Temporal Shifts in Biological Community Structure in Response to Wetland Restoration: Implications for Wetland Biodiversity Conservation and Management
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsLong-term studies of diversity and other parameters of individual populations and associations of amphibians are not always a rewarding, but necessary process. On the other hand, the authors studied populations removed from economic circulation - flooded fields for growing cranberries. In addition to the generalized characteristics, the authors used an analysis of indicator types (line 324), due to which the diversity dynamics was manifested. This approach is relevant. In addition to external factors, the diversity of the amphibian and reptile assembly can be affected by trophic links, as well as the consequences of anthropogenic transformation. The study is relevant and of interest, since the main long-term studies are conducted in reference areas.
In the fauna of amphibians and reptiles, 12 species are noted. Caudate amphibians – Ambystoma maculatum, tailless – Anaxyrus americanus, Pseudacris crucifer, Lithobates sylvaticus, Anaxyrus fowleri, Lithobates clamitans, Lithobates palustris, Dryophytes versicolor. Reptiles, turtles – Chrysemys picta, Chelydra serpentina and snake – Thamnophis sirtalis.
Notes:
Lines, 353-358. "(Lithobates catesbeianus), American toad (Anaxyrus americanus), common snapping turtle (Chelydra serpentina), Eastern painted turtle (Chrysemys picta), Fowler's toad (Anaxyrus fowleri), common garter snake (Thamnophis sirtalis), gray tree frog (Dryo phytes versicolor), green frog (Lithobates clamitans), Pickerel frog (Lithobates palustris), spotted salamander (Ambystoma maculatum), spring peeper (Pseudacris crucifer), and wood frog (Lithobates sylvaticus) (Table 1).". Full Latin names should be given and highlighted in italics.
Section "3.1. Overview", please pay attention to the analysis of the taxonomic composition, especially
General remarks, in
Section "4. Discussion", lines 615-617 "We observed nuanced patterns in community composition, total abundance, and richness between sites at varying post-restoration stages. Noteworthy distinctions have emerged between adult and larval amphibians, as well as reptiles, highlighting the multifaceted, complex, and incongruent responses by distinct taxa to restoration efforts." Please pay attention and provide information to evaluate reactions:
Lines, 626-629 “Our findings indicated the presence of both amphibians and reptiles in all restored wetlands, regardless of their restoration age. Given that herpetofauna occupy various trophic levels in food webs [81], these observations suggest that complex trophic interactions have likely been established, regardless of the time since restoration, potentially signaling successful restoration efforts.” The analysis indicates the presence of both predators in the assembly - Lithobates catesbeianus, Chelydra serpentina, Chrysemys picta, Thamnophis sirtalis, Lithobates clamitans, and poisonous species for predators - Anaxyrus americanus, Ambystoma maculatum and including the poisonous frog - Lithobates palustris. It is known that within the assembly, resistance of predatory species to poisons is noted, for example, for Lithobates palustris in Lithobates catesbeianus, Lithobates clamitans, Thamnophis sirtalis; Anaxyrus americanus in Thamnophis sirtalis. The presence of resistance to poisons in trophic links indicates a long-term coevolution and adaptation of predators. The ratio of the number of predators and their food supply is a classic example of the "hares and lynxes" ecological dependency models. Lines: 654-656. "The observed differences in amphibian richness and abundance as well as larval community composition between restoration trajectories are likely influenced by local drivers such as wetland depth and size, vegetation structure and biomass, substrate composition, hydroperiod, and predator density [96-99]." Analysis of factors influencing reproduction, including stability of hydrological (depth), hydrochemical (pH, mineralization, oxygen content) and microclimatic (illumination, overgrowth) factors, requires additions to the descriptions of amphibian habitats.
It is necessary to pay attention to the role of pathogens - helminths and fungi. The influence of pathogens is not always taken into account as a factor in changes in abundance, but their role in the global decline in amphibian and reptile populations has been proven, as the American bullfrog spreads the amphibian pathogen Batrachochytrium dendrobatidis. There are not many local studies, with the exception of helminth analysis (Sutherland et al., 2005, doi: 10.1525/california/9780520235922.003.0019), for example (Burger et al., 2024, doi: 10.3390/jof10020125).
Author Response
Reviewer 1
Reviewer comments (RC): Long-term studies of diversity and other parameters of individual populations and associations of amphibians are not always a rewarding, but necessary process. On the other hand, the authors studied populations removed from economic circulation - flooded fields for growing cranberries. In addition to the generalized characteristics, the authors used an analysis of indicator types (line 324), due to which the diversity dynamics was manifested. This approach is relevant. In addition to external factors, the diversity of the amphibian and reptile assembly can be affected by trophic links, as well as the consequences of anthropogenic transformation. The study is relevant and of interest, since the main long-term studies are conducted in reference areas.
Author response (AR): Thank you for your thoughtful comments. In response to your suggestions and the recommendations from two other reviewers, we have made substantial revisions to the manuscript. To facilitate your review, we have uploaded both a track changes version and a clean version of the manuscript for your consideration. Whenever relevant, we have included line numbers to help you easily cross-reference the edits we made. Please note that the line numbers correspond to the track changes version, not the cleaned version of the manuscript. We believe that the track changes version will allow you to clearly see the modifications we have implemented. Please attached track changes docx version to trace the improvements we made.
RC: Lines, 353-358. "(Lithobates catesbeianus), American toad (Anaxyrus americanus), common snapping turtle (Chelydra serpentina), Eastern painted turtle (Chrysemys picta), Fowler's toad (Anaxyrus fowleri), common garter snake (Thamnophis sirtalis), gray tree frog (Dryo phytes versicolor), green frog (Lithobates clamitans), Pickerel frog (Lithobates palustris), spotted salamander (Ambystoma maculatum), spring peeper (Pseudacris crucifer), and wood frog (Lithobates sylvaticus) (Table 1).". Full Latin names should be given and highlighted in italics.
AR: All scientific names have been italicized, as per standard convention. Additionally, we have included the taxonomic authority, as you requested for the “full” scientific name. Let us know if further clarification is needed.
RC: Section "3.1. Overview", please pay attention to the analysis of the taxonomic composition, especially in Section " 4. Discussion", lines 615-617 "We observed nuanced patterns in community composition, total abundance, and richness between sites at varying post-restoration stages. Noteworthy distinctions have emerged between adult and larval amphibians, as well as reptiles, highlighting the multifaceted, complex, and incongruent responses by distinct taxa to restoration efforts." Please pay attention and provide information to evaluate reactions:
AR: We appreciate your feedback but would like some clarification on your concern. The results section includes the statistical outputs that support these statements, and the discussion interprets these findings in relation to taxonomic composition, abundance, and richness across post-restoration stages. Since the results section provides the supporting statistical data, we intentionally refrain from repeating the same information in the discussion. If there are specific aspects that need further elaboration or additional analyses, we would be happy to address them.
