Developing a Model to Select Indicator Species Based on Individual Species’ Contributions to Biodiversity

Round 1

Reviewer 1 Report

Letter to Authors
applsci-1767233-v1
Developing a model to select indicator species based on individual species' contributions to biodiversity
Ta-Jen Chu, Yi-Jia Shih, Chun-Han Shih, Jia-Qiao Wang, Liang-Min Huang, Shu-Chen Tsai


220607


Dear authors,
I am pleased to read your very interesting and important MS challenging the past common sense on mangrove forest. You are making a survey on ecological succession and pulsing to role it back artificially. Planting mangroves promote succession to reach a plateau in which organisms live in a state of withering coexistence in a very competitive environment. Removing mangroves makes an ecological pulse, rolling the state back to a phase in which many organisms live temporarily in a state of prosperous coexistence. Breakdown of mangrove forests has been made historically or geologically by big typhoons, tsunamis, or volcanic ash fall-outs. Artificial pulsing emulates those events. You are examining how it was depicting ISs. It is thus very good publishing your MS in an international journal, if adequately written. I think, however, the current delivery is not very well prepared. Method description is incomplete, especially regarding temporal aspect of the locality. This is equivalent to "control missing" that is a criterion of major revision required. Several other miscellaneous issues also present. See below for detail.
Braced words indicate options, and those in brackets can be omitted.


L26
Spell out genus names at the first appearance.

L29
in-creased -> increased

L36 keywords
indicator species; biodiversity contribution -> replace
Avoid listing words which appear also in the title. Duplicate hits upon computer search do not make sense. Give words that do not appear in the title to draw attention from wider readership. Posting words that neither appear in the abstract is better, because even in full-text search/indexing robots may not weigh much on words deeper (posterior) in the text. Hint: pulsed ecosystem, habitat restoration, species richness, wetland, estuary, ecosystem service, etc.

L79
Siddig et al. [15] pointed out that -> delete
A merit of numbered citation is to save readers' short-term working memory spaces when reading without bothered by outflow of author names. What/how is it is more important than who did it. Reference #15 may be cited at the end of this sentence.

L84
between indicator species -> between IS[s]
Use abbreviation consistently.

L87-99
Using a matrix of 221 species .. directionality of taxa responses. -> delete
Do not make a simple reference list (A stated this, B analyzed that, C argued it, or alike). Simple reference lists bloat your MS, dilute your originality, and undersell your own research. Use noun phrases to make abstract contents of those references.

L105
(Ramsar Convention Bureau, 2005) -> cite the document and assign a number on it

L110-112
Buckland et 110 al. (2005) .. over time. They revealed that -> delete
If "they" are Buckland et al, you may cite it at the end of the following sentence.

L119
are available; therefore, -> are available. Therefore, (break sentence here)

L127-143
Biodiversity refers to .. determining ISs. (redundant) -> delete

L149
one particular -> number of individuals of {<i>i</i>th, one particular (<i>i</i>th)}

L150
total number of species -> total individuals [of all species]
ln is the natural log, Σ is the sum of the calculations -> delete

equation (3)
log -> ln ? or what is the bottom?

L181
Mangroves have been considered a good ecosystem
Reference(s) needed.

L182
Since 1992, a survey has been conducted
Reference(s) needed. It could be at L188.

L190
this initiated a debate
References needed.

L194
Habitat Rehabilitation Program
Reference(s) needed.

L201
the area before and after mangrove removal (does not make sense) -> areas with and without mangrove forest ?
See next.

L201-206
Time line information of the mangrove removal is absent. This paragraph describes spacial matters only. Is it OK?

L214-232
Move to result section.

L235
Equations -> in lower case

L236
are shown in Table A1 and Table A4, respectively. Table A1 and Table A4 show significant monthly changes.  -> showed significant monthly changes (Tables A1, A4).

L255
The spatial variations .. shown in Figure 2. -> delete
You may cite Fig. 2 at the end of next sentence in parentheses.

L263
Spatial -> Spatiotemporal ?

L264-273
Move to discussion.

L264
such as .. brine shrimp -> such as .. brine shrimp in captivity ?

