Spatial Pattern of Genetic Diversity and Demographic History Revealed by Population Genomic Analysis: Resilience to Climate Fluctuations of Acer truncatum Bunge

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The study titled "Spatial pattern of genetic diversity and demographic history revealed by population genomic analysis: resilience to climate fluctuations of Acer truncatum" impressively elucidates the spatial dynamics of genetic diversity and demographic history, showcasing the resilience of Acer truncatum to climate fluctuations through rigorous population genomic analysis. I have only several comments to improve the manuscript's quality. I suggest not using population abbreviations in the abstract - without explanation, this information is useless. In line 61, the authors state that the species has a broad range, but in lines 94-95, they contradict this statement. I recommend shortening the description of the species and its properties (lines 61-85). The aim of the study is poorly defined - it would be more valuable to formulate research hypotheses. Line 120: why were samples taken from 20 trees for one population? The authors do not explain this, and it complicates result interpretation significantly. Line 148: Mantel test? Lines 161-164 lack a description for all abbreviations used for genetic parameters. Line 192: are Q30 and GC values averages? Lines 210-217 are methodology descriptions, not results. Table 2 - XS04, where did this origin suddenly appear from? Is it mentioned in the materials description? Figure 2: The figure description is inconsistent with the image and contains unexplained abbreviations. Lines 264 - 265 please note that PCA describes a very low cumulative percentage of variability.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

The paper is well writen and have a significall sound. It could be accept in present form.

Author Response

Thanks for your comments.

Reviewer 3 Report

Comments and Suggestions for Authors

The findings presented by Liao et al. are intriguing and merit publication. However, there are some necessary corrections and enhancements required before acceptance, especially for the figures quality. Additionally, improvements to the methodology are essential, as certain sections are somewhat confusing.

 

For the title: I suggest enhance it maybe you can use this “Resilience of Acer truncatum: Insights from population genomic analysis revealing spatial pattern of genetic diversity and demographic history” or any more suggestions

Line 17: oscilliations ?

Line 21: “covering the entire range” it seems not complete this sentence , verify it !!

Line 86: when you talk about A. truncatum you have to add chromosome number and genome size. In the Introduction you have to add information about the draft genome of this specie i.e the first genome assembly when was done etc..

Line 102: oscilliations ?

Line 115 : subtitle 2.1 Sampling collection and whole genome sequencing

I suggest to split it in 2 different subsections giving more details for each sub section

2.1 Sampling collection

2.2 Whole genome sequencing

 

Lines 117 and 118: add the GPS data of the collected sites

Add picture showing an overview of the collected A. truncatum individuals

Line 134: add more details how you did the whole genome sequencing. You just mentioned very briefly what was done whithout giving details !!

Table 1: Add a column to show the provinces to be clear for readers to which province these populations belong to. If it is Liaoning, Hebei, Henan, Shanxi, Shaanxi or Gansu or a municipality (Beijing) or Inner Mongolia.

Line 151. Subtitle 2.3 Sampling strategy : this subtitle is not really showing the content it is better to modify it maybe as “Genetic diversity analysis or any other subtitle !!!

Besides in paragraph 2.4 there is redundancy you are talking of genetic , which should be in the same paragraph. So you have to re-organize these sections from lines 152 to 182.

I suggest to organize it in the 2 following subtitles:

-           Genetic diversity analysis

-           Population structure analysis.

Line 153. “WDT” why you selected only from WDT, you did not use the other locations ?? It is not clear what you did and why only WDT !!

 Line 166: “The LD decay” add the hole word if it is Linkage Disequilibrium and add what it determines!!!

Line 184: add one sentence to show why you did the demographic history.

Lines 187-188: is not clear !!

In table 2 you presented the sequencing information (Total reads, SNP num Q30, CG ..etc) but you did not mention that these parameters in material and methods section. So you have to add them and explain each parameter.

Change The title of the 1^st column as “Location Code” instead of “Code”; same for Table 3.

Enhance the quality of Figure 2 it is not clear, and explain a bit the results of this Figure.

Table 5: I suggest you to put the Fst an Nm values in different color background, if possible.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf