Species Differentiation of Two Endemic Montane Oaks in China: Population Genetics, Ecological Niche and Leaf Morphology Analyses
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsDear editor,
Thank you so much for sending this paper for me to review. I read this paper and I think it need corrections before the final acceptance. Here are my comments
- all the species name must be followed by their author name at the first mention.
- which markers have been used to detect genetic diversity? Authors must explain the used markers and their benefits in introduction section in more detail.
- in fig 1. author must delete results of structure analysis and also trees
- author must calculate the gene flow rate among each species and possible gene flow between these species.
- authors must explain the reproductive system of these species and explain how reproductive system can affect the genetic structure of these species.
- Authors must present gene flow diagram and explain how population similarities relate to gene flow rate.
- Authors must rewrite the abstract.
- all the best
Author Response
Comments 1: all the species name must be followed by their author name at the first mention.
Response 1: Thanks for the suggestion. We have carefully checked the species names mentioned in the submission and added the author name for species at the first mention.
Comments 2: which markers have been used to detect genetic diversity? Authors must explain the used markers and their benefits in introduction section in more detail.
Response 2: Thank you for pointing this out. In the study, nuclear microsatellite markers were used for population genetics due the high versatility and polymorphism features with low expense for microsatellite loci. We have explained this aspect in the INTRODUCTION part of the revised manuscript in lines 90-95.
Comments 3: in fig 1. author must delete results of structure analysis and also trees.
Response 3: Thanks for your valuable suggestion. We have modified figure one in relation to the information of sample collections for Q. baronii and Q. dolicholepis and rearranged the figures in the revision.
Comments 4: author must calculate the gene flow rate among each species and possible gene flow between these species.
Response 4: Thanks for the suggestion. We agree with this valuable comment and have added an estimation analysis on pairwise gene flow rates among populations within and between studied species in the revision, lines 128-129.
Comments 5: authors must explain the reproductive system of these species and explain how reproductive system can affect the genetic structure of these species.
Response 5: Thank you for pointing this out. We agree with the comment that the frequent and long distance dispersal of wind pollinated pollen gene flows among populations may influence the genetic structure of oak species. Discussion on this view was supplemented in the revision in lines 481-483.
Comments 6: Authors must present gene flow diagram and explain how population similarities relate to gene flow rate.
Response 6：Thanks for your valuable suggestion. As responded in Comments 4, we have performed an estimation on gene flow rates and presented the results in lines 333-341 and in figure 4 of our revision.
Comments 7：Authors must rewrite the abstract.
Response 7：Thanks for the suggestion. The abstract of this study was modified according to reviewers’ suggestions in the revised version.
Reviewer 2 Report
Comments and Suggestions for AuthorsPlease check the comments attached
Comments for author File: 
Comments.pdf
Author Response
Thanks for the revisions and suggestions on our submission. All revisions made for the submitted manuscript were accepted, and the unclear statements highlighted by the reviewer were rephrased and modified in the revision.
Additionally, we provided our point-by-point responses on some detailed comments below:
Comments 1: In total, 362 individuals of Q. baronii and 203 individuals of Q. dolicholepis have been analyzed. Why have you analyzed such small number of leaves?
Response 1: Thank you for pointing this out. We highly agree with the concern that small number of leaf samples might lead to uncertain results for the morphological analysis. Actually, the unbroken and adult leaves were adopted from herbariums of the two studied oaks, while not all of the sampled populations were represented by herbarium specimens deposited in our lab.
Comments 2: What about leaf dry mass?
Response 2: In the morphological analysis leaf dry mass (LM) were used to calculate specific leaf area (SLA) with LA/LM. Before morphological analysis we performed a Pearson correlation on the six leaf traits (LV, LWR, ANG, LA, LM and SLA), while the results showed significant and strong correlations of LM with LWR, ANG and LA. As a consequence, LM was removed from our morphological analysis. We have provided this statement in the revision in lines 238-240.
Comments 3: Could you compare these results with results obtained in some other studies?
Response 3: Thanks for the suggestion. We have made comparisons on genetic diversity of the two studied oaks with that obtained in previous researches in the revised version in lines 489-495.
Reviewer 3 Report
Comments and Suggestions for AuthorsSome comments and suggestions needs to be taken into consideration before acceptance, as reported in the attached file.
Comments for author File: Comments.pdf
Author Response
Comments 1: Abstract section: Line 32: Please add perspectives for future research to consolidate your findings. Based on the results obtained, could you clarify what yours envision as the next steps or implications of your findings?