L267
maintain -> control ?

L274
Furthermore, -> delete

L289
Add one sentence describing and outlining your present model to emphasize your originality.
Chu et al. [36] -> On the other hand, a previous study [36]

L292-294
The umbrella species concept .. for conservation planning [50]. -> delete
This reference may be cited elsewhere.

L294-297
When a species is present .. in the same community [36]. -> make compact
Do not make a simple reference list (A stated this, B analyzed that, C argued it, or alike). Simple reference lists bloat your MS, dilute your originality, and undersell your own research. Use noun phrases to make abstract contents of those references. This is also applicable to the previous lines.

L325
In the study of Kuo et al. [35], -> delete
This reference may be cited at the end of this sentence.

L329
Cite reference #51 also here (or other relevant literature).

L358
In the study of Chu et al. [36], they mentioned that -> delete
This reference may be cited at the end of this sentence.

L371
Kuo et al. (2010) [35] and Chu et al. (2021) [36] -> previous studies [35,36]

L409
Pander and Geist (2013) [60] proposed that -> delete
This reference may be cited at the end of this sentence.

L428-441
Delete (redundant).

L466 references
Check the reference list carefully again from the beginning. Reference lists are frequently hotbeds of errors. You might add, omit or swap citation in the main text on the way internal revision. Numbering of the references might then shift. If so, readers think you are making irrelevant citation. It is the authors' responsibility that all references are properly cited.

L483,538,546,etc
Make sure if book titles are in title case.

L519
Int. res. j. environ. -> Int. Res. J. Environ.

L524,556,etc
Make sure if paper titles are in lower case.

L553
Ocypodidae -> in Roman

Author Response

We are much grateful for your careful reading of our manuscript and your valuable comments and suggestions to help improve the paper. We have now carefully revised the paper in light of all the comments and suggestions. The following is a point-by-point response.

1. I am pleased to read your very interesting and important MS challenging the past common sense on mangrove forest. You are making a survey on ecological succession and pulsing to role it back artificially. Planting mangroves promote succession to reach a plateau in which organisms live in a state of withering coexistence in a very competitive environment. Removing mangroves makes an ecological pulse, rolling the state back to a phase in which many organisms live temporarily in a state of prosperous coexistence. Breakdown of mangrove forests has been made historically or geologically by big typhoons, tsunamis, or volcanic ash fall-outs. Artificial pulsing emulates those events. You are examining how it was depicting ISs. It is thus very good publishing your MS in an international journal, if adequately written. I think, however, the current delivery is not very well prepared. Method description is incomplete, especially regarding temporal aspect of the locality. This is equivalent to "control missing" that is a criterion of major revision required.

Answer: We are much grateful for your careful reading of our manuscript and your valuable comments and suggestions to help improve the paper. 

2. L26, Spell out genus names at the first appearance.

Answer: We have followed your comments, and have corrected these errors.

We fixed the “Mictyris brevidactylus, Macrophthalmus banzai, Uca arcuata, U. lacteal, and U. borealis.” Line 26-27.

3. L29, in-creased -> increased

Answer: We have followed your comments, and have corrected this error.

4. L36 keywords

indicator species; biodiversity contribution -> replace

Avoid listing words which appear also in the title. Duplicate hits upon computer search do not make sense. Give words that do not appear in the title to draw attention from wider readership. Posting words that neither appear in the abstract is better, because even in full-text search/indexing robots may not weigh much on words deeper (posterior) in the text. Hint: pulsed ecosystem, habitat restoration, species richness, wetland, estuary, ecosystem service, etc.

Answer: We have followed your comments, and have corrected and replaced the keywords. We fixed the “environmental monitoring; restoration; ” Line 36.

5. L79, Siddig et al. [15] pointed out that -> delete

A merit of numbered citation is to save readers' short-term working memory spaces when reading without bothered by outflow of author names. What/how is it is more important than who did it. Reference #15 may be cited at the end of this sentence.

Answer: We have followed your comments, and have corrected this sentence. We fixed the “Also, ISs can be selected based on some characteristics including abundance, sensitive, attractive, endangered, invasive species, or any combination of these [15].” Line 79-81.

