Genetic Diversity and Structure of a Diverse Population of Picea sitchensis Using Genotyping-by-Sequencing

Round 1

Reviewer 1 Report

The manuscript “Genetic diversity and structure of a diverse population of Picea sitchensis using genotyping-by-sequencing” from Byrne et al. provides insights into the genetic structure and diversity of Sitka spruce in its native range using GBS-derived genetic data. The results provide significant information on the biogeographical history of the species and will serve as a basis for breeding.

 The manuscript is very well written, methods and results are clearly presented. I have only a few questions and suggestions.

-          Table 1: I guess the column “Notes” is a remain of the review version.

-          Figure 1 has a poor resolution

-          Figure 2: the readers are not all familiar with the Pacific Coast geography. It would be easier if regions would be sorted per latitude and/or if the colors represent the latitude gradient (that should be easy to do in R), and would better highlight the spatial structure.

-          Figure 2B: I guess this is the result from a supervised DAPC (Regions as prior). This should be stated, because a supervised DAPC tends to show a higher genetic structure than an unsupervised DAPC associated with an optimization of K values. In other words, it might show a structure which is indeed very weak.

-           Figure 3A: that would be interesting to see the same graph without the two outlier regions, and better underline the isolation by distance between the mainland populations.

-          L328-331 Did you sample white spruce populations? Including those in an analysis (DAPC, STRUCTURE or alternatives) focusing in this region would certainly provide some insights on the hybrid status of some individuals. Such analysis work better when carried within each mean genetic cluster. It is worth a try.

Author Response

Please find the revised manuscript “Genetic diversity and structure of a diverse population of Picea sitchensis using genotyping-by-sequencing” for consideration as part of the special issue “Molecular genetics of forest trees and applications in breeding, conservation and management of genetic resources”.

We thank the reviewers and editor for their time spent with the manuscript. Here we have detailed our changes. Firstly we will provide high resolution versions of all figures included in the manuscript which should be most useful for Figures 1 and 6. With Figure 6, it is difficult to make it clearer without losing important detail so we have provided panels of regions of interest and have labelled these panels. High resolution versions of these panels will be made available in supplementary figures. We have reviewed our tables and cleaned up columns which were not necessary and fixed spelling and grammar mistakes.  We have altered our PCA to colour points by latitude rather than geographic region, making it clearer for readers. We have clarified the DAPC as supervised clustering in the figure legend and in the methods section. Upon the request of reviewer 1 we removed the outliers of Kodiak and Montague Islands from Figure 3a. This interestingly resulted in a weaker correlation coefficient (R=0.41) as compared to with the outlier islands (R=0.46) we have stated this in the manuscript but kept the original figure. To clarify, the IUFRO collection in this study is marked as spruce with one provenance being suspected as possible white spruce hybrid. We are working on an assay that would identify hybrids which would open up new possibilities for comparisons between the two species.

We hope you will find that our responses address the reviewer’s questions and concerns. Thank you for your consideration and we look forward to hearing your opinion on its suitability for publication in Forests.

Yours faithfully,

Dr. Susanne Barth

Reviewer 2 Report

Byrne et al. have used GBS techniques to further elucidate the population history of Picea sitchensis using an extensive sample from a IUFRO trial. I congratulate them on this excellent effort and have no objections for publishing the paper. In Fig. 6 the coloured circle seem a bit compressed, but otherwise the analysis performed and the presentation of the results is all very clear and well done.

Author Response

Please find the revised manuscript “Genetic diversity and structure of a diverse population of Picea sitchensis using genotyping-by-sequencing” for consideration as part of the special issue “Molecular genetics of forest trees and applications in breeding, conservation and management of genetic resources”.

We thank the reviewers and editor for their time spent with the manuscript. Here we have detailed our changes. Firstly we will provide high resolution versions of all figures included in the manuscript which should be most useful for Figures 1 and 6. With Figure 6, it is difficult to make it clearer without losing important detail so we have provided panels of regions of interest and have labelled these panels. High resolution versions of these panels will be made available in supplementary figures. We have reviewed our tables and cleaned up columns which were not necessary and fixed spelling and grammar mistakes.  We have altered our PCA to colour points by latitude rather than geographic region, making it clearer for readers. We have clarified the DAPC as supervised clustering in the figure legend and in the methods section. Upon the request of reviewer 1 we removed the outliers of Kodiak and Montague Islands from Figure 3a. This interestingly resulted in a weaker correlation coefficient (R=0.41) as compared to with the outlier islands (R=0.46) we have stated this in the manuscript but kept the original figure. To clarify, the IUFRO collection in this study is marked as spruce with one provenance being suspected as possible white spruce hybrid. We are working on an assay that would identify hybrids which would open up new possibilities for comparisons between the two species.

We hope you will find that our responses address the reviewer’s questions and concerns. Thank you for your consideration and we look forward to hearing your opinion on its suitability for publication in Forests.

Yours faithfully,

Dr. Susanne Barth