RC: Lines, 626-629 “Our findings indicated the presence of both amphibians and reptiles in all restored wetlands, regardless of their restoration age. Given that herpetofauna occupy various trophic levels in food webs [81], these observations suggest that complex trophic interactions have likely been established, regardless of the time since restoration, potentially signaling successful restoration efforts.” The analysis indicates the presence of both predators in the assembly - Lithobates catesbeianus, Chelydra serpentina, Chrysemys picta, Thamnophis sirtalis, Lithobates clamitans, and poisonous species for predators - Anaxyrus americanus, Ambystoma maculatum and including the poisonous frog - Lithobates palustris. It is known that within the assembly, resistance of predatory species to poisons is noted, for example, for Lithobates palustris in Lithobates catesbeianus, Lithobates clamitans, Thamnophis sirtalis; Anaxyrus americanus in Thamnophis sirtalis. The presence of resistance to poisons in trophic links indicates a long-term coevolution and adaptation of predators. The ratio of the number of predators and their food supply is a classic example of the "hares and lynxes" ecological dependency models.
AR: Thank you for raising this important point. Our initial statement was intended to highlight the presence of species across multiple trophic levels in the restored wetlands, based on the natural history of the species observed. While we did not explicitly consider predator-prey coevolution and resistance in our original analysis, we appreciate the relevance of these dynamics. However, we believe the specific discussion of predator resistance to toxins may be outside the scope of the current manuscript, as our focus was primarily on trophic interactions within the context of wetland restoration and not necessarily on long-term evolutionary adaptations. That said, we acknowledge the complexity of these interactions, and should you feel, it would enhance the discussion, we could explore this idea further in a future revision. At this point, we would like to keep the paper at a high level where we focus on the restoration outcome as opposed to these specific interactions and dynamics that are not directly connected with restoration actions.
RC: Lines: 654-656. "The observed differences in amphibian richness and abundance as well as larval community composition between restoration trajectories are likely influenced by local drivers such as wetland depth and size, vegetation structure and biomass, substrate composition, hydroperiod, and predator density [96-99]." Analysis of factors influencing reproduction, including stability of hydrological (depth), hydrochemical (pH, mineralization, oxygen content) and microclimatic (illumination, overgrowth) factors, requires additions to the descriptions of amphibian habitats.
AR: Thank you for pointing out these important factors. In response, we have expanded our description of amphibian habitats to include the stability of hydrological factors (e.g., depth), hydrochemical variables (e.g., pH, mineralization, oxygen content), and microclimatic factors (e.g., illumination, overgrowth). These additions are now reflected in the revised manuscript to better capture the full range of environmental variables influencing amphibian reproduction (L 737).
RC: It is necessary to pay attention to the role of pathogens - helminths and fungi. The influence of pathogens is not always taken into account as a factor in changes in abundance, but their role in the global decline in amphibian and reptile populations has been proven, as the American bullfrog spreads the amphibian pathogen Batrachochytrium dendrobatidis. There are not many local studies, with the exception of helminth analysis (Sutherland et al., 2005, doi: 10.1525/california/9780520235922.003.0019), for example (Burger et al., 2024, doi: 10.3390/jof10020125).
AR: Thank you for raising this important point. We have added a brief paragraph in the future directions section to emphasize the role of pathogens, such as helminths and fungi, in the context of amphibian and reptile population declines. We highlight the need for future studies to consider the impact of pathogens, including Batrachochytrium dendrobatidis, in restoration efforts. This addition aligns with the current understanding of pathogen-related declines and stresses the importance of incorporating pathogen monitoring into wetland restoration research (L 1093-1102).
Author Response File: 
Author Response.docx
Reviewer 2 Report
Comments and Suggestions for AuthorsDear Authors,
Your study presents an impressive and detailed examination of herpetofaunal responses to wetland restoration over time. The use of species richness, abundance, community composition analyses, and Indicator Species Analysis (ISA) provides a well-rounded approach to assessing restoration success. The statistical framework, including NMDS and PERMANOVA, is robust and allows for meaningful ecological interpretations. Furthermore, given that this study originates from an undergraduate honors thesis (https://vc.bridgew.edu/honors_proj/618/), the level of scientific rigor, methodological structure, and data analysis is exceptional. Congrats!!
However, I must emphasize that this article is exceptionally long and highly complex, making it very challenging to review thoroughly in a single attempt. The extensive statistical analyses, ecological interpretations, and dataset discussions require an enormous effort to evaluate comprehensively. While I have carefully reviewed the manuscript to the best of my ability (almost 2500 words for a review!!), given its length and complexity, I acknowledge that there may be minor errors or overlooked details in my comments. If that is the case, I appreciate your understanding, as this is one of the most technically dense manuscripts I have encountered.
That being said, I strongly recommend substantially shortening the manuscript by:
a. Streamlining the results section to focus on the most ecologically meaningful findings while removing excessive statistical details that could be moved to supplementary materials - move some parts to supplementary materials.
b. Condensing the discussion by eliminating repetitive statements and ensuring that all interpretations directly align with the statistical results.
c. Shortening overly detailed figure descriptions, particularly when the information is already conveyed within the text.
Despite its length, this manuscript has significant potential for publication after careful revisions. I appreciate the effort that has gone into this work and look forward to seeing an improved version that is more concise and accessible to readers.
Introduction
Your introduction provides a comprehensive background on wetland restoration and its ecological significance, highlighting the role of herpetofauna as bioindicators and the importance of post-restoration monitoring. The discussion on wetland degradation, restoration mechanisms, and legislative frameworks is well-structured and establishes the broader relevance of the study. However, several key aspects require improvement to better define the research gap, refine the hypothesis, and strengthen the ecological rationale.
A major issue is the lack of a clearly defined research gap. In Lines 91–96, you mention that assessing the biological effectiveness of restoration, particularly temporal biodiversity shifts, is essential for ensuring restoration success. However, you did not explicitly state what remains unknown in the field or how previous studies have fallen short. In Lines 98–105 you highlight that past restoration monitoring efforts have often lacked statistical rigor and focus, but you do not specify how this study directly addresses those shortcomings. I recommend explicitly stating which aspects of wetland restoration remain poorly understood—for example, whether the rate and trajectory of species recovery over time are well documented or whether species turnover and functional recovery have been systematically analyzed in similar settings. Clarifying this gap will strengthen the justification for the study and make its contributions more apparent.
Moreover, in Lines 114–118 you stated that “herpetofauna display a wide range of sensitivity to environmental quality, thus widely regarded as indicators of ecosystem integrity”. While this is accurate, the introduction does not fully explain why amphibians and reptiles are particularly suitable for monitoring wetland restoration success. You can strengthen the justification by discussing why herpetofaunal responses are useful indicators of restoration success (e.g., amphibians’ reliance on hydroperiod stability and reptiles’ dependence on habitat complexity). Cite specific studies demonstrating the effectiveness of herpetofauna as bioindicators in wetland ecosystems.
The hypothesis in Lines 119–123 is also overly simplistic and does not fully consider the complexity of ecological succession and community assembly. The assumption that species richness and abundance will increase with restoration age does not account for species turnover, dispersal constraints, or habitat filtering mechanisms. Wetland succession is often non-linear, and different species may respond at different temporal scales, with some early colonizers declining as habitat conditions change. I recommend revising the hypothesis to include explicit expectations about how species composition, rather than just species richness, may shift over time. A more refined hypothesis could state that older restored wetlands will exhibit distinct community compositions due to the establishment of late-successional species and the potential decline of early colonizers. Successful restoration is often defined by not just the return of species, but the reestablishment of ecological functions and interactions. I recommend discussing whether this study focuses solely on taxonomic recovery or if functional aspects of biodiversity, such as trophic structure or habitat use, are also considered. This addition would provide a clearer understanding of how success is being measured and whether certain species are expected to play key roles in restored wetland ecosystems.
