Regional Trends of Biodiversity Indices in the Temperate Mesic United States: Testing for Influences of Anthropogenic Land Use on Stream Fish while Controlling for Natural Landscape Variables
Round 1
Reviewer 1 Report
I has reviewed the ms (Water-2313591). The authors summarized stream fish assemblages from 10,522 locations by multiple biodiversity indices and then quantified index responsiveness to natural landscape variables and anthropogenic land use in stream network catchments across five freshwater ecoregions in the temperate mesic portion of the United States. The results indicated complex influences of natural and anthropogenic landscape variables on unique elements of biodiversity and offer insights that may inform conservation of stream fish assemblage biodiversity now and into the future. Our analyses show that taxonomic distinctness in freshwater fishes characterize a unique element of biodiversity in relationships with anthropogenic land uses in a streams network catchment. Based on the results, the authors recommend using multiple biodiversity measures to capture unique attributes of stream fish assemblages when testing for effects of anthropogenic stressors. The study has important implications for development of multimetric indices of biotic integrity and emphasizes the importance of identifying species-specific targets when implementing actions to conserve or protect biodiversity in stream systems. This study is very nice, and also is important to management and conservation of fish biodiversity. I provide some comments in detail below and hope these will be useful to the authors. Furthermore, I am not a native English speaker, so my comments will mainly not involve the issues of language.
Major concern:
Mostly, I am curious in data of fish assemblages used in this study. The authors did not describe detailed information of fish data to rationalize their processing method. The data were collected from 10,522 locations of five ecoregions between years 1990 to 2010. how many locations are in each ecoregion? Were data intensity same among different ecoregions and sampling years? Sometimes, I need to guess the temporal relationships between fish data and anthropogenic landscape variables, because fish data spanned 20 yeras and may be different among ecoregions. I suggested the authors added these information to provide readers that data is not unbalanced.
Specific concerns:
Abstract: it is better to condense the Abstract.
Introduction: the authors introduced all indices such as species richness, Shannon’s diversity, Pielou’s evenness,taxonomic diversity, and taxonomic distinctness in this part. However, the beta diversity was missed. Why?
Line 140: delete redundant spaces.
Table 1: the descriptions of precipitation and Urban (%) seemed inaccurate, i.e. “average mean annual precipitation” and “Developed, open space, low , medium, & high intensity in network catchment”.
Line 276: “ A standardized regression coefficient (β) value” was introduced here, however “ adjusted R2” was stressed in the Results.
Line 491: some references were cited in text, which seem strange to me. For example, reference [76] in line 491, [89] in line 563, [41] in line 603.
Line 563: the full name of “IBI” should be added here.
References: I think there are too many references for a research paper.
Author Response
Reviewer 1
Each of the reviewer major and specific concerns have been addressed and a response provide below.
Major concern:
[X]Mostly, I am curious in data of fish assemblages used in this study. The authors did not describe detailed information of fish data to rationalize their processing method. The data were collected from 10,522 locations of five ecoregions between years 1990 to 2010. how many locations are in each ecoregion? Were data intensity same among different ecoregions and sampling years? Sometimes, I need to guess the temporal relationships between fish data and anthropogenic landscape variables, because fish data spanned 20 years and may be different among ecoregions. I suggested the authors added these information to provide readers that data is not unbalanced.
-Response: Added additional descriptions and detail regarding sampling sites included in study which were chosen to appropriately match temporal relationship with natural landscape variables and anthropogenic lands use information included in the study. Also referenced in the manuscript was [60,61] for further descriptions of fish data. The number of sites in analysis can be inferred by the degrees of freedom in Table 4 by the study regions. I added the number of sample sites by region in Table 1.
Specific concerns:
[X] Abstract: it is better to condense the Abstract.
-Response: I reduced the length of the Abstract.
[X]Introduction: the authors introduced all indices such as species richness, Shannon’s diversity, Pielou’s evenness, taxonomic diversity, and taxonomic distinctness in this part. However, the beta diversity was missed. Why?
-Response: Added description introducing beta diversity in the introduction
[X]Line 140: delete redundant spaces.
