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Dear Authors,
Please note the latest recommendations from the reviewers so that the manuscript can complete the review process.
Sincerely
[# PeerJ Staff Note - this decision was reviewed and approved by Dezene Huber, a PeerJ Section Editor covering this Section #]
**PeerJ Staff Note:** Although the Academic and Section Editors are happy to accept your article as being scientifically sound, a final check of the manuscript shows that it would benefit from further editing. Therefore, please identify necessary edits and address these while in proof stage.
The authors have implemented the suggested grammatical corrections, improved sentence clarity, and rephrased problematic passages (e.g., Lines 18, 277, and 308–310). Figures and abbreviations were revised for clarity, and the manuscript’s readability has improved.
The authors clarified their methodological choices, notably the use of IRI > 1000 as a threshold for dominant species, supporting this decision with appropriate references. They also explained how rare species were excluded from the RDA, ensuring replicability and methodological transparency.
The discussion of invasive species was expanded, and conservation strategies were more explicitly articulated. The ecological classification criteria were defined and supported by authoritative literature. These revisions strengthen the ecological and management implications of the study
Overall, the authors responded constructively and carefully to all of my comments. The manuscript is clearer, better justified methodologically, and more robust in its conclusions. I am satisfied that my concerns have been adequately addressed. I agree with the changes made and recommend the manuscript for publication in its current form
Clear and unambiguous, professional English used throughout.
Literature references, sufficient field background/context provided
Professional article structure.
Change the keywords so they don’t repeat the exact words in the article’s title
Improve the quality of figures except the map
Original primary research within Aims and Scope of the journal
Methods described with sufficient detail & information to replicate.
All underlying data have been provided; they are robust, statistically sound, & controlled.
Conclusions are well stated, linked to original research question
Dear Authors,
Based on reviewer's comments, the manuscript requires major revisions.
Check all the notes and comments in the attached files, particularly Experimental design and Validity of the findings, which need attention.
Thanks again for your submission and we look forward to receiving your corrected manuscript.
Sincerely
**PeerJ Staff Note:** Please ensure that all review and editorial 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.
**Language Note:** The review process has identified that the English language must be improved. PeerJ can provide language editing services - please contact us at [email protected] for pricing (be sure to provide your manuscript number and title). Alternatively, you should make your own arrangements to improve the language quality and provide details in your response letter. – PeerJ Staff
The article draws a very clear analysis of the diversity of a stretch of an important river, however, the introduction must be better founded with studies that have been carried out at least
which possem to be comparative. These pigtails occur in different months and years, making it difficult to compare in terms of seasonal differences. The mal doesn’t exist, it’s important to understand the section of the river was sampled.
The experimental design use differents ways to capture the fishes however there are a lacks in the samples of the years could be difficult to have a sazonal differences
The analysis are good, the types of analyses helped the understanding of the findings. Despite the problems in sampling, the results are very well explained.
Improve the introduction with papers about fish diversity studies
Put the map of the sample sites
Improve the discussion about the why don’t have differences between the sites
English language and clarity: The manuscript is generally well-written, but some sentences would benefit from grammatical and stylistic polishing.
For instance:
Line 18: “...and their relationship...”, should be “its relationship” to agree with singular subject “structure”.
Line 277: consider rephrasing for clarity, e.g., “nutrient input from irrigation return flows” instead of “pollution caused by irrigation projects”.
Lines 308–310: long sentence with many commas; suggest breaking it up for better readability.
Literature coverage and context: The introduction (Lines 44–76) includes relevant and recent references. However, the knowledge gap could be more sharply defined by connecting historical fish records (Lines 270–271) with the rationale for the present study.
Structure and figure quality: The manuscript adheres to PeerJ structural standards. Tables and figures are clear and informative.
Raw data availability: Data collection and availability are described appropriately (Line 94). The methodology complies with data-sharing policies.
Research scope and relevance: The study addresses an ecologically critical and underrepresented river stretch (Lines 69–70), with strong justification for monitoring freshwater fish biodiversity.
Sampling design and effort: Seasonal sampling across 15 stations (Lines 81–84) with multiple gear types (Lines 85–89) demonstrates methodological rigor.