Materials and Methods
The Materials and Methods section is well-structured and provides a detailed description of the study sites, survey techniques, and statistical analyses. The study’s methodology is based on widely accepted field protocols and employs standardized techniques for herpetofaunal monitoring, including trap surveys and visual encounter surveys. The efforts to ensure replicability and methodological consistency are commendable. However, several aspects require clarification and refinement to ensure the robustness of the study design, the accuracy of data interpretation, and the validity of the statistical approaches used.
The description of the study sites in Lines 150–170 provides a good overview of the restoration history and habitat modifications. However, site comparability is a concern, as the 5-year-since-restoration (5-YSR) site is significantly larger than the 1-year-since-restoration (1-YSR) site (481 acres vs. 128 acres). This size disparity may influence species richness and abundance independently of restoration age, potentially confounding results. I recommend explicitly discussing whether site area differences were accounted for in the statistical analyses or including site area as a covariate in subsequent models.
Additionally, in Lines 161–165, you described the restoration interventions that were applied at both sites, such as dam removal, construction of ponds, and placement of large woody debris. However, it does not clarify whether both sites experienced the same degree of intervention or if certain restoration actions were more intensive at one site than the other. I recommend clarifying whether restoration treatments were standardized across both sites to ensure that any observed differences in species composition or abundance are due to restoration age rather than differential intervention intensity.
The field survey methodology is well-documented in Lines 178–205, detailing trap deployment, visual encounter surveys, and active searches. However, sampling effort varies across habitat types and sites, which may introduce bias in species detectability. In particular, the number of traps and survey plots differs between the 1-YSR and 5-YSR sites, as described in Lines 206–220. Since species richness is often correlated with sampling effort, I recommend standardizing sampling intensity across habitats and sites.
In Lines 186–191, you stated that sampling was conducted from May to August, with three consecutive trap nights per week. However, it is unclear whether all habitats were sampled with the same intensity. Some habitats (e.g., ponds, streams, and marshes) may inherently differ in species detectability, necessitating corrections for sampling effort. I recommend calculating Catch Per Unit Effort (CPUE), which normalizes captures based on trap deployment time and survey effort. This approach will improve comparability across habitat types and ensure that species richness and abundance estimates are not biased by unequal sampling effort.
The field methods rely on two standard techniques: baited aquatic traps and visual encounter surveys (Lines 179–183). While these methods are widely used in herpetofaunal research, they are susceptible to detection bias. Certain species may be underrepresented due to differences in habitat use, behavior, or seasonality. For example, some amphibians may be more detectable in early summer, whereas certain reptiles may only become active later in the season. Additionally, trap effectiveness may vary based on environmental conditions. In Lines 194–196, you described how traps were deployed based on water depth, flow, and surrounding structures. However, environmental conditions fluctuate throughout the season, potentially affecting species detectability. I recommend explicitly acknowledging detection biases and, if possible, incorporating occupancy models or detection probability estimates to improve the accuracy of species occurrence data.
Finally, in the statistics section I recommend to explicitly report the results of the betadisper test to confirm whether dispersion differences influenced PERMANOVA outcomes. If dispersion effects are significant, consider alternative models such as PERMDISP (to adjust for dispersion).
Results
In Lines 348–351, you stated that nine amphibian and three reptile species were recorded at 1-year-since-restoration (1-YSR) sites, while nine amphibian and five reptile species were recorded at 5-YSR sites. However, in Table 1, the species totals do not align perfectly with these numbers. I recommend carefully cross-checking species presence/absence data with Table 1 to ensure consistency.
In Lines 374–376, you reported that adult amphibian richness and abundance were significantly higher at 1-YSR sites (F = 0.47, p < 0.0001), while adult reptile richness was higher at 5-YSR sites (F = -0.38, p ~ 0.001). However, F-values should never be negative, as ANOVA statistics represent variance components that are always non-negative. The presence of negative F-values suggests either a reporting error or a misunderstanding of how F-statistics are interpreted.
Similarly, in Line 381, you reported that "total herpetofauna abundance significantly differed between 1-YSR and 5-YSR (F = -1.29, p < 0.0001)." Again, an F-value of -1.29 is not possible. The F-statistic represents the ratio of variance between groups to variance within groups, meaning that it should always be positive. I strongly recommend double-checking the output of the ANOVA models and correcting these errors.
You also reported pairwise comparisons among habitat types (Lines 388–402) but you did not consistently indicate whether p-values were corrected for multiple comparisons. In Lines 389–391, you stated: “Significant differences in adult herpetofaunal abundance between large ponds and marshes (t = 1.65, p < 0.001), large ponds and streams (t = 1.14, p < 0.0001), marshes and small ponds (t = 1.39, p < 0.001), and small ponds and streams (t = 1.15, p < 0.001)” This raises the question of whether a post-hoc correction was applied (e.g., Bonferroni or Tukey HSD). Given that multiple comparisons increase the likelihood of false positives, I recommend applying a multiple comparison correction and reporting adjusted p-values.
Figure 2 presents adult herpetofaunal abundance and species richness across habitat types. It is unclear whether individual trap nights were treated as independent replicates or whether traps were pooled across sampling events before resampling. The use of small grey dots in the figure needs to be described more clearly. What do these dots represent? Are they raw abundance values or bootstrapped estimates?
In Lines 495–496, you stated that habitat type (F = 17.030, p < 0.0001), time since restoration (F = 28.60, p < 0.0001), and their interaction (F = 4.930, p < 0.0001) significantly influenced adult herpetofaunal community composition. However, in Lines 503–504, it is stated that the effects of surface water coverage and time since restoration were non-significant (F = 0.70, p > 0.05; F = 1.89, p > 0.05). This contradiction should be clarified by distinguishing whether results differ between adult and larval herpetofauna or whether the difference arises due to habitat vs. surface water coverage effects. Additionally, you reported percentages of explained variance (SS values, Lines 497–498) but do not provide confidence intervals or effect sizes, which are necessary for understanding the strength of the effects.
In Lines 448–454, the manuscript states that "the 1-YSR sites displayed greater variation in the community composition than the 5-YSR sites." However, this contradicts the assertion in Lines 522–524 that states "the test for multivariate homogeneity of group dispersions demonstrated significantly greater among-group dispersion than within-group dispersion (F = 98.66, p < 0.0001)."If 1-YSR sites had greater variation, then the betadisper test should show higher dispersion in 1-YSR sites than in 5-YSR sites. However, you stated that among-group dispersion was greater than within-group dispersion, which suggests that 5-YSR sites were more variable—contradicting the earlier claim.
Moreover, you stated that "the covariance ellipses for 1-YSR and 5-YSR overlapped almost entirely" (Lines 485–486), which suggests weak differentiation, yet you simultaneously claims significant differences. If differences are statistically significant, how strong are they? What is the effect size?
The NMDS Shepard plot (Lines 435–437) is described as showing "strong correlation" (R² = 0.96 for adults, R² = 0.93 for larvae), but no scree plot information is provided to determine how many dimensions were retained.
The indicator species analysis (Lines 561–573, Table 2 & Table 3) is an important aspect of the study, but its ecological relevance is not sufficiently explained. You found that American bullfrog, common snapping turtle, and Fowler’s toad as indicators of 1-YSR, while eastern painted turtle and musk turtle are indicators of 5-YSR. However, no ecological explanation is provided. Why are these species more abundant in specific restoration stages? For instance, American bullfrogs are opportunistic breeders that prefer open water conditions, which may explain their association with recently restored sites. Musk turtles are known to prefer more stable wetland conditions, which may explain their association with 5-YSR sites.
