Phylogeography of the Endangered Endemic Perkinsiodendron macgregorii Based on Chloroplast Genome Data

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The article uses chloroplast genomes from populations of an endangered species, P. macgregorii, to understand the structure of its populations and propose conservation strategies.

- The introduction is generally well structured, but needs some adjustments: 1) The text leads the reader to believe that aspects of adaptive evolution will be discussed. Although the markers obtained and analyzed are useful in this type of approach, this approach was not carried out in-depth in this manuscript. I even suggest removing the term “adaptive evolution” from the title, since no concrete results were obtained in this regard. 2) The end of the penultimate paragraph (lines 88-95) seems to me to be a discussion and not an introduction topic. Maybe it could be used in the discussion of the manuscript, which should be improved.

- The objectives of the article (last paragraph of the introduction) should be revised and should coincide exactly with the topics of the discussion. As for the second objective, it does not seem to me that evolutionary relationships were elucidated. The article presents a population and phylogeographic approach, which can be discussed in light of evolution, but this was not done.

 

- Review the titles of tables and figures; they should be complete, including the acronyms cited in them.

- I suggest positioning the map in Figure 5 in the country and/or continent.

- The last paragraph of the “results” item mixes the presentation of results with discussion. For example: Arguing that adaptive pressures may have shaped the pattern is already a speculation that could have been better developed in the discussion. The proposal that Clade A is a refuge deserves discussion and cannot be confirmed with these results.

- The first subitem of the discussion, entitled “Population Genomic Variation and Adaptive Marker Development”, in my view is not in line with the first proposed objective, which is to elucidate the structural variation and genetic diversity of chloroplast genomes across populations. Instead, I would discuss how hypervariable regions are distributed across populations. The first objective is not associated with the adaptive issue. This first subitem is also repetitive with the results, it should be reviewed and improved.

- In my opinion, the second objective of the article should be discussed in the second subitem of the discussion. I repeat that this objective addresses evolutionary relationships, which were not effectively tested, there are no concrete hypotheses. An example of issues that should be improved: How can we affirm that you are in the face of microrefugia? Based on what? Are there other examples to compare? The entire discussion lacks comparisons with the literature in a more effective way.

- The conclusions report habitat fragmentation. This was never mentioned or tested in your results. Furthermore, there are no concrete hypotheses of isolation. Distance? Type of environment? This should be clearer when discussing the results found in the formation of the clades.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

The authors have completed the work at the modern molecular genetic level. The chloroplast genome of Perkinsiodendron macgregorii was studied, its phylogeny and trends of adaptive evolution were revealed. Not all conclusions can be made based on the chloroplast genome alone, which the authors rightly wrote about in the Conclusions. The conservation of the object is not sufficiently described, although this is stated in the title.

There are several comments:

15 Despite its conservation urgency

• Add information on the need to conserve Perkinsiodendron macgregorii

27 AMOVA attributed 51.19% of genetic..

• ANOVA?

33 Keywords: Conservation genetics

 –          the text does not provide sufficient information specifically on conservation genetics

100 3) propose priority conservation areas and management strategies based on genetic diversity patterns and population differentiation mechanisms.

-           management strategies should be described below

Materials and Methods

-           Were leaves from one plant collected to extract DNA? Each sample is represented by one plant?

Results

Table 1. Nucleotide diversity and variables of 134 chloroplast genome accessions

-           what formula was used to calculate Nucleotide diversity?

269 - Clade B includes four populations (TS, LS, XN, SL) from southern Hunan/eastern Zhejiang and Fujian…

-           What is the reason that the XN population from clade B differs in geographic location from the TS, LS and SL populations of the same clade?

306 Abbreviations: H, number of haplotypes; Hd, haplotype diversity; N, sample size; S, number of polymorphic sites; Pi, nucleotide diversity. * p < 0.05.

-           probably mixed up: N - number of polymorphic sites, S - sample size

318 This paradox - low sequence divergence coupled with high population differentiation - was corroborated by AMOVA…

-           ANOVA?

Discussion

375 To address the geographic genetic structure and diversity patterns of P. macgregorii, an integrated conservation framework combining in situ protection, ex situ conservation, and sustainable utilization is urgently needed

-           Please provide information on why there is an urgent need to conserve this species?

-           ex situ conservation: what methods of ex situ conservation do you propose?

-           Which methods will be most effective?

 

 

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

After the second review, I noticed that the authors accepted all the suggestions, incorporating them throughout the text. I consider that the manuscript is much more balanced and robust in its current format. In my opinion, I think that small adjustments are necessary, as described below. If these changes are made, I consider that the article can be published, and no need to return to the reviewer.

- In item 4.2 of the discussion, some terms should be attenuated so that some statements are more consistent with reality:

1) Line 388. Instead of “we infer that” I propose “we proposed that”.

2) Line 389. Instead of “served as” I suggest “may have served as”.

3) Line 391. Instead of “constituted a secondary” it would be better to write “might be a secondary”.

4) Line 420. Instead of “is associated” I propose “might be associated”.

- For me, the conclusions, as they are written, are not really conclusions. If there is no journal’s rule that requires this subitem to be included, I suggest removing it or change it to “final considerations”.

Author Response

Please see the attachment.

Author Response File: Author Response.docx