Effect of Canal Bank Engineering Disturbance on Plant Communities: Analysis of Taxonomic and Functional Beta Diversity
Round 1
Reviewer 1 Report
The authors intensively investigated how canal bank engineering affected bank and aquatic plant communities. The study is well-designed, and the methods and results were well-described. The introduction and discussion, however, should be revised before the manuscript can be considered for publication.
Abstract: Please use 2-3 sentences to give some background information about this study.
Introduction: This section should include a paragraph giving the definition of 'canal bank engineering' and relevant information to this study; otherwise, it is very difficult to understand the aim of this research.
Materials & Methods: I doubt if it is really a good idea to log transform the data. Instead of checking the normality of the data, the authors should check the normality of the residuals of the models they built.
Results: Quite well described.
Discussion: The sentences in this section are rather long. Some sentences even run over 5 lines.
Conclusion: The section is where to conclude what has been found and discussed in a concise way and should not bring new information to open new topics. Please shorten the section into one paragraph.
Minor comments:
Line 30: Please give at least an example of human modification of landscape relevant to this study, so that readers can expect what information this study will bring.
Line 95: Please add the coordinates of the Basingstoke Canal and the information on through which county and country the canal runs. Please cite the Figure 2.
Line 106: Please define 'soft bank-engineering'.
Line 122: 'm2' -> 'm2'
Line 184: 'using RStudio 1.3.1' -> 'using the statistical software R version xxx'. RStudio is a development environment for R. Please check the version of R utilised in the data analysis. The authors cited R Core Team 2020, but the version was 1.3.1 , which was published in September 2001.
Lines 324-326: Results is the section where the results are described. The authors should move the description of what they have done to the Materials & Methods section.
Lines 454-473: It is better to mention the results of this study first, and then compare the results with previous research.
Line 518: Delete 'record'.
The English is in general good, but for some reason, in the Discussion, the sentences are rather long (over 3 lines!!!) and very difficult for readers to understand. The authors must avoid using ambiguous words, such as using 'this' alone, because the readers would be confused by what 'this' refers to. 'This' problem appeared throughout the manuscript, e.g. in Lines 61, 107, 251, 266, 270, 409, 429, 479, 501, 505, 518, 539, 610.
Author Response
Note: the reviewer comments and suggestions are indicated, point by point, with ‘>’ and our responses start with ‘Response:’
>The authors intensively investigated how canal bank engineering affected bank and aquatic plant communities. The study is well-designed, and the methods and results were well-described. The introduction and discussion, however, should be revised before the manuscript can be considered for publication.
Response: Thank you for your assessment, which we think is fair and balanced. Please see our responses below, to the specific comments about the introduction and discussion.
>Abstract: Please use 2-3 sentences to give some background information about this study.
Response: We added the following sentence of background information near the start of the abstract:
“We utilized a pseudo-experimental setting on the Basingstoke Canal, UK, where sections of canal bank have been repaired over a four-year period, interspersed with sections left undisturbed.”
We think is sufficient for the abstract. The journal’s recommended length for the whole abstract is only 200 words, and that is not compatible with 2-3 sentences on background alone. And we need to maintain a balance of background, aim, methods, results and conclusions in the abstract. We were already slightly over the 200 words for the abstract, and did not want to remove too much from the version of abstract that was already approved by the guest editors for this special issue. The new version of our abstract is 223 words, which we hope is acceptable to the journal.
>Introduction: This section should include a paragraph giving the definition of 'canal bank engineering' and relevant information to this study; otherwise, it is very difficult to understand the aim of this research.
