Genetic Diversity and Profile of Red Algae Pterocladiella capillacea (Gelidiales, Rhodophyta) along the Coast of China
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsSome corrections need to be made to the MS prior to acceptance.
Add a population location map.
Line 32: add authors to the species name.
Tables 1 and 2: There is a discrepancy in the number of samples in the two tables. It's obvious from the Line 193 that some sequences are incorrect. If they were not used in the analysis, why include them in the Table 1?
Figure 1: add bootstrap values
Figure 2: stretch the drawing horizontally, showing the P. caerulescens branch with a dotted line and indicating its length with a number.
Line 101: delete (1994), relocate refs 12,23 to this place
Lines 111-112: delete “optimized 111 by Tamura (2021)”. What alignment method was used?
Line 114: outer group > outgroup
Line 116: delete “created by Saitou & Nei (1987)”; Ref [27] does not describe a method for constructing a MP tree.
Line 117: delete “established by Tamura & Nei (1993)”; Ref [28] is not about ML tree construction.
Was bootstrap analysis used when constructing the trees?
Line 118: Ref [29] is not about PopART
The length of concatenated alignment and rbcL and cpx1 separately are not specified. The new sequences should be deposited to GenBank.
Lines 146-48 are poor and need to be rewritten
Lines 158-59: ”Hasegawa-Kishino-Yano (HKY) model was selected as the optimal model and then constructed the samples’ haplotype phylogenetic tree using MEGA [31]” shoud be placed in Methods.
Lines 177-78: “variation sites and haplotype 177 diversity of the rbcL were much less than those of cox1.” This result should be described in Results
Line 193: It is not correct to compare the diversity of algae and fish.
Lines 204-05: Dxy values Between NZ and other populations are also high.
Line 205: “the Fst values of CD, NA, and NZ were relatively high”. However, Fst values of CD and all other populations are about the same.
Lines 211-214: describe in more detail what could be causing the negative values of Tajima's D, because they are usually associated with population expansion after a recent bottleneck.
Author Response
Comment 1: [Add a population location map.]
Response 1: [The suggestion was taken and Figure 1 has been improved.]
Comment 2: [Line 32: add authors to the species name.]
Response 2: [The authors was add (Line 32, “Pterocladiella capillacea (S.G.Gmelin) Santelices & Hommersand”).
Comment 3: [Tables 1 and 2: There is a discrepancy in the number of samples in the two tables. It's obvious from the Line 193 that some sequences are incorrect. If they were not used in the analysis, why include them in the Table 1?]
Response 3: [SL population was categorized into XM according to reviewer’s suggestion. And Table 1, 2 has been rearranged.]
Comment 4: [Figure 1: add bootstrap values]
Response 4: [The suggestion was taken (Figure 2, 4).]
Comment 5: [Figure 2: stretch the drawing horizontally, showing the P. caerulescens branch with a dotted line and indicating its length with a number.]
Response 5: [The figure was revised (Figure 4).]
Comment 6: [Line 101: delete (1994), relocate refs 12,23 to this place]
Response 6: [The suggestion was taken (Line 105).]
Comment 7: [Lines 111-112: delete “optimized by Tamura (2021)”. What alignment method was used?]
Response 7: [The sentence was changed, and the alignment method was explained (Line 114-115: “were performed using Clastal W algorithm in MEGA 11”).]
Comment 8: [Line 114: outer group > outgroup]
Response 8: [The phrase was revised (Line 118). ]
Comment 9: [Line 116: delete “created by Saitou & Nei (1987)”; Ref [27] does not describe a method for constructing a MP tree.]
Response 9: [The suggestion was taken (Line 118).]
Comment 10: [Line 117: delete “established by Tamura & Nei (1993)”; Ref [28] is not about ML tree construction.]
Response 10: [The sentence was changed (Line 118-120).]
Comment 11: [Was bootstrap analysis used when constructing the trees?]
Response 11: [Sure. And the bootstrap was indicated (Figure 2 and 4).]