Discussion
Your discussion provides a comprehensive synthesis of the study's findings, effectively linking species responses to wetland restoration with broader ecological processes. The interpretation of species richness and abundance changes across time since restoration is valuable. However, several aspects require substantial revisions to enhance clarity, avoid contradictions, and strengthen the ecological interpretations.
In Lines 620–622, you claim that "reptile diversity increased while amphibian diversity decreased with restoration age." However, this is not fully supported by the results, which indicate that adult amphibian abundance and richness declined at 5-YSR sites, while reptile richness and abundance increased. The phrase "diversity" is vague here—are you referring to species richness, Shannon diversity, or functional diversity? If referring to species richness, this statement needs to be aligned with the statistical results and explicitly stated.
Additionally, Lines 624–626 you state that "the re-establishment of carbon and nutrient cycles through food webs is a fundamental objective in ecological restoration." While this is ecologically relevant, there is no direct evidence from the study measuring these trophic interactions. If the intention is to hypothesize potential implications, this should be clearly stated rather than framed as a direct conclusion.
The use of NMDS and indicator species analysis is an appropriate methodological approach, but its interpretation in Lines 628–630 oversimplifies the findings. The manuscript states that "herpetofauna occupy various trophic levels in food webs, suggesting that complex trophic interactions have likely been established, regardless of time since restoration." However: The NMDS only provides compositional dissimilarities and does not infer trophic relationships. There is no direct evidence of predator-prey dynamics, competition, or trophic interactions in the results. The presence of herpetofauna at both 1-YSR and 5-YSR sites does not necessarily indicate successful trophic re-establishment, as species may persist despite changes in food availability. I recommend to avoid inferring trophic relationships from NMDS and species presence alone. Instead, suggest further studies on predator-prey interactions, stable isotope analyses, or gut content studies to assess trophic structuring.
Author Response
Reviewer comments (RC): Your study presents an impressive and detailed examination of herpetofaunal responses to wetland restoration over time. The use of species richness, abundance, community composition analyses, and Indicator Species Analysis (ISA) provides a well-rounded approach to assessing restoration success. The statistical framework, including NMDS and PERMANOVA, is robust and allows for meaningful ecological interpretations. Furthermore, given that this study originates from an undergraduate honors thesis (https://vc.bridgew.edu/honors_proj/618/), the level of scientific rigor, methodological structure, and data analysis is exceptional. Congrats!!
Author Responses (AR): Thank you for your kind words of encouragement. This work initially began as an undergraduate summer research project, which was later expanded into an honors thesis, and we are pleased that it has now evolved into this publication. We appreciate the thorough review and your recognition of the rigor and structure behind this study.
RC: However, I must emphasize that this article is exceptionally long and highly complex, making it very challenging to review thoroughly in a single attempt. The extensive statistical analyses, ecological interpretations, and dataset discussions require an enormous effort to evaluate comprehensively. While I have carefully reviewed the manuscript to the best of my ability (almost 2500 words for a review!!), given its length and complexity, I acknowledge that there may be minor errors or overlooked details in my comments. If that is the case, I appreciate your understanding, as this is one of the most technically dense manuscripts I have encountered.
That being said, I strongly recommend substantially shortening the manuscript by:
- Streamlining the results section to focus on the most ecologically meaningful findings while removing excessive statistical details that could be moved to supplementary materials - move some parts to supplementary materials. b. Condensing the discussion by eliminating repetitive statements and ensuring that all interpretations directly align with the statistical results.
- Shortening overly detailed figure descriptions, particularly when the information is already conveyed within the text.
AR: We acknowledge that the manuscript is lengthy and dense with information. With the helpful feedback from you and two other reviewers, we were able to reduce the manuscript by approximately five pages and make it more accessible for readers. We appreciate the thoroughness and constructive nature of your comments. While we made significant reductions in the introduction and discussion sections, we chose to minimize changes in the methods and results to maintain transparency and ensure reproducibility of our work. Regarding the detailed figure captions, we would prefer to retain the current level of detail. Our aim is to make the figures and tables stand alone, allowing readers to fully understand the results by reviewing the graphics without needing to refer to the main text. While we attempted to reduce the details on statistical methods, we retained the critical information necessary for readers to understand the rationale behind our approach, ensuring full transparency. In many published studies, complex statistical models are often used without providing sufficient context or justification. Our goal was to address this gap by including relevant details about our statistical approach. This not only supports reproducibility but also aids readers in better understanding the rationale and suitability of our methods within the context of our study.
RC: Despite its length, this manuscript has significant potential for publication after careful revisions. I appreciate the effort that has gone into this work and look forward to seeing an improved version that is more concise and accessible to readers.
AR: We are grateful for your recognition of the importance of our work. We hope that the revised version meets your expectations, as we have made an effort to incorporate nearly all of your valuable comments. Throughout the revisions, we kept readability in mind. The manuscript's length was, in part, a result of our aim to make the paper accessible to a broader audience of ecologists, conservation scientists, and wetland scientists, not just herpetologists. That said, we fundamentally agree with your feedback and have worked to streamline the manuscript in this round of revisions. To facilitate your second round of review, we have uploaded both a track changes version and a clean version of the manuscript for your consideration. Where relevant, we have included line numbers to help you easily cross-reference the edits. Please note that the line numbers correspond to the track changes version, not the clean version. We believe the track changes version will clearly highlight the modifications we have made. Please attached track changes docx version to trace the improvements we made.
Introduction
RC: Your introduction provides a comprehensive background on wetland restoration and its ecological significance, highlighting the role of herpetofauna as bioindicators and the importance of post-restoration monitoring. The discussion on wetland degradation, restoration mechanisms, and legislative frameworks is well-structured and establishes the broader relevance of the study. However, several key aspects require improvement to better define the research gap, refine the hypothesis, and strengthen the ecological rationale.
A major issue is the lack of a clearly defined research gap. In Lines 91–96, you mention that assessing the biological effectiveness of restoration, particularly temporal biodiversity shifts, is essential for ensuring restoration success. However, you did not explicitly state what remains unknown in the field or how previous studies have fallen short. In Lines 98–105 you highlight that past restoration monitoring efforts have often lacked statistical rigor and focus, but you do not specify how this study directly addresses those shortcomings. I recommend explicitly stating which aspects of wetland restoration remain poorly understood—for example, whether the rate and trajectory of species recovery over time are well documented or whether species turnover and functional recovery have been systematically analyzed in similar settings. Clarifying this gap will strengthen the justification for the study and make its contributions more apparent.
AR: We agree with this excellent comment. We have addressed the gaps in current knowledge (lines 96–98), and lines 102–105 outline the shortcomings of past restoration monitoring efforts. To further clarify the research gap, we have explicitly stated the aspects of wetland restoration that remain poorly understood, such as the rate and trajectory of species recovery over time, as well as the systematic analysis of species turnover and recovery in similar settings. We believe this strengthens the justification for our study and makes its contributions clearer. Additionally, we have emphasized the strengths of our study, including the statistical rigor and design, in the discussion section (lines 706–708), where the strengths and weaknesses of the study are typically addressed.