Response: The aim of this research is to better understand effects of small-scale disturbances on plant communities. We use disturbance created by canal bank engineering as pseudo-experimental system for studying that. So we argue that the aim is already clear. However, we agree that it is helpful to provide more information on that study system – canal bank engineering – so that readers can better understand the methods and results. We have added a paragraph giving this information, as requested, in lines 54-77:
“In this research, to study plant assemblage response to small-scale disturbance, we utilized a pseudo-experimental system produced by canal bank engineering. The disturbance comprises the total removal of above- and belowground biomass and replacement with dredged material from the canal, following annual bank engineering work, each winter across a four-year period. Dredged materials vary greatly in chemical properties, often containing high concentrations of nutrients and pollutants including heavy metals (Bromhead and Beckwith, 1994; Singh et al, 1996) and have been associated with increased likelihood of seedling establishment (Hoosein, 2016). Although they do not undergo flooding events, highly fragmented towpath habitats are analogous to urbanised riparian plant communities. They are vulnerable to invasive species introductions from private gardens (Mayer et al, 2017), meaning that even if the disturbance causes loss of native species, invasive species may lead to net increases in beta-diversity (Olden and Poff, 2003). For example, a study on urbanisation of riparian habitats concluded that functional-beta and taxonomic-beta increased under urbanisation due to invasive species and environmental heterogeneity (Brice et al, 2017). However, even when disturbance date is known (e.g. flooding or fire events) many studies use only phenomenological data (e.g. Alignier and Baudry, 2016; Brice et al, 2017; Freeman et al, 2019), complicating interpretation of results due to variation in initial biomass (Fukami et al, 2005; Smart et al, 2006). An experimental study altering initial composition of grassland communities reported reduction of functional-beta diversity through time, due to environmental filtering (Fukami et al, 2005). But the same study also reported maintenance of high taxonomic beta-diversity due to stochastic biotic interactions of founding species. Although experimental studies are relatively uncommon, by controlling complicating variables (e.g. dispersal) they can be utilised to better understand small-scale compositional drivers (Hulme and Bremner, 2006; Götzenberger et al, 2011). Pseudo-experimental studies additionally allow dispersal of species often not considered in experimental studies, such as rare species or ornamental invasive species.”
>Materials & Methods: I doubt if it is really a good idea to log transform the data. Instead of checking the normality of the data, the authors should check the normality of the residuals of the models they built.
Response: We have clarified in the text that the normality we were addressing was in the residuals of the models (line 198). We are fully aware that it is the residuals of the models that matter for normality – indeed, the corresponding author of our paper has published several works that stress this exact point.
The reviewer does not mention why s/he doubts the suitability of the log-transformations. Perhaps it is no more than the point about the residuals being what matters rather than the raw data. The log-transformations cured skew in the residuals. In addition, we give a biological explanation for the two log-transformations we applied, and support this reasoning with citation of appropriate literature.
We have adapted the current text to improve the clarity of justification for log transformations, as follows:
“Seed mass and plant height data were positively skewed (as is typical), resulting in ecologically relevant differences between low trait values being underrepresented by the raw data (Májeková et al, 2016). Following Májeková et al. (2016), who tested effects of transformations on functional trait data and found that log-transformations best improved normality and led to greater accuracy in FD indices for contexts in which the exact values of traits are not important (as here), we log(10)-transformed both variables. This greatly reduced skew in the residuals of our models. For SLA, for which there was low skew, we did not apply a transformation.” Lines 192-199.
>Results: Quite well described.
Response: Thank you. Please note that we have tried to improve this description further in the revision, in particular in some of the Figures (prompted by comments by another reviewer).
>Discussion: The sentences in this section are rather long. Some sentences even run over 5 lines.
Response: Agreed. We had to rush the submission of the manuscript, to meet the deadline, and the Discussion and Conclusion sections had been written by a different author to the Methods and Results. We have now applied consistency of style throughout the manuscript, a key focus of which was to improve readability in the Discussion.
>Conclusion: The section is where to conclude what has been found and discussed in a concise way and should not bring new information to open new topics. Please shorten the section into one paragraph.
Response: We agree that it was too long, and have shortened it to one paragraph, as recommended.
>Minor comments:
>Line 30: Please give at least an example of human modification of landscape relevant to this study, so that readers can expect what information this study will bring.
Response: done (now line 31).
>Line 95: Please add the coordinates of the Basingstoke Canal and the information on through which county and country the canal runs. Please cite the Figure 2.