-Response: deleted redundant space in line 140
[X]Table 1: the descriptions of precipitation and Urban (%) seemed inaccurate, i.e. “average mean annual precipitation” and “Developed, open space, low, medium, & high intensity in network catchment”.
-Response: Edited descriptions for Urban (%) and Precipitation descriptions to improve clarity as reviewer suggested
[X]Line 276: “A standardized regression coefficient (β) value” was introduced here, however “adjusted R2” was stressed in the Results.
-Response: The standardized regression coefficients were the basis of identifying the most important and significant natural landscape variables and anthropogenic land use predictors of biodiversity indices and the predictors negative or positive influence on the indices. The standardized regression coefficients are conferred in relative terms as importance as a predictor of biodiversity indices and discussed in a large portion of the results section.
[X]Line 491: some references were cited in text, which seem strange to me. For example, reference [76] in line 491, [89] in line 563, [41] in line 603.
-Response: Edited in text references in line 491, 563, and 613 and moved them to the end of sentence.
[X]Line 563: the full name of “IBI” should be added here.
-Response: Added full name of Index of Biotic Integrity before the use of acronym (IBI).
[X]References: I think there are too many references for a research paper.
-Response: The topic of biodiversity indices has a rich history in the scientific literature and has also had a resurgence in topic debate within the scientific community, e.g. [25, 27] hence the larger amount of references for this research paper.
Submission Date
14 March 2023
Date of this review
23 Mar 2023 03:59:30
Reviewer 2 Report
The title can be shorter, I suggest it
The references may be the relevant ones and some that are not pertinent are reduced.
Improve figure 4
The research design is pertinent, the use of biological indices generates baseline information, which can be rescued and according to a history in each ecoregion and strengthen the objective of the water magazine.
It should be noted that the results of the study suggest that multiple measures of fish biodiversity could be used to better characterize the response of baseline stream fish assemblages. To support the development of multimetric indices of biotic integrity to assess streams and emphasizes the importance of identifying species-specific targets when implementing actions to conserve or protect biodiversity in stream systems.
Author Response
Reviewer 2
Each of the reviewer comments and suggestions have been addressed and a response provide below.
Comments and Suggestions for Authors
[X]The title can be shorter, I suggest it
-Response: The title was shortened
[X]The references may be the relevant ones and some that are not pertinent are reduced.
-Response: The topic of biodiversity indices has a rich history in the scientific literature and has also had a resurgence in topic debate within the scientific community, e.g. [25, 27] hence the larger amount of references for this research paper.
[X]Improve figure 4
-Response: There is no figure 4 in this manuscript.
Submission Date
14 March 2023
Date of this review
21 Mar 2023 05:19:30
Reviewer 3 Report
Basic remarks
Abstract is too big.
Materials and Methods
L 132-140 and 143-154: The information is redundant for this section and can be moved to the Introduction.
L 160: Unclear meaning needs to be rephrased.
L 162 and 164: Replace with “dataset”.
Table 1: Table 1 is too cumbersome. Perhaps it should be moved to Supplementary.
L 255: Was not indicated a tool used for calculation of the descriptive statistics.
Results: More illustrations could improve the quality of presentation.
Supplementary Materials: Data presented in Supplementary Table are poorly organized. Unable to read.
Resume: Accept after minor revision (corrections to minor methodological errors and text editing).
Comments for author File: 
Comments.pdf
Author Response
Reviewer 3
Each of the reviewer comments and suggestions have been addressed and a response provide below.
Comments and Suggestions for Authors
Basic remarks
[X]Abstract is too big.
-Response: the length of the abstract was reduced.
Materials and Methods
[X]L 132-140 and 143-154: The information is redundant for this section and can be moved to the Introduction.
-Response: I disagree with the reviewer that this information describing the study area is redundant for the materials and methods section and should be moved to the introduction. The study area is a key part of the research design for this study and is appropriately described and placed in the materials and methods sections. I did not alter the placement of, or the description of the study area as suggested by the review.
[X]L 160: Unclear meaning needs to be rephrased.