RC: Moreover, in Lines 114–118 you stated that “herpetofauna display a wide range of sensitivity to environmental quality, thus widely regarded as indicators of ecosystem integrity”. While this is accurate, the introduction does not fully explain why amphibians and reptiles are particularly suitable for monitoring wetland restoration success. You can strengthen the justification by discussing why herpetofaunal responses are useful indicators of restoration success (e.g., amphibians’ reliance on hydroperiod stability and reptiles’ dependence on habitat complexity). Cite specific studies demonstrating the effectiveness of herpetofauna as bioindicators in wetland ecosystems.
AR: Thank you for pointing this out. We have added a more detailed justification for why herpetofauna are particularly suitable for monitoring wetland restoration success, as you suggested. Specifically, we discussed amphibians' reliance on hydroperiod stability and reptiles' dependence on habitat complexity, as well as citing studies demonstrating the effectiveness of herpetofauna as bioindicators in wetland ecosystems (lines 119–125).
RC: The hypothesis in Lines 119–123 is also overly simplistic and does not fully consider the complexity of ecological succession and community assembly. The assumption that species richness and abundance will increase with restoration age does not account for species turnover, dispersal constraints, or habitat filtering mechanisms. Wetland succession is often non-linear, and different species may respond at different temporal scales, with some early colonizers declining as habitat conditions change. I recommend revising the hypothesis to include explicit expectations about how species composition, rather than just species richness, may shift over time. A more refined hypothesis could state that older restored wetlands will exhibit distinct community compositions due to the establishment of late-successional species and the potential decline of early colonizers. Successful restoration is often defined by not just the return of species, but the reestablishment of ecological functions and interactions. I recommend discussing whether this study focuses solely on taxonomic recovery or if functional aspects of biodiversity, such as trophic structure or habitat use, are also considered. This addition would provide a clearer understanding of how success is being measured and whether certain species are expected to play key roles in restored wetland ecosystems.
AR: Thank you for your insightful comment. We have revised the hypothesis to better reflect the complexity of ecological succession and community assembly. Specifically, we now address how species composition, rather than just species richness, may shift over time, with older restored wetlands potentially exhibiting distinct community compositions due to the establishment of late-successional species and the decline of early colonizers (lines 127–131, 140-144, 147-150). We also highlight the role of dispersal constraints and habitat filtering in shaping species responses to restoration (line 111), as you rightly pointed out. Furthermore, we acknowledge that successful restoration is not only about taxonomic recovery but also the reestablishment of ecological functions and interactions. This is now addressed in the discussion under future directions (lines 1117–1119). Additionally, we clarify the taxonomic focus of our study (lines 143–144), and mention that functional aspects of biodiversity, such as trophic structure, will be explored in future research in the discussion section (lines 1117–1119).
Materials and Methods
RC: The Materials and Methods section is well-structured and provides a detailed description of the study sites, survey techniques, and statistical analyses. The study’s methodology is based on widely accepted field protocols and employs standardized techniques for herpetofaunal monitoring, including trap surveys and visual encounter surveys. The efforts to ensure replicability and methodological consistency are commendable. However, several aspects require clarification and refinement to ensure the robustness of the study design, the accuracy of data interpretation, and the validity of the statistical approaches used.
The description of the study sites in Lines 150–170 provides a good overview of the restoration history and habitat modifications. However, site comparability is a concern, as the 5-year-since-restoration (5-YSR) site is significantly larger than the 1-year-since-restoration (1-YSR) site (481 acres vs. 128 acres). This size disparity may influence species richness and abundance independently of restoration age, potentially confounding results. I recommend explicitly discussing whether site area differences were accounted for in the statistical analyses or including site area as a covariate in subsequent models.
AR: Thank you for highlighting this concern. We acknowledge that the size disparity between the 5-year-since-restoration (5-YSR) site and the 1-year-since-restoration (1-YSR) site could potentially influence species richness and abundance independently of restoration age. While it is difficult to fully control for this size disparity, our survey design did account for this variation. Nevertheless, as you suggested, we have included the size disparity as a potential driver for observed community distinctions in the discussion section. We believe this will provide further clarity on the influence of site area on the results.
RC: Additionally, in Lines 161–165, you described the restoration interventions that were applied at both sites, such as dam removal, construction of ponds, and placement of large woody debris. However, it does not clarify whether both sites experienced the same degree of intervention or if certain restoration actions were more intensive at one site than the other. I recommend clarifying whether restoration treatments were standardized across both sites to ensure that any observed differences in species composition or abundance are due to restoration age rather than differential intervention intensity.
AR: Thank you for pointing this out. We agree with your observation. The restoration actions and types were indeed similar between the two sites, although the intensity of some interventions may not have been identical, but certainly comparable. We have clarified this in the revised manuscript and have addressed these potential differences in the discussion (lines 749-752, 868-869, 1013-1017), specifically regarding their possible influence on community structure and diversity metrics.
RC: The field survey methodology is well-documented in Lines 178–205, detailing trap deployment, visual encounter surveys, and active searches. However, sampling effort varies across habitat types and sites, which may introduce bias in species detectability. In particular, the number of traps and survey plots differs between the 1-YSR and 5-YSR sites, as described in Lines 206–220. Since species richness is often correlated with sampling effort, I recommend standardizing sampling intensity across habitats and sites.
AR: We agree with your point. As already outlined in the statistical analysis (lines 243-269), we standardized the sampling effort by calculating the per-trap capture rate to account for differences in sampling intensity across habitats and sites. This approach allows us to mitigate potential biases you pointed out.
RC: In Lines 186–191, you stated that sampling was conducted from May to August, with three consecutive trap nights per week. However, it is unclear whether all habitats were sampled with the same intensity. Some habitats (e.g., ponds, streams, and marshes) may inherently differ in species detectability, necessitating corrections for sampling effort. I recommend calculating Catch Per Unit Effort (CPUE), which normalizes captures based on trap deployment time and survey effort. This approach will improve comparability across habitat types and ensure that species richness and abundance estimates are not biased by unequal sampling effort.
AR: We agree with your suggestion. We have already calculated Catch Per Unit Effort (CPUE) to normalize captures based on trap deployment time and survey effort, as explained in the statistical analysis section. Additionally, sampling at both sites was conducted concurrently, which we clarified in the revised manuscript (line 209). If by "sampling intensity" you are referring to the variation in survey effort between habitats, we believe that the CPUE calculation sufficiently addresses this concern by accounting for differences in effort across habitat types. This pint is related to your previous comment as well, therefore, the response we provided therein is also applicable here.
RC: The field methods rely on two standard techniques: baited aquatic traps and visual encounter surveys (Lines 179–183). While these methods are widely used in herpetofaunal research, they are susceptible to detection bias. Certain species may be underrepresented due to differences in habitat use, behavior, or seasonality. For example, some amphibians may be more detectable in early summer, whereas certain reptiles may only become active later in the season. Additionally, trap effectiveness may vary based on environmental conditions. In Lines 194–196, you described how traps were deployed based on water depth, flow, and surrounding structures. However, environmental conditions fluctuate throughout the season, potentially affecting species detectability. I recommend explicitly acknowledging detection biases and, if possible, incorporating occupancy models or detection probability estimates to improve the accuracy of species occurrence data.
Finally, in the statistics section I recommend to explicitly report the results of the betadisper test to confirm whether dispersion differences influenced PERMANOVA outcomes. If dispersion effects are significant, consider alternative models such as PERMDISP (to adjust for dispersion).