6. L84, between indicator species -> between IS[s]

Use abbreviation consistently.

Answer: We have followed your comments, and have corrected this sentence. We fixed it in Line 84.

7. L87-99, Using a matrix of 221 species .. directionality of taxa responses. -> delete

Do not make a simple reference list (A stated this, B analyzed that, C argued it, or alike). Simple reference lists bloat your MS, dilute your originality, and undersell your own research. Use noun phrases to make abstract contents of those references.

Answer: We have followed your comments, and have corrected this paragraph. We fixed the “Several quantitative models have been developed to select IS, including principal component analysis [33], context-sensitive joint species distribution model (JSDM) [34], probability of species occurrence combined with environmental factors [35], maximum conditional co-occurrence [36], and threshold indicator taxa analysis (TITAN) [37].” Line 86-90.

8. L105, (Ramsar Convention Bureau, 2005) -> cite the document and assign a number on it

Answer: We have followed your comments, and have corrected this paragraph. We fixed the “Biodiversity is one of the primary criteria used in the protection of wetlands [9].” Line 94-95.

9. L110-112, Buckland et 110 al. (2005) .. over time. They revealed that -> delete

If "they" are Buckland et al, you may cite it at the end of the following sentence.

Answer: We have followed your comments, and have corrected this sentence. We fixed the “Species abundance could be measured either in terms of biomass or the number of individual species [40]. B” Line 100-101.

10. L119, are available; therefore, -> are available. Therefore, (break sentence here)

Answer: We have followed your comments, and have corrected this sentence. We fixed it in Line 107.

11. L127-143, Biodiversity refers to .. determining ISs. (redundant) -> delete

Answer: We have followed your comments, and have deleted these paragraphs.

12. L149, one particular -> number of individuals of, one particular

Answer: We have followed your comments, and have corrected this sentence. We fixed the “pi is the proportion (ni/N) of number of individuals of species found (ni) divided by the total individuals found (N),” Line 120-121.

13. L150, total number of species -> total individuals [of all species]

ln is the natural log, Σ is the sum of the calculations -> delete

Answer: We have followed your comments, and have corrected this error. We fixed it in Line 120-121.

14. equation (3), log -> ln ? or what is the bottom?

Answer: We have followed your comments, and have corrected equations (3).

15. L181, Mangroves have been considered a good ecosystem Reference(s) needed.

Answer: We have followed your comments, and have cited the reference [49]. We fixed the “Mangroves have been considered a good ecosystem for the past three decades [49].” Line 150.

16. L182, Since 1992, a survey has been conducted. Reference(s) needed. It could be at L188.

Answer: We have followed your comments, and have added the reference [47,50]. We fixed the “Since 1992, a survey has been conducted, and it was revealed that the area contains ap-proximately 5300 mangrove trees. In 1995, the area occupied by these trees was separately estimated by the Taiwanese Government and Endemic Species Research Institute of Taiwan to be 0.1 ha. Due to the original mudflat geology, hydrology, and estuary effect, the mangrove area expanded rapidly to 107 ha by 2003, as reported by the Hsinchu City Wild Animal Sanctuary Habitat Rehabilitation and Mangrove Research Program [47,50].” Line 151-157.

17. L190, this initiated a debate. References needed.

Answer: We have followed your comments, and no documentation. Only news and media reports here.

18. L194, Habitat Rehabilitation Program. Reference(s) needed.

Answer: We have followed your comments, and have added the reference [51,52]. We fixed the “the 2011 National Important Wetland Ecological Environment Investigation and Rehabilitation Project [51] and Assessment of Wetland Habitat Restoration in Siangshan Wetland Program [52].” Line 162-164.

19. L201, the area before and after mangrove removal (does not make sense) -> areas with and without mangrove forest ? See next.

Answer: We have followed your comments. Sorry. We hope to keep this sentence.

20. L201-206, Time line information of the mangrove removal is absent. This paragraph describes spacial matters only. Is it OK?