Comment 12: [Line 118: Ref [29] is not about PopARTs]
Response 12: [The citation was relocated (Line 123, 334-335).]
Comment 13: [The length of concatenated alignment and rbcL and cox1 separately are not specified. ]
Response 13: [The suggestion was taken (Line 127: “In total, 161 rbcL sequences (838 bp) and 161 cox1 sequences (1395 bp) were generated.”).]
Comment 14: [The new sequences should be deposited to GenBank.]
Response 14: [Sure, we’ve already submitted the sequences.]
Comment 15: [Lines 146-48 are poor and need to be rewritten]
Response 15: [The suggestion was taken (Line 146-152).]
Comment 16: [Lines 158-59: ”Hasegawa-Kishino-Yano (HKY) model was selected as the optimal model and then constructed the samples’ haplotype phylogenetic tree using MEGA [31]” shoud be placed in Methods.]
Response 16: [The suggestion was taken (Line 120-122).]
Comment 17: [Lines 177-78: “variation sites and haplotype diversity of the rbcL were much less than those of cox1.” This result should be described in Results]
Response 17: [The suggestion was taken (Line 133-134).]
Comment 18: [Line 193: It is not correct to compare the diversity of algae and fish.
Response 18: [The wrong part was deleted.]
Comment 19: [Lines 204-05: Dxy values Between NZ and other populations are also high.]
Response 19: [Table 3 is on Dxy. All of the Dxy values are less than 0.01. ]
Comment 20: [Line 205: “the Fst values of CD, NA, and NZ were relatively high”. However, Fst values of CD and all other populations are about the same.]
Response 20: [Table 4 is on Fst. All the Fst values of CD, NA, and NZ are more than 0.5, while the others three are less than 0.1.]
Comment 21: [Lines 211-214: describe in more detail what could be causing the negative values of Tajima's D, because they are usually associated with population expansion after a recent bottleneck.]
Response 21: [More information has been presented (Line 222-225).]
Reviewer 2 Report
Comments and Suggestions for AuthorsI reviewed the manuscript entitled “Genetic diversity and profile of red algae Pterocladiella capillacea (Gelidiales, Rhodophyta) along the coast of China” by Li and collaborators. This manuscript could have potential but lacks a more constructed narrative. The first issue of the manuscript is that Pterocladiella capillacea belongs to the family Pterocladiaceae and not Gelidiaceae. Please check "Perrone et al. 2006. Botanica Marina" and Algaebase.
The introduction and conclusion are weak. In the introduction, there is a very long paragraph about using genetic markers for phylogeny, but this research is about population genetics. Therefore, the background is not there, and I could not find why studying the genetic diversity of P. capillacea is important. I would not agree that P. capillacea contribute to carbon sequestration. Please, check recent literature about seaweed uses for carbon sequestration.
The discussion needs to be clarified and the results are not well linked. A deeper discussion about population genetics and why it is important should be demonstrated.
The methods are good, and the results are well presented. However, these results are meaningless without a history. I also missed a map showing the collection sites. Population genetics relies on geography, and this should be discussed as well.
The manuscript has potential, but the history needs to be much improved.
Author Response
Comment 1: The first issue of the manuscript is that Pterocladiella capillacea belongs to the family Pterocladiaceae and not Gelidiaceae. Please check "Perrone et al. 2006. Botanica Marina" and Algaebase.]
Response 1: [The part was revised (Line 29, 31).]
Comment 2: The introduction and conclusion are weak. In the introduction, there is a very long paragraph about using genetic markers for phylogeny, but this research is about population genetics. Therefore, the background is not there, and I could not find why studying the genetic diversity of P. capillacea is important. ]
Response 2: [The suggestion was taken (Line 35-37; 41-44).]
Comment 3: I would not agree that P. capillacea contribute to carbon sequestration. Please, check recent literature about seaweed uses for carbon sequestration.]
Response 3: [The unsolved argument is no longer presented in this paper.]
Comment 4: The discussion needs to be clarified and the results are not well linked. A deeper discussion about population genetics and why it is important should be demonstrated.]