AR: Thank you for this insightful point. While we did not perform occupancy modeling in this study, we recognize its potential value in addressing detection biases, particularly given the complex and fluctuating environmental conditions that can affect species detectability. However, it is challenging to quantify these fluctuations in a way that would allow them to be incorporated as covariates in an occupancy model, especially since some species had low capture rates, which could lead to convergence issues. Nonetheless, we agree with your suggestion and have added a brief discussion on the importance of occupancy modeling under ‘future directions’ (1074-1103) in the revised manuscript. Regarding the PERMANOVA analysis, it is generally robust to differences in dispersion, though not entirely immune. We used the `adonis` function, which is particularly robust to this issue, and we also performed a Principal Coordinate Analysis (PCoA) as an additional method, which strengthens our inferences. However, we appreciate your suggestion to explicitly report the results of the betadisper test and the results we originally reported already included these results in the revised manuscript.
Results
RC: In Lines 348–351, you stated that nine amphibian and three reptile species were recorded at 1-year-since-restoration (1-YSR) sites, while nine amphibian and five reptile species were recorded at 5-YSR sites. However, in Table 1, the species totals do not align perfectly with these numbers. I recommend carefully cross-checking species presence/absence data with Table 1 to ensure consistency.
AR: We have double-checked the species counts, and the numbers in the text are consistent with those reported in Table 1. Please note that "B" in the table indicates species present at both the 1-year-since-restoration (1-YSR) and 5-year-since-restoration (5-YSR) sites. If you noticed any discrepancies, please let us know, and we will review them again.
RC: In Lines 374–376, you reported that adult amphibian richness and abundance were significantly higher at 1-YSR sites (F = 0.47, p < 0.0001), while adult reptile richness was higher at 5-YSR sites (F = -0.38, p ~ 0.001). However, F-values should never be negative, as ANOVA statistics represent variance components that are always non-negative. The presence of negative F-values suggests either a reporting error or a misunderstanding of how F-statistics are interpreted.
Similarly, in Line 381, you reported that "total herpetofauna abundance significantly differed between 1-YSR and 5-YSR (F = -1.29, p < 0.0001)." Again, an F-value of -1.29 is not possible. The F-statistic represents the ratio of variance between groups to variance within groups, meaning that it should always be positive. I strongly recommend double-checking the output of the ANOVA models and correcting these errors.
AR: Thank you for pointing out this issue. We agree that F-statistics cannot be negative, as they represent the ratio of variance between groups to variance within groups. This was indeed a typo, and we have corrected the F-values in the manuscript accordingly.
RC: You also reported pairwise comparisons among habitat types (Lines 388–402) but you did not consistently indicate whether p-values were corrected for multiple comparisons. In Lines 389–391, you stated: “Significant differences in adult herpetofaunal abundance between large ponds and marshes (t = 1.65, p < 0.001), large ponds and streams (t = 1.14, p < 0.0001), marshes and small ponds (t = 1.39, p < 0.001), and small ponds and streams (t = 1.15, p < 0.001)” This raises the question of whether a post-hoc correction was applied (e.g., Bonferroni or Tukey HSD). Given that multiple comparisons increase the likelihood of false positives, I recommend applying a multiple comparison correction and reporting adjusted p-values.
AR: Thank you for your observation. We agree that the use of post-hoc correction is crucial for multiple comparisons. As detailed in the Methods section (lines 280–283), we applied the Benjamini-Hochberg procedure to adjust p-values and control the false discovery rate. We believe that this detail is sufficiently addressed in the Methods and, therefore, is not repeated in the Results section. However, we will make sure the methods are clearly highlighted to ensure transparency regarding the correction for multiple comparisons
RC: Figure 2 presents adult herpetofaunal abundance and species richness across habitat types. It is unclear whether individual trap nights were treated as independent replicates or whether traps were pooled across sampling events before resampling. The use of small grey dots in the figure needs to be described more clearly. What do these dots represent? Are they raw abundance values or bootstrapped estimates?
AR: Thank you for your comment. Individual trap nights were treated as independent replicates for these calculations, while the grey dots in Figure 2 represent raw abundance values. We have clarified this in the Figure 2 caption (lines 442-450).
RC: In Lines 495–496, you stated that habitat type (F = 17.030, p < 0.0001), time since restoration (F = 28.60, p < 0.0001), and their interaction (F = 4.930, p < 0.0001) significantly influenced adult herpetofaunal community composition. However, in Lines 503–504, it is stated that the effects of surface water coverage and time since restoration were non-significant (F = 0.70, p > 0.05; F = 1.89, p > 0.05). This contradiction should be clarified by distinguishing whether results differ between adult and larval herpetofauna or whether the difference arises due to habitat vs. surface water coverage effects. Additionally, you reported percentages of explained variance (SS values, Lines 497–498) but do not provide confidence intervals or effect sizes, which are necessary for understanding the strength of the effects.
AR: Thank you for pointing this out. As you suspected, the first statement refers to adults, while the second pertains to larvae. We have clarified this distinction in lines 552–562. Regarding effect size, we reported R² values as they are appropriate measures of effect magnitude, directly derived from the adonis output. Both sum of squares (SS) and R² are standard metrics for assessing effect size in this analysis.
RC: In Lines 448–454, the manuscript states that "the 1-YSR sites displayed greater variation in the community composition than the 5-YSR sites." However, this contradicts the assertion in Lines 522–524 that states "the test for multivariate homogeneity of group dispersions demonstrated significantly greater among-group dispersion than within-group dispersion (F = 98.66, p < 0.0001)."If 1-YSR sites had greater variation, then the betadisper test should show higher dispersion in 1-YSR sites than in 5-YSR sites. However, you stated that among-group dispersion was greater than within-group dispersion, which suggests that 5-YSR sites were more variable—contradicting the earlier claim.
AR: We do not believe there is a contradiction in our statements. The statement in Line 448 refers to a comparison of within-group variability, indicating that 1-YSR sites exhibit greater variation in community composition than 5-YSR sites. This pattern is visually evident in the NMDS plot. Meanwhile, the test for multivariate homogeneity of group dispersions assesses overall among-group vs. within-group dispersion, demonstrating that variation in community structure is greater between 1-YSR and 5-YSR sites than within each group. These results are consistent with our interpretation.
RC: Moreover, you stated that "the covariance ellipses for 1-YSR and 5-YSR overlapped almost entirely" (Lines 485–486), which suggests weak differentiation, yet you simultaneously claims significant differences. If differences are statistically significant, how strong are they? What is the effect size?
AR: Thank you for raising this point. As you previously noted, the inclusion of effect sizes enhances the interpretation of significant results. We have now reported effect sizes for the PERMANOVA tests and added a statement clarifying whether the observed differences were weak or strong (Lines 552–562).
RC: The NMDS Shepard plot (Lines 435–437) is described as showing "strong correlation" (R² = 0.96 for adults, R² = 0.93 for larvae), but no scree plot information is provided to determine how many dimensions were retained.
AR: As explained in the methods, we generated scree plots to determine the appropriate number of NMDS dimensions. However, since this step serves as a validation rather than a direct result, we chose to report only the R² values in the main text. Including the scree plot in the results would not enhance the interpretation of our findings. If necessary, we can provide it as supplementary material, but given the manuscript’s length, we aimed to prioritize essential content.