-Response: Edited to clarify and reference study that methods were followed.
[X]L 162 and 164: Replace with “dataset”.
-Response: Replaced NHDPlusV1 with NHD throughout manuscript.
[X]Table 1: Table 1 is too cumbersome. Perhaps it should be moved to Supplementary.
-Response: Revised table 1 to make more condensed
[X]L 255: Was not indicated a tool used for calculation of the descriptive statistics.
-Response: Added the R package that was used to calculate the descriptive statistics.
[X]Results: More illustrations could improve the quality of presentation.
-Response: I have already reduced the number of illustrations to balance the relevant information to describe the research and keep the text and length of the manuscript to a pertinent minimum.
[X]Supplementary Materials: Data presented in Supplementary Table are poorly organized. Unable to read.
-Response: Reviewed supplementary materials and found there to be nothing wrong with the excel spreadsheet provided. It is a species list organized logically for all species included in the study and needed to calculate the taxonomic measures used in the study. Therefore, I did not change the supplementary material provided.
Submission Date
14 March 2023
Date of this review
04 Apr 2023 11:15:07
Reviewer 4 Report
The manuscript „Regional trends of biodiversity indices in the temperate mesic 2 United States: testing for influences of anthropogenic land use 3 on stream fish while controlling for natural landscape variables " is well prepared and worthy of publication in Water.
I think it need small corrections.
Firstly, authors should provide the abundance of individual fish species and provide specific values for individual research regions. The list of only species is of little use for comparative purposes.
Secondly, the analysis should be supported by some multivariate analysis. An example of such analysis (different landscape parameters) you could find in articles:
Pakulnicka J., Buczyński P., Dąbkowski P., Buczyńska E., Stępień E., Stryjecki R., Szlauer-Łukaszewska A., Zawal A. 2016. Aquatic beetles (Coleoptera) in springs of a small lowland river: habitat factors vs landscape factors. Knowledge and Management of Aquatic Ecosystems. 417, 29: 1-13. DOI: 10.1051/kmae/2016016
Author Response
Reviewer 4
Each of the reviewer comments and suggestions have been addressed and a response provide below.
I think it need small corrections.
[X]Firstly, authors should provide the abundance of individual fish species and provide specific values for individual research regions. The list of only species is of little use for comparative purposes.
-Response: The supplemental material is not provided for a comparative purpose it is a species list for all species included in the study and needed to calculate the taxonomic measures used in the study. The number of sites in analysis can be inferred by the degrees of freedom in Table 4 by the study regions. The number of sample sites by region was added in Table 1. The abundances of individual fish species for 10522 sites in the study will not be provided.
[X]Secondly, the analysis should be supported by some multivariate analysis. An example of such analysis (different landscape parameters) you could find in articles:
-Response: Additional analysis for this manuscript will not be completed but is taken into consideration for future avenues of research the reference to examples of appropriate multivariate analysis is appreciated.
Submission Date
14 March 2023
Date of this review
28 Mar 2023 15:03:34
Reviewer 5 Report
Review comments on the manuscript by Thornbrugh et al
Regional trends of biodiversity indices in the temperate mesic United States: testing for influences of anthropogenic land use on stream fish while controlling for natural landscape variables
The aim of the study was to investigate on a large scale, over five ecoregions in the United States, the response of freshwater stream fish assemblages to anthropogenic landscape stressors. To undertake the analysis, the authors summarised stream fish assemblage data from 10,522 locations collected over 20 years and then calculated six biodiversity indices for each of the five ecoregions. The authors initially tested for correlations between indices across ecoregions. They then tested for correlations between indices across ecoregions. Finally, they used multiple linear regression to identify significant natural and anthropogenic landscape variables across the ecoregions.
The results of the study showed that across the bioregions the biodiversity indices were influenced by both natural landscape variables and anthropogenic land uses. The results of this comprehensive study will inform future studies investigating stream fish assemblages and the factors that influence fish assemblages in different regions, and differences in land use and anthropogenic impacts. Overall, the authors have achieved the study aims. As such, I consider that a revised paper addressing the comments detailed below would be suitable for publication.