Response 1: Thanks for the suggestions. The abstract section of this study was modified in the revised version based on reviewers’ suggestions.
Comments 2: “Quercus robur” YOU SHOULD ADD GENOME SIZE AND PLOIDY LEVEL AND CHROMOSOME NUMBER. IN THE INTRODUCTION SECTION (Information of this specie is missing I mean their use and why it is important to make this study on this Quercus specis) Quercus robur is not only valued for its practical uses but also plays a significant role in supporting biodiversity and cultural traditions.
Response 2: Thank you for pointing this out. We have added information in relation to Quercus robur in the revision in lines 51-61.
Comments 3: you described what you did in your study but I don’t see a clear objective of this. You should add your main objectives from this study to be clear for readers.
Response 3: Thank you for pointing this out. We have made some modifications on the purposes of this study in lines 90-100 based on the reviewers’ suggestions.
Comments 4: Laboratory storage” at which T° ?? ; “DNA isolation” ?? you mean DNA extraction ?? you should rectify.
Response 4: Thank you for pointing this out. We have modified the statement of this sentence in the revised manuscript in line 106.
Comments 5: Ten polymorphic markers were selected " which are the criteria for selecting these SSR.
Response 5: Thank you for pointing this out. The ten microsatellite markers were selected and used in this study because they showed 100% amplification rates in a subset of samples from the two studied oaks. We have rewritten the description in the revised version in lines 108-111.
Comments 6: You should let in this figure only a and b related to data of your sampling site and distribution map. The “c, d ..to h” of this Figure 1 is results and should appear where the results of these analysis were reported in the manuscript and not in this Figure 1.
Response 6: Thanks for pointing this out. We have made some changes to figures included in the revision according to the reviewers’ suggestions.
Comments 7: "for each population and species" but in the results section you reported the results for only 2 species wheareas it should be for the 3 species.
Response 7: Thanks for pointing this out. The objectives of this study were to investigate species differentiation and evolution of two Chinese montane oaks Quercus baronii and Quercus dolicholepis. The Quercus oxyphylla was adopt as an outgroup for the analyses of genetic relationships including NJ tree, PCoA and species level population structures, and for ABC simulation.
Genetic information was not estimated for Q. oxyphylla due to limited sample collections for this species, which could cause bias inference when compared with Q. baronii and Q. dolicholepis. In the revision we have provided a label “outgroup” for Q. oxyphylla to make it clear.
Comments 8: and what about Q. oxyphylla why not used in this analysis.
Response 8: Thanks for pointing this out. As responded in Comment 7, we only performed species divergence models on Q. baronii and Q. dolicholepis to estimate potential species divergence pattern between them. For Q. oxyphylla the limited samples sizes largely influenced the likelihood estimation and led to non-convergence results in simulations of species divergence models in Migraine v 0.5.
Comments 9: "Eight bioclimatic 206 factors showing low correlations (r < 0.8) were retained" : WY THOSE SHOWING LOW CORRELATION WERE RETAINED.... IT IS NOT CLEAR.
Response 9: Thanks for pointing this out. The unclear statements were modified in the revised manuscript in lines 210-212.
Comments 10: why the Q. oxyphylla was not included in this leaf traits analysis
Response 10: Thanks for pointing this out. In our study, only 47 individuals from Q. oxyphylla were collected and used as outgroup for analyses of phylogenetic relationships and species demographic simulations. Six herbarium specimens were retained for species identification of Q. oxyphylla, which might show insufficient statistical significance if these samples were used for leaf traits analysis.
Comments 11: where is the Q. oxyphylla In Results section, sometimes you report data analysis of 3 scpecies and sometime of only 2 which is confusing
Response 11: Thanks for pointing this out. We realize that some descriptions in the results were unclear. According to the reviewers’ suggestions, we have made changes in relation to the aims of our study and marked Q. oxyphylla an outgroup species for genetic data analysis with the two studied Ilex oak species.
Comments 12: in conclusion section add few sentences regarding the perspectives and how to valorize the data you found and the actions to be taken.
Response 12: Thanks for the suggestions. We have accordingly made some changes to the conclusion part to emphasize the perspectives of our study in the revised submission.
Round 2
Reviewer 1 Report
Comments and Suggestions for AuthorsDear editor,
This paper can be published in the current form.
All the best
Author Response
Thanks for the comments.
We highly appreciate your valuable suggestions on the research.
