Phylogeography and Genetic Structure of Sand Dune Specialist Stilpnolepis centiflora (Asteraceae) in Northwest China Revealed by Molecular Data
Round 1
Reviewer 1 Report
Please see the attached PDF file that consisted of my general comments (2 pages) and detailed edits/comments/questions in tracks directly on the manuscript.Comments for author File: 
Comments.pdf
Author Response
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Author Response File: Author Response.pdf
Reviewer 2 Report
The aim of the manuscript titled “Evolutionary history of the sand dune specialist Stilpnolepis centiflora (Asteraceae) couple the formation of sand deserts in Northwest China in the Pleistocene” is clear and, due to the lack of knowledge in the bibliography for the species, the paper is potentially of interest. However, the authors have to re-write all sections, there are several incongruences, many information are redundant and, in the results section, it is very difficult to highlight the main results and/or follow the single approach used for the characterization. In addition, since the whole chloroplast genome is available for S. centiflora, (Shi and Xie, 2020) it is not clear because the authors used only 2 intergenic spacer and 1 ITS. The lack of discrimination could be related to the low number of sequences used. In my opinion the authors should increase the number of region analyzed
Major comments
The authors have to add different and more specific paragraphs in material and methods section (in the present version there is only - 2.1. Sample Source and DNA Analysis). It is very difficult understand what has been done for the specific section/analysis.
It is not clear why the authors analysed 120 out of 280 samples in the second step (ITS) - line 108…and the other samples? In addition in the results (line 291-292) the authors wrote “Ribotype reconstruction of ITS sequences in PHASE resulted in highly supported ribotype pairs (P > 0.90) for 250 individuals (500 sequences in total)”…please check and explain
I didn’t find the sequences used for analysis. The authors have to provide all information (obviously the sequences obtained) to both verify the results obtained and to share them to the scientific community.
Line 183: the sentence is related to a result (2 clades) but this a mat&met section. Rewrite this sentence
How do the authors explain that the cpDNA data revealed high haplotype and low nucleotide diversity?
Line 249-250: the authors wrote “However, if single-population clusters were left out, as is 249 usual in SAMOVA”, is it a correct procedure? please support this sentence with ref or other information,
Where is the SAMOVA output? Please add the figure (also eventually in supplementary material)
For the Population structure the authors have to test also an approach without a priori information using (e.g.) STRUCTURE or BAPS. The results could support the possible admixture profiles of populations studied (as reported by the authors in the text).
In the phylogenetic analysis there are three outgroup never listed in the previous part of the MS. Check and add them in all sections.
Many information and results were repeated several time…check the text and delete this redundancy.
Minor comments
Reduce the size and reformat Table 1 and table 3;
The first and last affiliation of the authors are the same;
The figure S4 is missed
Did the authors use Paup or mega for the tree development?
Author Response
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Author Response File: Author Response.pdf
Round 2
Reviewer 1 Report
See a few comments and some edits in the attached PDF file
Comments for author File: Comments.pdf
Author Response
Thanks for your comments, we have made some modifications in the revised manuscript. Please see the detailed responses in the attached PDF file.
Reviewer 2 Report
The authors improved the paper following the suggestions but some lacks remain opened.
All sequences produced MUST be available (this is MANDATORY) not only the two sequences loaded on NCBI (MF416962-MF417003). Therefore all 280 chloroplast and ITS sequences, both raw data (electropherograms) and FASTA files must be added to the manuscript to check the polymorphism and results obtained. About the sequences, there is (again) an incongruence between cpDNAs (280 samples) and ITS (250 samples), why?
The authors run STRUCTURE but it is not clear why they chosen also k=4 in the first run...only K=2 can be selected as the best K (figure S3B). The different between the two runs is not explained in material and methods but only in the results. The authors have to change this section modifying results and discussion.
The manuscript must necessarily be corrected by a native English speaker. This aspect is also mandatory for the publication of the paper, as well as making available all the sequences produced.
Author Response
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Author Response File: Author Response.pdf