Specific comments on the manuscript are detailed below.
In lines 31 and 32 in the abstract, add land use after urban and agriculture to clarify these terms.
In line 248, insert the … using the function….
In line 250, insert a comma ….. Before analysis, variables and ……
In line 358, insert the …. In the Middle Missouri.
In lines 367 and 369, change, the spelling of Species richness to a lower case
In line 412, insert a comma ….. biodiversity indices, except for ……
In line 426, remove the hyphen from an-thropogenic.
In line 495 insert species …..such as species richness…
In line 531, insert a comma ….. Lakes ecoregions, but were ……
In line 564 define the abbreviation of IBI scores
In lines 607 and 608, should the spelling of lithophils and reheophils be lithophil and reheophil or lithophilic and reheophilic?
In line 609, remove the second full stop after 4.4 . . Spatial….
In line 632, insert was ….. distinctiveness was found to….
In a number of places in the manuscript e.g., lines 319, 339, 341, 378, 389, 446, 539, 541 etc, the authors use the plural ecoregions when referring to a single ecoregion.
In references No 9, 11 and 53 the publication year has been included twice in the reference after the authors names.
In line 800, correct the spelling of regional.
Author Response
Reviewer 5
Each of the reviewer comments and suggestions have been addressed and a response provide below. All suggested specific line edits as suggested by reviewer were excepted and edited appropriately in the manuscript.
Specific comments on the manuscript are detailed below.
[X]In lines 31 and 32 in the abstract, add land use after urban and agriculture to clarify these terms.
-Response: Added land use following urban and agricultural in lines 31 and 32
[X]In line 248, insert the … using the function….
-Response: Added ‘the’ as suggested by reviewer in line 248
[X]In line 250, insert a comma ….. Before analysis, variables and ……
-Response: Inserted a comma as suggested by reviewer in line 250
[X]In line 358, insert the …. In the Middle Missouri.
-Response: inserted ‘the’ in line 358 as suggested by reviewer in line 358
[X]In lines 367 and 369, change, the spelling of Species richness to a lower case
-Response: changed Species richness to lower case in line 367 and 369 as suggested by reviewer
[X]In line 412, insert a comma ….. biodiversity indices, except for ……
-Response: Inserted a comma in line 412 as suggested by reviewer
[X]In line 426, remove the hyphen from an-thropogenic.
-Response: Removed the hyphen from anthropogenic in Table 4 description as suggested by reviewer
[X]In line 495 insert species …..such as species richness…
-Response: Inserted species to species richness in line 495 as suggested by reviewer
[X]In line 531, insert a comma ….. Lakes ecoregions, but were ……
-Response: Inserted a comma in line 532 as suggested by reviewer
[X]In line 564 define the abbreviation of IBI scores
-Response: I defined the abbreviation of Index of Biotic Integrity (IBI) as suggested by reviewer on line 564
[X]In lines 607 and 608, should the spelling of lithophils and reheophils be lithophil and reheophil or lithophilic and reheophilic?
-Response: Edited lithophils and reheophils spelling as suggested by reviewer to lithophilic and reheophilic species in line 607 and 608.
[X]In line 609, remove the second full stop after 4.4 . . Spatial….
-Response: Removed the second period in line 609 as suggested by reviewer.
[X]In line 632, insert was ….. distinctiveness was found to….
-Response: Inserted was as suggested by reviewer in line 632.
[X]In a number of places in the manuscript e.g., lines 319, 339, 341, 378, 389, 446, 539, 541 etc, the authors use the plural ecoregions when referring to a single ecoregion.
-Response: Edited manuscript for plural use of ecoregions when it should be singular and incorporated all suggested edit as suggested by reviewer.
[X]In references No 9, 11 and 53 the publication year has been included twice in the reference after the authors names.
-Response: Deleted duplicate publication years for reference [9,11,53] as suggested by reviewer
[X]In line 800, correct the spelling of regional.
-Response: Corrected spelling of regional in line 800 reference [61]
Submission Date
14 March 2023
Date of this review
31 Mar 2023 10:57:15