Answer: We have followed your comments. We have added new paragraphs. We fixed the “The Hsinchu City Government ran a large-scale mangrove removal project from October 2015 to March 2016 to restore the wetland. From October 2015 to September 2016, the biological effects of mangrove removal on benthic crabs and their adjacent habitat were investigated.” Line 170-173.

21. L214-232, Move to result section.

Answer: We have followed your comments, and have move to result section. We fixed it in Line 188-206.

22. L235, Equations -> in lower case

Answer: We have followed your comments, and have corrected these errors. We fixed it in Line 207.

23. L236, are shown in Table A1 and Table A4, respectively. Table A1 and Table A4 show significant monthly changes. -> showed significant monthly changes (Tables A1, A4).

Answer: We have followed your comments, and have corrected this sentence. We fixed it in Line 208.

24. L255, The spatial variations .. shown in Figure 2. -> delete. You may cite Fig. 2 at the end of next sentence in parentheses.

Answer: We have followed your comments, and have deleted and noted Figure 2. We fixed the “Three crab species, namely, U. arcuata, U. borealis, and M. banzai, were observed at the sampling sites within the mangrove region before mangrove removal (Figure 2).” Line 227-228.

25. L263, Spatial -> Spatiotemporal ?

Answer: We have followed your comments, and have corrected these errors. We fixed it in Line 293.

26. L264-273, Move to discussion.

Answer: We have followed your comments. But we don't have a proper discussion chapter to move this paragraph. Sorry. We hope to keep this paragraph.

27. L264, such as .. brine shrimp -> such as .. brine shrimp in captivity ?

Answer: We have followed your comments, and have corrected this error.

28. L267, maintain -> control ?

Answer: We have followed your comments, and have corrected this error.

29. L274, Furthermore, -> delete

Answer: We have followed your comments, and have corrected this error.

30. Add one sentence describing and outlining your present model to emphasize your originality. Chu et al. [36] -> On the other hand, a previous study [36]

Answer: We have followed your comments, and have corrected this statement.

31. L292-294, The umbrella species concept .. for conservation planning [50]. -> delete. This reference may be cited elsewhere.

Answer: We have followed your comments, and have deleted this paragraph.

32. L294-297, When a species is present .. in the same community [36]. -> make compact. Do not make a simple reference list (A stated this, B analyzed that, C argued it, or alike). Simple reference lists bloat your MS, dilute your originality, and undersell your own research. Use noun phrases to make abstract contents of those references. This is also applicable to the previous lines.

Answer: We have followed your comments, and have corrected this paragraph. We fixed the “When a species exists in a habitat with other species, the status of these species is most likely to represent other species living in the same community [36].” Line 261-263.

33. L325, In the study of Kuo et al. [35], -> delete. This reference may be cited at the end of this sentence.

Answer: We have followed your comments, and have corrected this paragraph. We fixed the “In order to increase the biodiversity of artificial structures, the selection of ISs helps to realize the design of coastal structures based on biological considerations [35].” Line 290-292.

34. L329, Cite reference #51 also here (or other relevant literature).

Answer: We have followed your comments, and have cited this reference [51].

35. L358, In the study of Chu et al. [36], they mentioned that -> delete. This reference may be cited at the end of this sentence.

Answer: We have followed your comments, and have corrected this paragraph. We fixed the “The expansion of mangrove lands changed the state of the habitat substrate, and U. formosensis, for example, was forced to move outwards or even disappeared. When man-groves are removed, the habitat gradually returns to its original state [36]. ” Line 323-325.

36. L371, Kuo et al. (2010) [35] and Chu et al. (2021) [36] -> previous studies [35,36]

Answer: We have followed your comments, and have corrected this paragraph. We fixed the “Integrating the ideas of previous studies [35,36], more complex conditions will be presented to select ISs.” Line 335-336.

37. L409, Pander and Geist (2013) [60] proposed that -> delete. This reference may be cited at the end of this sentence.

Answer: We have followed your comments, and have corrected this paragraph. We fixed the “The evaluation of conservation or restoration requires a holistic approach that integrates the consideration of several endpoints on different scales (target species, indicator groups, and an ecosystem scale) [63].” Line 373-375.