Response: Figure 2 is cited in line 112. We have included co-ordinates in Figure 2.
>Line 106: Please define 'soft bank-engineering'.
Response: Done (now line 120-125).
>Line 122: 'm2' -> 'm2'
Response: Corrected. Thanks for spotting this.
>Line 184: 'using RStudio 1.3.1' -> 'using the statistical software R version xxx'. RStudio is a development environment for R. Please check the version of R utilised in the data analysis. The authors cited R Core Team 2020, but the version was 1.3.1 , which was published in September 2001.
Response: We have updated the versions of R and RStudio and provided relevant citations, thank you for bringing this up!
>Lines 324-326: Results is the section where the results are described. The authors should move the description of what they have done to the Materials & Methods section.
Response: Thanks for pointing this out. Now moved to the methods section.
>Lines 454-473: It is better to mention the results of this study first, and then compare the results with previous research.
Response: Thanks. Done.
>Line 518: Delete 'record'.
Response: Done.
>Comments on the Quality of English Language
>The English is in general good, but for some reason, in the Discussion, the sentences are rather long (over 3 lines!!!) and very difficult for readers to understand. The authors must avoid using ambiguous words, such as using 'this' alone, because the readers would be confused by what 'this' refers to. 'This' problem appeared throughout the manuscript, e.g. in Lines 61, 107, 251, 266, 270, 409, 429, 479, 501, 505, 518, 539, 610.
Response: As explained with respect to the comments on the Discussion, above, we have gone through the entire manuscript, improving readability. As part of that process, we have reviewed all instances of the word ‘this’ (including, but not limited to, those specified by the reviewer), and made revisions as recommended.
Please note that we did not find the word ‘this’ in line 518 of the original submission, nor any occurrence of the word that might have been problematic within the 10 lines before or after line 518.
Reviewer 2 Report
General Comments
The topic of this scientific article review is of significant importance as it sheds light on the impact of small-scale disturbances on plant communities and their corresponding biotic functions. The study focused on determining the patterns of functional and taxonomic dissimilarity in disturbed and undisturbed plant communities, providing insights into the effects of human activities on biodiversity. The research findings revealed high levels of taxonomic and functional dissimilarity between disturbed and undisturbed sites, primarily driven by turnover, and indicated that small-scale disturbances may increase taxonomic and functional between-community dissimilarity in anthropogenic habitats. These results highlight the importance of local-scale conservation efforts to promote habitat heterogeneity and enhance taxonomic diversity, which is critical for maintaining ecosystem functions and services. Therefore, this study has significant implications for policymakers, conservationists, and land managers who are concerned with protecting and preserving biodiversity in human-altered landscapes. I am unsure if they would fall under the heading of ‘major changes’ or ‘minor changes’ to the manuscript, but I believe they can be easily handled or refuted by the authors. Some general comments are included below.
I will look forward to seeing the published paper and congratulate the authors on the work done here.
Sincerely,
Comments for author File: 
Comments.pdf
Author Response
Note: the reviewer comments and suggestions are indicated, point by point, with ‘>’ and our responses start with ‘Response:’
>General Comments
>The topic of this scientific article review is of significant importance as it sheds light on the impact of small-scale disturbances on plant communities and their corresponding biotic functions. The study focused on determining the patterns of functional and taxonomic dissimilarity in disturbed and undisturbed plant communities, providing insights into the effects of human activities on biodiversity. The research findings revealed high levels of taxonomic and functional dissimilarity between disturbed and undisturbed sites, primarily driven by turnover, and indicated that small-scale disturbances may increase taxonomic and functional between-community dissimilarity in anthropogenic habitats. These results highlight the importance of local-scale conservation efforts to promote habitat heterogeneity and enhance taxonomic diversity, which is critical for maintaining ecosystem functions and services. Therefore, this study has significant implications for policymakers, conservationists, and land managers who are concerned with protecting and preserving biodiversity in human-altered landscapes. I am unsure if they would fall under the heading of ‘major changes’ or ‘minor changes’ to the manuscript, but I believe they can be easily handled or refuted by the authors. Some general comments are included below.