Response 4: [The suggestion was taken (Line 239-244)]
Comment 5: The methods are good, and the results are well presented. However, these results are meaningless without a history. I also missed a map showing the collection sites. ]
Response 5: [The suggestion was taken (Line 41-44, Figure 1).]
Comment 6: Population genetics relies on geography, and this should be discussed as well. The manuscript has potential, but the history needs to be much improved.]
Response 6: [The suggestion was taken (218-219).]
Reviewer 3 Report
Comments and Suggestions for AuthorsIn this article, the authors investigate the genetic diversity of red algae Pterocladiella capillacea in China. Additionally, they analyse the genetic profile about different populations of P. capillacea and make an analysis. I have a few recommendations before publication:
1) I recommend using maximum likelihood method to construct phylogenetic trees and show bootstrap support.
2) Tell why only 8 samples were collected in SL population, so as DZ.
3) Compare the previous research results on other seaweed, such as Gelidium.
4）Please double-check the whole manuscript to make it more readable.
Author Response
Comment 1: [I recommend using maximum likelihood method to construct phylogenetic trees and show bootstrap support.]
Response 1: [The suggestion was taken (Line 119-120; Fiure 2, 4).]
Comment 2: [Tell why only 8 samples were collected in SL population, so as DZ.
Response 2: [SL population was categorized into XM according to the comments and Table 1 shows it.]
Comment 3: [ Compare the previous research results on other seaweed, such as Gelidium.]
Response 3: [The suggestion was taken (Line 203-206)]
Comment 4: [Please double-check the whole manuscript to make it more readable.]
Response 4: [Sure, efforts have been made to the article for a better version.]
Reviewer 4 Report
Comments and Suggestions for AuthorsThe work is interesting, it demonstrates a problem with Pterocladiella capillacea and I like that it is very concise.
I think it is very worthwhile, I only think that they should improve the writing of some paragraphs, make the summary clearer because it is difficult to read, it is tangled, and the quality of the figures, especially figure 2.
Line 29 – Delete and replace the phrase “The common name red algae are given to members of the phylum Rhodophyta” is extremely general for a manuscript of this style.
Lines 32-33 This phrase that means “stand in the important niche in China is” to improve this phrase and make it more explanatory, it is strange.
Line 37 “the ocean nature” would not be a better expression like in the environments where it develops naturally or something like that, again it is a strange phrase.
Line 83 Avoid starting paragraphs with numbers, rewrite.
Line 129 Indicate the total number of haplotypes, it is a very important value that must be indicated in the text.
Comments on the Quality of English LanguageThe work is easy to understand in terms of the language, there are some phrases that need to be better explained.
Author Response
Comment 1: [I think it is very worthwhile, I only think that they should improve the writing of some paragraphs, make the summary clearer because it is difficult to read, it is tangled, and the quality of the figures, especially figure 2.]
Response 1: [The suggestion was taken, and the figure was changed (Figure 3).]
Comment 2: [Line 29 – Delete and replace the phrase “The common name red algae are given to members of the phylum Rhodophyta” is extremely general for a manuscript of this style.]
Response 2: [Sure, the redundant sentence was deleted.]
Comment 3: [Lines 32-33 This phrase that means “stand in the important niche in China is” to improve this phrase and make it more explanatory, it is strange.( The sentence was changed.)]
Response 3: [The sentence was improved (Line 31-32).]
Comment 4: [Line 37 “the ocean nature” would not be a better expression like in the environments where it develops naturally or something like that, again it is a strange phrase. ]
Response 4: [The phrase was deleted.]
Comment 5: [Line 83 Avoid starting paragraphs with numbers, rewrite.
Response 5: [The sentence was changed (Line 83).]
Comment 6: [Line 129 Indicate the total number of haplotypes, it is a very important value that must be indicated in the text.]
Response 6: [The total number of haplotypes was indicated (Line 138; Table 2).]
Comment 7: [The work is easy to understand in terms of the language, there are some phrases that need to be better explained.]
Response 7: [Sure, your suggestions have been seriously considered and improvements have been made to the manuscript. ]