RC: The indicator species analysis (Lines 561–573, Table 2 & Table 3) is an important aspect of the study, but its ecological relevance is not sufficiently explained. You found that American bullfrog, common snapping turtle, and Fowler’s toad as indicators of 1-YSR, while eastern painted turtle and musk turtle are indicators of 5-YSR. However, no ecological explanation is provided. Why are these species more abundant in specific restoration stages? For instance, American bullfrogs are opportunistic breeders that prefer open water conditions, which may explain their association with recently restored sites. Musk turtles are known to prefer more stable wetland conditions, which may explain their association with 5-YSR sites.
AR: We fully agree that the ecological relevance of ISA results is important. However, we believe that this interpretation belongs in the discussion rather than the results section. As noted in Lines 945–979, we already address species-specific associations with restoration stages. While natural history context is relevant, we have kept it concise to maintain focus on broader ecological patterns, in line with the journal’s scope.
Discussion
RC: Your discussion provides a comprehensive synthesis of the study's findings, effectively linking species responses to wetland restoration with broader ecological processes. The interpretation of species richness and abundance changes across time since restoration is valuable. However, several aspects require substantial revisions to enhance clarity, avoid contradictions, and strengthen the ecological interpretations.
In Lines 620–622, you claim that "reptile diversity increased while amphibian diversity decreased with restoration age." However, this is not fully supported by the results, which indicate that adult amphibian abundance and richness declined at 5-YSR sites, while reptile richness and abundance increased. The phrase "diversity" is vague here—are you referring to species richness, Shannon diversity, or functional diversity? If referring to species richness, this statement needs to be aligned with the statistical results and explicitly stated.
AR: We agree that 'diversity' is too vague in this context. We have revised the statement to explicitly refer to species richness and abundance to align with the statistical results (line 680-690).
RC: Additionally, Lines 624–626 you state that "the re-establishment of carbon and nutrient cycles through food webs is a fundamental objective in ecological restoration." While this is ecologically relevant, there is no direct evidence from the study measuring these trophic interactions. If the intention is to hypothesize potential implications, this should be clearly stated rather than framed as a direct conclusion.
AR: We agree with this point, and another reviewer raised a similar concern. To avoid implying unsupported conclusions, we have removed this statement.
RC: The use of NMDS and indicator species analysis is an appropriate methodological approach, but its interpretation in Lines 628–630 oversimplifies the findings. The manuscript states that "herpetofauna occupy various trophic levels in food webs, suggesting that complex trophic interactions have likely been established, regardless of time since restoration." However: The NMDS only provides compositional dissimilarities and does not infer trophic relationships. There is no direct evidence of predator-prey dynamics, competition, or trophic interactions in the results. The presence of herpetofauna at both 1-YSR and 5-YSR sites does not necessarily indicate successful trophic re-establishment, as species may persist despite changes in food availability. I recommend to avoid inferring trophic relationships from NMDS and species presence alone. Instead, suggest further studies on predator-prey interactions, stable isotope analyses, or gut content studies to assess trophic structuring.
AR: We agree with this point, which also aligns with your previous comment. As a result, we have removed this statement from the discussion to avoid inferring trophic relationships without direct evidence.
Author Response File: Author Response.docx
Reviewer 3 Report
Comments and Suggestions for AuthorsKeith et al. have completed a nice study that will provide a significant contribution to the literature on wetland restoration. They exploited a unique opportunity by studying herpetofaunal diversity and abundance in different stages and habitats following wetland restoration. My only criticism is that the manuscript, in my opinion, is overwritten. There is a tendency toward redundancy, a focus on extraneous detail in discussing previous work, and it borders on being a bit platitudinal. For example, the Future directions and Conclusions sections should be more related to their own work. Rather, they are heavily laden with statements which are already the broad consensus among conservation scientists, such as the values of wetlands, There is discussion and explanation of the data within the Results, and the Discussion is long and gets a bit tedious at times. I think both sections could easily be streamlined significantly without the major points losing any strength.
Also, the References need to be thoroughly checked for consistency. For example, some journal names are not abbreviated or fully capitalized (e.g., line 104). In some, abbreviations are followed by periods (e.g., line 1029) but not for most.
Other than that, I have a few, minor corrections following line numbers given below:
18 replace “where” with “with”
25 make “challenged” present tense
47+ “such as” is a prepositional phrase and should not be led by a comma
104 insert “are” before “unsuitable”
123 Is “future” out of place here? It makes no sense to me.
124+ use past tense when referring to what you did in your study (e.g., “our aims were,” “we hypothesized,” etc.)
159 add a comma after “2017” as it is a compound sentence
185 change “herpetofauna” to “herpetofaunal”
251 change “as” to “the” [or delete “was”]
305-309 This sentence is too long. I would break it into two, the first ending on line 308 with “measure.”
350-359 italicize scientific names
358 the currently accepted scientific name for wood frog is Boreorana sylvatica
378 insert “were” after “reptiles”
381 change “herpetofauna” to “herpetofaunal”
479 “much” is used for amounts, whereas “many” is used for countable quantities. Therefore, the phrase should be either “much dissimilarity” or “many dissimilarities”
579+ because p-values are given within the table, explanations of values are redundant
624-626 This statement seems out of place and does not strongly relate to the rest of the paragraph.
649 change “challenged” to “challenge”
731 add “are” before “in accord”
754-755 make sure tenses agree
822-827 the detail about red-eared sliders seems superfluous
Author Response
Reviewer 3
RC: Keith et al. have completed a nice study that will provide a significant contribution to the literature on wetland restoration. They exploited a unique opportunity by studying herpetofaunal diversity and abundance in different stages and habitats following wetland restoration. My only criticism is that the manuscript, in my opinion, is overwritten. There is a tendency toward redundancy, a focus on extraneous detail in discussing previous work, and it borders on being a bit platitudinal. For example, the Future directions and Conclusions sections should be more related to their own work. Rather, they are heavily laden with statements which are already the broad consensus among conservation scientists, such as the values of wetlands, There is discussion and explanation of the data within the Results, and the Discussion is long and gets a bit tedious at times. I think both sections could easily be streamlined significantly without the major points losing any strength.
AR: We appreciate your thoughtful feedback and your recognition of the value of our study. We are grateful for your constructive comments regarding the manuscript’s length and the need for streamlining. In response to your suggestions, we took significant steps to reduce redundancy throughout the manuscript. Specifically, we trimmed approximately 5 pages from the overall length, focusing particularly on the Introduction and Discussion sections. We removed extraneous details from previous work and reduced unnecessary repetition in the data interpretation, ensuring that the main points remain strong without being overelaborated. Regarding the Future Directions section, we acknowledge that this section could be seen as addressing broader conservation themes, but we believe that framing our work within this larger context is essential. Our goal in this section was to place our findings within the broader discourse on wetland restoration and conservation, suggesting potential avenues for future research in this field. We believe this broader perspective adds value, as it connects our study to ongoing ecological restoration efforts and helps guide future directions for related research. Last but not the least, the minor modifications you suggested were included into consideration. But, as we cut down the manuscript as you suggested foremost, we might have removed some of these sentences entirely. Again, we thank you for your thoughtful review. Your comments have been invaluable in improving the clarity and focus of our manuscript.
RC: Also, the References need to be thoroughly checked for consistency. For example, some journal names are not abbreviated or fully capitalized (e.g., line 104). In some, abbreviations are followed by periods (e.g., line 1029) but not for most.