38. L428-441, Delete (redundant).

Answer: We have followed your comments, and have deleted this paragraph.

39. L466 references. Check the reference list carefully again from the beginning. Reference lists are frequently hotbeds of errors. You might add, omit or swap citation in the main text on the way internal revision. Numbering of the references might then shift. If so, readers think you are making irrelevant citation. It is the authors' responsibility that all references are properly cited.

Answer: We have followed your comments and carefully checked.

40. L483,538,546,etc. Make sure if book titles are in title case.

Answer: We have followed your comments, and have corrected these errors.

41. L519, Int. res. j. environ. -> Int. Res. J. Environ.

Answer: We have followed your comments, and have corrected this error.

42. L524,556,etc. Make sure if paper titles are in lower case.

Answer: We have followed your comments, and have corrected these errors.

43. L553, Ocypodidae -> in Roman

Answer: We have followed your comments, and have corrected this error.

Author Response File: Author Response.docx

Reviewer 2 Report

The manuscript of Chu et al. is very well written and structured text, which describes the newly developed model for the selection of the species used as indicator of the ecolological health of an environment. 

However, I have some minor suggestions to improve the clarity of the manuscript:

line 26: When the species Latin names first used in the text it is better to avoid abbreviation in the genus for the first of them (M.brevidactylus, U.arcuata) and use the name fully written. Also it is convenient to mention that these species are crab: "...we identified five indicator crab species..."

In the Material and Methods there are some parts that are better fit to Introduction or Results:

lines 127-143: the definition of biodiversity and ISs are already explained in Introduction. You can enlarge the explanation there adding things from this Method's paragraph and start the Material and methods section straight from "Numerous methods..."

lines 214-232: Here you rather describe the results and it better should be moved to the corresponding part.

 

Author Response

We are much grateful for your careful reading of our manuscript and your valuable comments and suggestions to help improve the paper. We have now carefully revised the paper in light of all the comments and suggestions. The following is a point-by-point response.

1. line 26: When the species Latin names first used in the text it is better to avoid abbreviation in the genus for the first of them (M.brevidactylus, U.arcuata) and use the name fully written. Also it is convenient to mention that these species are crab: "...we identified five indicator crab species..."

Answer: We thank Reviewer #2 for these helpful comments. We corrected these errors.

2. In the Material and Methods there are some parts that are better fit to Introduction or Results:

Answer: We have followed your comments, and some adjustments have been made.

3. lines 127-143: the definition of biodiversity and ISs are already explained in Introduction. You can enlarge the explanation there adding things from this Method's paragraph and start the Material and methods section straight from "Numerous methods..."

Answer: We have followed your comments, and have removed and corrected statements.

4. lines 214-232: Here you rather describe the results and it better should be moved to the corresponding part.

Answer: We have followed your comments, and some adjustments have been made.

Author Response File: Author Response.docx

Round 2

Reviewer 1 Report

Letter to Authors
applsci-1767233-v2
Developing a model to select indicator species based on individual species' contributions to biodiversity
Ta-Jen Chu, Yi-Jia Shih, Chun-Han Shih, Jia-Qiao Wang, Liang-Min Huang, Shu-Chen Tsai


220630


Dear authors,
I am pleased again to read a well-revised MS. Addition of time line description of the study site cleared when and where. Only one point remained.
Citing line numbers are of a pdf file showing track changes.

L197
a debate -> a debate in news/media

I am looking forward to seeing your interesting paper in the journal.

Author Response

We are much grateful for your careful reading of our manuscript and your valuable comments and suggestions to help improve the paper. We have now carefully revised the paper in light of all the comments and suggestions. The following is a point-by-point response.

1. I am pleased again to read a well-revised MS. Addition of time line description of the study site cleared when and where. Only one point remained.

L197, a debate -> a debate in news/media

Answer: We have followed your comments, and have corrected these errors.

We fixed the “Furthermore, this initiated a debate in news/media regarding the positive and negative effects of mangroves, both in civil society and academic institutions.” Line 159-161.

Author Response File: Author Response.docx