this purpose, three specific objectives are set out: (1) to describe the snake species composition in a locality at the Cerrado-Amazonia ecotone; (2) to test the hypothesis that species turnover is higher during the rainy season compared to the dry season, likely due to increased resource availability (e.g., prey) and, (3) to evaluate community stability over time through biotic mechanisms.
Studying the temporal or spatial change of snake communities in a tropical landscape is a major challenge, since, due to their habits, it is not easy to record the different species that make up an assemblage in a location. I recognize that the topic of temporal (seasonal) dynamics of a community of snake species and examining or determining what factors affect or determine it is an interesting topic. However, there are several issues in the study that concern me and that I think compromise its robustness and scope. This is mainly related to the formulation of two specific objectives, as well as the study design, part of the data analysis, and the interpretation of results.
Given the study design, objective 2 is not addressed, since a hypothesis is not being tested; the study does not examine availability or quantity of resources (e.g. prey nor any other resource). What is being done is to describe a pattern of changes in species richness and species turnover between contiguous seasons (dry and wet), but the cause of these changes is unknown. That is, the factors that affect the temporal dynamics of the community are not examined. Regarding objective 3, I think that it is not being addressed either, as no biotic mechanisms affecting the stability or instability of the snake community are evaluated. The authors assume the observed changes to different mechanisms (as a hypothesis) but do not prove it. There is no evidence that the observed changes are due to competition, predation, parasitism, commensalism, or any other biotic mechanism; they only assume possible biotic mechanisms involved in the dynamics. For this reason, objective 3 also does not contribute to examining or determining the factors that affect the temporal dynamics of the snake community. The only objective that is addressed is objective 1, but this does not allow us to address the overall purpose of the study, because it only describes the number and composition of snake species at the study site (recorded by the authors themselves and by authors of other studies).
Regarding the study design, the methods are not described in sufficient detail, making it impossible to replicate the study at a later time or in another landscape (to compare results over time or with another location). For example, the authors do not explain the criteria for locating the 25 pitfall traps within the study area. There are four vegetation types in the study area, but it is not indicated whether traps were set in all vegetation types, nor how many traps per vegetation type, nor the distance between pitfall traps. This is relevant because the species richness and species composition of a faunal community is strongly associated with the vegetation type, its structure and vegetal composition, in addition to the abiotic conditions prevailing in that vegetation type. Additionally, it is not reported whether the traps (or how many traps) were placed near water bodies, inside or at the edges of forest fragments. Furthermore, the collecting effort related to active searches should be indicated (how many people actively searched for snakes and for how long). That is, there is not enough information on community sampling to allow the study to be replicated in the future or in another landscape, nor to compare it with the results of other studies (because the species richness, turnover, and known species composition of a locality are closely linked to the sampling methods used, the sampling effort, and the size of the sampled area).
Regarding the analysis methods, I think there is a misunderstanding regarding the estimated number of species (when the species estimation is extrapolated, see lines 182-188 and Figure 5). The sample size, according to the various publications by Ann Chao et al. or Robert Colwell et al., refers to the number of individuals or number of traps, search time, etc., but not to the number of species recorded. In the case of this study, the sample size is 146 individuals (and twice that is 292 snakes); the sample size does not refer to 34 species. So, what's indicated on lines 185-187 isn't correct. The default endpoint for calculations isn't 68 species, but 292 individuals and about 38 species, according to Figure 2A. That curve won't reach 68 species because it's already very close to the asymptote. By the way, Figure 2B is related to sample coverage, but the methods section doesn't specify why it was calculated or how to interpret it.
In this regard, a significant shortcoming of the study is that there is no analysis of sample coverage by season; there is only a general one. As this study compares six seasons over two years, there should be an analysis of sample coverage for each season to validate the comparisons of both species richness and species turnover. I see a significant shortcoming here, since according to the supplementary data, between 60% and 100% of the species recorded in each season were represented by only one or two individuals (singletons or doubletons, respectively). This indicates that the sample completeness (the representativeness of the community) is insufficient, since for most species in that season, only one or two individuals were recorded (when the number of singletons or doubletons is proportionally high, as in the case of this study, the completeness of the sample is poor). If this sample completeness is insufficient, then it is impossible to know whether differences in species richness or species turnover are due to sampling insufficiencies or truly reflect a biological/ecological phenomenon.
Regarding the methods associated with objectives 2 and 3, they are actually intended to reflect or distinguish patterns of change in species richness and composition, but not to examine the factors affecting the temporal dynamics of snake communities. In the discussion, the authors attribute the observed changes in the community to one factor or another, but with the methods used, it is impossible to truly examine which factors are affecting the community; these are only assumptions. Additionally, each method used must clearly state what objective or question it answers. It seems to me that the way the data analyses are designed makes it unclear how each analysis method relates to each objective.
All of these design issues influence the results and their interpretation, so I think the robustness of the results, discussion, and conclusions themselves is compromised. For example, the authors attribute the greater species turnover in the 2019 wet season to the emergence of species due to a greater quantity and variety of prey, but the highest species richness, greatest turnover, and greatest abundance of snakes were recorded in the 2019 dry season. Why were the highest values of species richness, abundance, and species turnover observed in this season? If prey abundance influences these community values, why is that argument not used here to explain what was observed during the dry season of that year? Since there was no assessment of prey availability (or prey abundance), the justifications for what was observed (the factors that affect community dynamics) are only based on assumptions or hypotheses, but they are solid foundations. I also think that several of the interpretations of the results are not the most appropriate. For example (see lines 253-254) that the variation in the community composition over time (classified as unstable) is due to the contact of two biomes. One issue is that a community is composed of species from different biomes, and another is that the variation in composition over time is due to the species being from different biomes; the analysis to confirm the latter was not performed in this study.
Table 1 shows 35 species with N values, but Figure 2 and the text indicate that there are 34 species.
From table 3 to 5 I think they should go in supplementary material, not in the main text.
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