AR: We have corrected the journal abbreviations. We used the endnote style as recommended by the journal.
Other than that, I have a few, minor corrections following line numbers given below:
RC: 18 replace “where” with “with”
AR: corrected
RC: 25 make “challenged” present tense
AR: corrected
RC: 47+ “such as” is a prepositional phrase and should not be led by a comma
AR: Good catch, I think this point only pertains to restrictive clauses. I removed commas from all restrictive clauses.
RC: 104 insert “are” before “unsuitable”
AR: corrected
RC: 123 Is “future” out of place here? It makes no sense to me.
AR: this was a typo, it should be “further”
RC: 124+ use past tense when referring to what you did in your study (e.g., “our aims were,” “we hypothesized,” etc.)
AR: We consistently used the past tense as suggested, and yes, we agree with the recommendation. Thank you
RC: 159 add a comma after “2017” as it is a compound sentence
AR: corrected
RC: 185 change “herpetofauna” to “herpetofaunal”
AR: changed
RC: 251 change “as” to “the” [or delete “was”]
AR: changed
RC: 305-309 This sentence is too long. I would break it into two, the first ending on line 308 with “measure.”
AR: We broke this sentence into two sentences.
RC: 350-359 italicize scientific names
AR: all scientific names are now italicized
RC: 358 the currently accepted scientific name for wood frog is Boreorana sylvatica
AR: much appreciated pointing this out we used this new name
RC: 378 insert “were” after “reptiles”
AR: corrected
RC: 381 change “herpetofauna” to “herpetofaunal”
AR: corrected
RC: 479 “much” is used for amounts, whereas “many” is used for countable quantities. Therefore, the phrase should be either “much dissimilarity” or “many dissimilarities”
AR: corrected as “many dissimilarities”
RC: 579+ because p-values are given within the table, explanations of values are redundant
AR: This is a tricky point. The tables and figures are supposed to be standalone from the text and vice versa. It is generally expected to report the stats in parentheses in general, otherwise, it might look odd or even speculative. For that reason, we are opting to keep them as is.
RC: 624-626 This statement seems out of place and does not strongly relate to the rest of the paragraph.
AR: agreed and, we removed the entire sentence
RC: 649 change “challenged” to “challenge”
AR: corrected
RC: 731 add “are” before “in accord”
AR: corrected
RC: 754-755 make sure tenses agree
AR: We modified this sentence, the initial phrase was a bit awkward
RC: 822-827 the detail about red-eared sliders seems superfluous
AR: agreed, we cut down a lot of text from this point
Round 2
Reviewer 1 Report
Comments and Suggestions for AuthorsThe authors made significant changes to the manuscript. Thanks for updating the article. Most of the comments have been taken into account.
Explanations:
RC: Section "3.1. Overview", please pay attention to the analysis of the taxonomic composition, especially in Section " 4. Discussion", lines 615-617 "We observed nuanced patterns in community composition, total abundance, and richness between sites at varying post-restoration stages. Noteworthy distinctions have emerged between adult and larval amphibians, as well as reptiles, highlighting the multifaceted, complex, and incongruent responses by distinct taxa to restoration efforts." Please pay attention and provide information to evaluate reactions:
AR: We appreciate your feedback but would like some clarification on your concern. The results section includes the statistical outputs that support these statements, and the discussion interprets these findings in relation to taxonomic composition, abundance, and richness across post-restoration stages. Since the results section provides the supporting statistical data, we intentionally refrain from repeating the same information in the discussion. If there are specific aspects that need further elaboration or additional analyses, we would be happy to address them.
The information is provided in the results, in particular, differences between reptiles and amphibians were revealed. I propose to supplement the information by indicating at the expense of which species the reactions of "increased diversity", "decreased diversity", "no change" are realized.
In general, overgrowing of reservoirs, siltation, decreased flow can affect the diversity of aphiubia differently than the diversity of reptiles. The analyzed species differ significantly in life cycle, activity of resource use, and some are predators and invaders outside their natural range. Brief information on each species with discussion will increase interest in the publication and development of recommendations for the conservation and maintenance of biodiversity, including planning work to maintain the optimal state of amphibian breeding and development sites (clearing, deepening, maintaining the hydrological regime) and possible reduction of trophic pressure - creation of additional shelters and partial isolation of spawning reservoirs.
Notes:
1. Design of figures. Please provide figures 3, 4 and 5 in the same scale and text font size as figure 2.
Author Response
Reviewer comment: The information is provided in the results, in particular, differences between reptiles and amphibians were revealed. I propose to supplement the information by indicating at the expense of which species the reactions of "increased diversity", "decreased diversity", "no change" are realized.
In general, overgrowing of reservoirs, siltation, decreased flow can affect the diversity of aphiubia differently than the diversity of reptiles. The analyzed species differ significantly in life cycle, activity of resource use, and some are predators and invaders outside their natural range. Brief information on each species with discussion will increase interest in the publication and development of recommendations for the conservation and maintenance of biodiversity, including planning work to maintain the optimal state of amphibian breeding and development sites (clearing, deepening, maintaining the hydrological regime) and possible reduction of trophic pressure - creation of additional shelters and partial isolation of spawning reservoirs.
Author response: Thank you for your detailed feedback. We have provided extensive information on the species driving the observed shifts in richness and abundance in both the Results (see Table 1, Table 2, Sections 3.3 and 3.4) and the Discussion (Lines 643–655, 750–770). Our use of NMDS and indicator species analyses was specifically intended to elucidate these patterns, and reiterating species-specific details earlier in the Results would only introduce redundancy and potential confusion. Regarding management recommendations, we have incorporated additional text addressing these points (Lines 836–846). We also note that the primary aim of our article is to present a high-level theoretical framework and an applied framework to test efficacy of restoration, rather than a detailed natural history account of each species, thereby ensuring the work remains accessible to a broad audience beyond specialists in herpetology. With respect to discussions on predator/invader dynamics, although these mechanisms are intriguing, two other reviewers advised against extensive elaboration given the lack of direct observational evidence in our study. Consequently, we have limited discussion of these aspects to maintain focus on our core results. We trust that these revisions adequately address your concerns.
Reviewer comments: Design of figures. Please provide figures 3, 4 and 5 in the same scale and text font size as figure 2.
Author response: Thank you for your detailed feedback. We prepared Figures 3, 4, and 5 with the same font size and formatting as Figure 2 at the time of submission. Unfortunately, the journal’s production process has led to manual resizing of the figures, which is beyond our control. Furthermore, the figures intentionally use different scales because each represents data with inherently different ranges (for example, Fig. 1a’s Y-axis ranges from 0 to 12, whereas Fig. 3a’s ranges from 0 to 200, and Figures 4 and 5 depict multivariate axes). Standardizing these scales would misrepresent the underlying data and lead to misleading visualizations. Lastly, regarding the comment on “research design,” it seems there may have been a misunderstanding between study design and manuscript formatting. We believe the study design is robust, and the issues raised pertain solely to the presentation of figures—a matter handled by the journal's editorial staff. Two other reviewers did not raise any concerns about the study design either.
Reviewer 2 Report
Comments and Suggestions for AuthorsThis is a very interesting article! Thak you for your effort to make it even better!
Author Response
Thank you for reviewing the revised version we submitted. Much appreciate the quick respond and your fantastic comments we received from the round 1.