>I will look forward to seeing the published paper and congratulate the authors on the work done here.
Response:
Thank you for this positive overall assessment. We agree with the comments, which are addressed point by point below.
>It is important to note that the article under review requires improvements in the quality of its graphics and images. The current visual representations are not adequate to fully convey the data and information being presented and may hinder the reader's understanding of the research findings. Higher quality and more visually appealing graphics and images are necessary to enhance the overall presentation and impact of the article. Improving the quality of the graphics and images in the article can also help to increase the likelihood of the research being published in a reputable journal, as it demonstrates attention to detail and an overall commitment to producing high-quality research. Therefore, I recommend that the authors revise the graphics and images in the article before submitting it for publication.
Response: Thank you for pointing this out. We absolutely agree that some of the figures could be improved, which we have now done. In particular, we have improved Figure 2 (the site map), which now includes coordinates (pointed out by another reviewer). Additionally, Figure 1 has been changed to only include high-resolution photos of the bank engineering sites due to the lower resolution of available diagrams provided by the engineering consultants. A graphical abstract will be included with the submission of this paper, which should help to improve visual interpretability of the study for the reader. We have also modified Figures 3 and 4 and removed Figure 8. We hope that these changes fully address this criticism.
>Although the article under review contains valuable research findings, it is important to address the inconsistencies in the formatting of the bibliography. While the changes required may be small, inconsistent formatting can detract from the clarity and quality of the article and may raise questions about the rigor and attention to detail of the research. Therefore, I recommend that the authors thoroughly review and correct any inconsistencies in the formatting of the bibliography to ensure that it is consistent with the guidelines and standards of the publication. This will not only enhance the professionalism and credibility of the research but also demonstrate the authors' commitment to producing high-quality, well-researched work.
Response: Agreed. We had to rush the submission of the manuscript, to meet the deadline, and as a result our reference list had these problems, as well as including references that are not cited in the text. We have completely redone the reference list, which is also now numbered.
>I would like to commend the authors of the reviewed article for the comprehensive supplementary materials provided alongside the main research paper. These materials, which include a list of the species studied, are incredibly valuable in providing readers with a better understanding of the extensive research conducted by the authors. The list of species studied is particularly important as it provides insight into the scope and scale of the research, highlighting the amount of work that went into collecting and analyzing the data. By including these supplementary materials, the authors have demonstrated a commitment to transparency and thoroughness in their research, and have provided a valuable resource for researchers and practitioners in the field.
Response:
Thank you for this commendation!
Reviewer 3 Report
I only have two concerns for this study. The first is language. Several sentences are too long and researchers in non-English countries may find difficulty to understand. Therefore, we suugest the authors to rephrase the long sentences in the article. The second is the trait data. Did the authors measure the traits in situ, or just exteact the data from TRY database? If the authors just extract the data from database, I recommend the authors to collect the data in the field. And I do not know if the TRY database reflect the true scenario in the field.
The English quality is fine but several phrases need minor improvement since several long sentences are difficult to understand.
Author Response
Note: the reviewer comments and suggestions are indicated, point by point, with ‘>’ and our responses start with ‘Response:’
>I only have two concerns for this study. The first is language. Several sentences are too long and researchers in non-English countries may find difficulty to understand. Therefore, we suugest the authors to rephrase the long sentences in the article.
Response: Agreed, and now addressed. We had to rush the original submission of the manuscript, to meet the deadline, and the Discussion and Conclusion sections had been written by a different author to the Introduction, Methods and Results. We have now applied consistency of style throughout the manuscript, a key focus of which was to improve readability, particularly in the Discussion.
>The second is the trait data. Did the authors measure the traits in situ, or just exteact the data from TRY database? If the authors just extract the data from database, I recommend the authors to collect the data in the field. And I do not know if the TRY database reflect the true scenario in the field.