Reproducibility and methodological clarity: Indices and statistical methods are well described (Lines 103–161).
Two points need clarification:
Line 119: Explain why IRI > 1000 is used as a dominance threshold; While the Index of Relative Importance (IRI) is a widely used metric, the choice of a fixed cutoff is context-dependent and not universally accepted. Without a clear rationale or supporting references, the classification of species as "dominant" may appear arbitrary and limit comparability with other studies.
Line 152: Specify how rare species were excluded from RDA analysis. RDA is sensitive to low-frequency taxa, and exclusion decisions can significantly affect ordination results. Failure to report how rare species were filtered undermines the interpretability and replicability of the analysis and may bias the ecological patterns observed.
Ethical standards: Animal use and ethics compliance are clearly stated (Lines 98–99; 380–382).
Robustness and Interpretation: The manuscript applies appropriate statistical tools to assess diversity (lines 103–111), dominance (lines 114–119), ecological traits (lines 120–124), and ordination (lines 140–150; 246–257). However, the following concerns must be addressed:
Unmeasured Anthropogenic Pressures
Lines 64–68: Anthropogenic stressors and invasive species are cited as causes of fish community decline, but no empirical data or literature are presented to substantiate these claims. This creates an analytical dissonance: the manuscript invokes human-induced impacts (dams, pollution, exotic species) but does not quantify or include them in the analysis.
Lines 79–99: The methods do not include land use metrics, proximity to dams, or pollution indicators — despite being presented as major drivers in the introduction. This undermines the study's objective to assess environmental relationships with community structure.
Ecological Classification Not Integrated
Lines 120–124: Although fish were categorized into habitat and trophic types, the criteria used (field observation, literature, databases?) are not explained. More critically, these classifications are not integrated into any of the community analyses. Functional shifts may be more sensitive indicators of disturbance than taxonomic changes — this represents a missed analytical opportunity.
Habitat Variables Omitted
Only five water quality variables (temperature, DO, pH, ammonia, chlorophyll-a) are measured. No physical habitat variables (substrate, vegetation, depth, flow) are included. This weakens environmental interpretation and limits potential ecological insights.
Community Similarity and Ordination
Lines 140–150: Bray-Curtis, hierarchical clustering, and NMDS are correctly applied. The use of stress values is appropriate (<0.1). However, the interpretation is superficial — there is no discussion of weak clustering or overlapping assemblages. This could suggest biotic homogenization or species replacement, but such processes are not explored. Moreover, ordination results are not contextualized with ecological groups or habitat variables.
Stability and ABC Curves
Lines 289–299:While ABC curves and W-statistics are used, their interpretation is limited. Patterns of disturbance (e.g., from exotic species or recruitment failure) are not linked to the results. Dominant species traits are not discussed, and no spatial heterogeneity is analyzed.
Strengths:
i. Seasonal dataset from 15 stations;
ii. Use of multiple biodiversity and ordination metrics;
iii. Identification of environmental gradients through RDA;
iv. Valuable regional baseline for freshwater conservation.
Weaknesses and Points for Revision:
i. Expand discussion on invasive species and management responses (Lines 286–294);
ii. Translate ecological findings into actionable conservation strategies (Lines 343–371);
iii. Strengthen analysis of hydrological fragmentation and fish migration (Lines 278–280);
iv. Clearly define criteria for ecological classification and integrate functional groups into analyses;
v. Add disturbance metrics (e.g., dominance of exotic species, proportion of r-strategists) to complement ABC results;
vi. Deepen interpretation of NMDS and clustering outcomes to address possible biotic homogenization.
1. It is necessary to reread an article and improve the content.
2. Need to add more information about the background.
3. Need to improve the quality of figures, as it is mentioned in the article.
4. Uncommon abbreviations should be spelled out at first use.
1. Yes, original primary research within the Aims and Scope of the journal.
2. Methods are described with sufficient detail & information to replicate.
1. Need to assess impact and novelty.
2. The conclusion should be appropriately stated, should be connected to the original question investigated, and should be limited to those supported by the results. In particular, claims of a causative relationship should be supported by a well-controlled experimental intervention. Correlation is not causation.
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