Comparing the Effectiveness of Exome Capture Probes, Genotyping by Sequencing and Whole-Genome Re-Sequencing for Assessing Genetic Diversity in Natural and Managed Stands of Picea abies

Round 1

Reviewer 1 Report

This is a very interesting and useful study, although the segment of readership of Forests, for which it is of interest, might be a bit limited. This, however, may the the case of other papers as well.

I would suggest accepting the ms as it stands, but

1. the ms lacks an abstract
2. the 1st paragraph of the Introduction is a bit out of topic. I do not see a link between seed orchard pollen contamination rates and genomics

The material is not representative for Norway spruce as species, as the part of the distribution range south of the Polish disjunction (strongly differentiated from the Nordic populations) is represented by just Blizyn and Toplita, but this does not affect the validity of the results.

Author Response

(our answers are given in red)

Reviewer 1

This is a very interesting and useful study, although the segment of readership of Forests, for which it is of interest, might be a bit limited. This, however, may the the case of other papers as well.

I would suggest accepting the ms as it stands, but

1. the ms lacks an abstract

An abstract has been added.

2.the 1st paragraph of the Introduction is a bit out of topic. I do not see a link between seed orchard pollen contamination rates and genomics

We find it relevant to help explain the ecology behind the existing genetic differences we observe in our samples used later in the manuscript.

The material is not representative for Norway spruce as species, as the part of the distribution range south of the Polish disjunction (strongly differentiated from the Nordic populations) is represented by just Blizyn and Toplita, but this does not affect the validity of the results.

We have added a note that the material used, mainly represents the Nordic domain of Norway spruce (lines 278-279).

Reviewer 2 Report

The manuscript presents results of a high-quality research on an important tree species, with employing advanced methods and markers (Targeted capture probes and GBS). The results obtained could be useful as a guide for genotyping other conifers with complex genomes, as the conifer genomes usually are.

The paper is well written and would be very interesting to the scientific community, and particularly, to forest geneticists, but also, to evolutionary biologists.

The authors are advised to go through the text once again. Some sentences could be rewritten in order to remove tautology and/or to make the sentences and expressions more elegant.

Another minor remark:

Page 1, row 34
Not all conifers have chromosome number 2n=24. This is true for Pinaceae, while, for example, most of Cupressaceae species have 2n=22.
Here it could be worthy also to cite a very recent book: Neale D.B., Wheeler N., 2019. The Conifers. Genomes, Variation and Evolution. Springer, xviii+590 pp.

Although the paper could be published as it is, it could benefit of one more critical reading.

Author Response

(our answers are given in red)

Reviewer 2

 

The manuscript presents results of a high-quality research on an important tree species, with employing advanced methods and markers (Targeted capture probes and GBS). The results obtained could be useful as a guide for genotyping other conifers with complex genomes, as the conifer genomes usually are.

The paper is well written and would be very interesting to the scientific community, and particularly, to forest geneticists, but also, to evolutionary biologists.

The authors are advised to go through the text once again. Some sentences could be rewritten in order to remove tautology and/or to make the sentences and expressions more elegant.

We have gone through the text and addressed any awkward sentences we could find. 

Another minor remark:

Page 1, row 34
Not all conifers have chromosome number 2n=24. This is true for Pinaceae, while, for example, most of Cupressaceae species have 2n=22.
Here it could be worthy also to cite a very recent book: Neale D.B., Wheeler N., 2019. The Conifers. Genomes, Variation and Evolution. Springer, xviii+590 pp.

Conifers have been changed to Pinaceae and we have added the citation as suggested.

Although the paper could be published as it is, it could benefit of one more critical reading.

Reviewer 3 Report

Dear authors,

I made some comments directly in the pdf of your submission. You might find them useful.

kind regards

Comments for author File: Comments.pdf

Author Response

Dear authors,

I made some comments directly in the pdf of your submission. You might find them useful.

Line 69: add names of both stands

Names of the 4 populations have been added and unique population numbers have been added to Table 1.

Line 101: please add a comment on if the samples for the two data sets were analysed in the same way. If they weren't, please what you did to make the two data sets comparable.

The two data sets were analysed according to the same general pipeline, This is now stated in the text (lines 141-142).

Line 108: please add the method that you used for measuring the DNA concentrations.

We measured all samples using Qubit and this is now noted in the text (lines 183-184).

Line 181: here you refer to Fig 2A, please add "A" to the Figure and to the Figure caption. Also to all subsequent Figures with A nd B.

We have clarified figure 2 and 3 with an added A and B throughout the text

Line 203: please add a table with all populations and their location/despcription which aou are using within the results section.

We have added names to the populations presented in Table 1 in the Methods section.