Response: We used data from databases. We appreciate that using species-level trait values from global databases in local studies can be problematic. However, measuring traits in the field was not possible for two key reasons. First, the fieldwork was conducted during a brief interval in Covid lockdown, so time in the field was extremely limited. Second, for one of the three core traits (seed mass), most of the plants encountered in our plots were not seeding.
Additionally, without significant extra fieldwork measuring traits for plants in the local area, but separate to the measured plots, measuring the traits in situ would not have been appropriate. This is because we are interested in the strategies of the plant species in the assembly, not in the specifics of the plant individuals. For example, with respect to plant height, measuring height of individuals within disturbed and undisturbed sampling plots for perennial plants would introduce circularity, given that the treatments differ in the amount of time that the plants have had to grow since disturbance. Instead, our focus is on typical height of mature individuals of the species concerned, rather than on the heights of the (often seedling or juvenile) plants encountered in our plots.
We therefore extracted traits from the global TRY database on seed mass, plant height (generative), and specific leaf area. This is because TRY provided the most complete coverage of traits for species in this study. However, trait values for all species were manually inspected and any suspicious values were compared with categorical trait values within the Grime et al (1988) database. To maximise comparability of functional and taxonomic diversity in this study, missing trait values in TRY were hierarchically infilled using the following system:
- If the species’ trait was in TRY, specifically from the ECOFLORA database (most representative of UK plant data) – ECOFLORA values were used
- If the species’ trait was in TRY but not in ECOFLORA – LEDA values were used (considered to be the second most representative dataset in TRY for UK plants, as still within Europe)
- If the species’ trait was in TRY but not in ECOFLORA or LEDA – trait values from other datasets within TRY were used
- If the species’ trait was not in TRY at all – the trait value was extracted from the categorical mean of Grime et al, (1988)
- If the trait value was also not in Grime et al, (1988) – the PFAF database was used
- If the trait value was in none of the datasets above – the species was removed from the functional diversity analysis
In practice this resulted in 11 trait values not present in TRY being infilled by categorical mean values from Grime et al, (1988) and 2 trait values infilled by PFAF. Additionally, before trait infilling, we compared TRY species-level trait values to categorical mean traits from Grime et al, (1988). This quality control constitutes a section of the results in our paper (Section 3.1). Although we did not use the Grime et al (1988) data in the functional diversity analysis (as the betapart package in R could not take categorical traits), these data are from the UK, so are more ‘locally representative’ than TRY. Such ‘trait validation’ is rarely done in studies using species-level plant traits and clearly demonstrates that SLA values from TRY were less ‘locally representative’ than those for plant height or seed mass (Figure 4). This could be an important source of uncertainty in results, both for this study and other studies using trait databases.
We hope that this is now more clearly expressed in our paper, in which we have changed the wording to:
“Trait values for 130 species in this study were extracted from the TRY database (Kattge et al, 2020). Where possible, trait values extracted from TRY were drawn from the Ecological Flora of the British Isles (ECOFLORA; Fitter and Peat, 1994) and LEDA datasets (Kleyer et al, 2008). However, if no trait values were available from ECOFLORA and LEDA, other TRY datasets were utilised. Functional-beta calculations are sensitive to missing values, so the Plants for a Future (PFAF) and Grime et al (1988) datasets were used to infill data missing from all TRY databases (Fern, 1997; Májeková et al, 2016). To account for intraspecific variability (e.g. collection area and sampling strategy) and estimate local-representativeness of traits from TRY datasets, pre-infilled TRY traits were compared with ordinal UK trait data extracted from Grime et al, (1988) using Spearman’s rank correlation.” (Lines 179-188)
>Comments on the Quality of English Language:
>The English quality is fine but several phrases need minor improvement since several long sentences are difficult to understand.
Response: We have edited the text to address this issue – please see our response to this reviewer’s first point, above.
Round 2
Reviewer 1 Report
The authors had put sufficient efforts in the revision. I suggest the manuscript accepted for publication.
Author Response
>The authors had put sufficient efforts in the revision. I suggest the manuscript accepted for publication.
Response: Many thanks for your positive assessment!
