Incipient sympatric speciation in wild barley caused by geological-edaphic divergence

Sympatric speciation is still contentious but here based on genome-wide analysis; we show incipient sympatric speciation of an emerging new wild barley species from Hordeum spontaneum, the progenitor of all cultivated barleys at “Evolution Plateau” (EP), Upper Galilee, Israel.

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Thank you for this interesting contribution to Life Science Alliance. We are looking forward to receiving your revised manuscript. --An editable version of the final text (.DOC or .DOCX) is needed for copyediting (no PDFs).
--High-resolution figure, supplementary figure and video files uploaded as individual files: See our detailed guidelines for preparing your production-ready images, http://www.life-sciencealliance.org/authors --Summary blurb (enter in submission system): A short text summarizing in a single sentence the study (max. 200 characters including spaces). This text is used in conjunction with the titles of papers, hence should be informative and complementary to the title and running title. It should describe the context and significance of the findings for a general readership; it should be written in the present tense and refer to the work in the third person. Author names should not be mentioned.

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Full guidelines are available on our Instructions for Authors page, http://www.life-sciencealliance.org/authors We encourage our authors to provide original source data, particularly uncropped/-processed electrophoretic blots and spreadsheets for the main figures of the manuscript. If you would like to add source data, we would welcome one PDF/Excel-file per figure for this information. These files will be linked online as supplementary "Source Data" files. ***IMPORTANT: It is Life Science Alliance policy that if requested, original data images must be made available. Failure to provide original images upon request will result in unavoidable delays in publication. Please ensure that you have access to all original microscopy and blot data images before submitting your revision.*** ---------------------------------------------------------------------------Reviewer #1 (Comments to the Authors (Required)): I think the paper should be published, perhaps using a different title. I see no evidence of speciation, but population isolation and differential selection due to environmental differentiation is indeed obvious. Unfortunately for one of the primary tenets of this paper, it's also quite common.
Reviewer #2 (Comments to the Authors (Required)): This is an important contribution based upon a very useful environment for study of evolution in wild plant populations. The manuscript lacks a methods section. More details of the experimental materials and methods would aid in understanding the work. Other aspects of the manuscript are all satisfactory.
Reviewer #3 (Comments to the Authors (Required)): This MS presents significant genomic evidence for the incipient microevolution of a new lineage of Wild Barley (WB) at "Evolution Plateau" (EP). The phylogenetic and statistical analysis clearly shows the separation of WB into two differentially selected populations on the chalk and basalt regions of the EP site. However, the data are not yet sufficient to conclude that a truly novel species has formed. As their own analysis in Table 1 and Figure 4 indicates, there is evidence for continuing but reduced genetic exchange between the two populations. No attempts at hybridizing the two populations are reported. In my opinion, the incomplete nature of the genetic separation process should be incorporated into the title, abstract and text. For example, adding the phrase "Early stages of" at the start of the tile would produce a more accurate statement of the conclusions that can legitimately be drawn from the sequence data analysis presented in the MS.
The research presented here depends on a number of generic sequence data analysis tools. It would make the paper clearer for the reader to explain the logic and significance of each analytical procedure when it first appears in the text. Naming the tool and providing a reference are not adequate.
Line 18: add (SS) after "sympatric speciation" Line 22: "separation" should read "SS separating" Line 30: "were" for "was" Line 44: "illuminate" for "highlight" Line 48: "might it" for "it might" Line 98: "shared" in what way(s)? Table S3: define "lv" and "ls" The chromosome comparisons seem to show more similarity than difference between the two populations. These data require a more detailed discussion and presentation. It would be appropriate to have quantitative figures on the indels similar to those for SNPs. Since these will come later, mention that fact here.
Line 184: The computation of effective population size based on SNP data needs more explanation.
Line 220: The computation and meaning of the fastsimcoal2 numbers in Table 1 requires explanation.
Lines 221-233: The logic of this argument needs to be articulated more full, both for determining "best fit" and for the exclusion of allopatry. Line 428: "controversy" reads better as "debate" Line 443: "Originated" a new species of WB may be an overinterpretation of the evidence presented here. "Initiated formation" of a new species would be better.
Line 459: It's questionable that "free breeding" is the right description for self-fertilizing plants such as WB. Reviewer #1 (Comments to the Authors (Required)): I think the paper should be published, perhaps using a different title. I see no evidence of speciation, but population isolation and differential selection due to environmental differentiation is indeed obvious. Unfortunately for one of the primary tenets of this paper, it's also quite common.
My colleague, Dr Kexin Li, will resubmit the MS LSA-2020-00827-T with all needed revision. I wish to briefly explain, as also shortly explained in the summary blurb below, why we retain in the title, abstract, and main text, the concept of "sympatric speciation" although we added for clarification incipient sympatric speciation, across the MS, and fully explained the issue in our discussion.
The concepts of biological species and speciation are still contentious despite the long span since the origin of species have been deeply theorized by Darwin, and since he suggested, in principle, that new species can originate in an interbreeding metapopulation with gene flow (although his phrasing was different and did not use the term sympatric speciation (SS).

Reviewer #2 (Comments to the Authors (Required)):
This is an important contribution based upon a very useful environment for study of evolution in wild plant populations. The manuscript lacks a methods section. More details of the experimental materials and methods would aid in understanding the work. Other aspects of the manuscript are all satisfactory.

The materials and methods parts were transferred from the supplement to the main text.
Reviewer #3 (Comments to the Authors (Required)): This MS presents significant genomic evidence for the incipient microevolution of a new lineage of Wild Barley (WB) at "Evolution Plateau" (EP). The phylogenetic and statistical analysis clearly shows the separation of WB into two differentially selected populations on the chalk and basalt regions of the EP site. However, the data are not yet sufficient to conclude that a truly novel species has formed. As their own analysis in Table 1 and Figure 4 indicates, there is evidence for continuing but reduced genetic exchange between the two populations. No attempts at hybridizing the two populations are reported. In my opinion, the incomplete nature of the genetic separation process should be incorporated into the title, abstract and text. For example, adding the phrase "Early stages of" at the start of the tile would produce a more accurate statement of the conclusions that can legitimately be drawn from the sequence data analysis presented in the MS.

Please find our responses to reviewer 1
The research presented here depends on a number of genetic sequence data analysis tools. It would make the paper clearer for the reader to explain the logic and significance of each analytical procedure when it first appears in the text. Naming the tool and providing a reference are not adequate.

Detailed methods were moved from the supplementary to the main text, and readers can find and repeat our data analyses.
Line 18: add (SS) after "sympatric speciation" Yes, added Line 22: "separation" should read "SS separating" Yes, corrected Line 30: "were" for "was" Yes, corrected Line 44: "illuminate" for "highlight" Yes, corrected Line 48: "might it" for "it might" Yes, corrected Line 98: "shared" in what way(s)? It was changed to "present in both" Table S3: define "lv" and "ls" lt was corrected to ts, transition; lv to tv: transversion; Line 120: define "PCA" (princple component analysis)

This was defined in line 105
Line 135: What is the parameter k and what do the different colors indicate in Fig 1E  histograms? k was the number of clusters and was defined The different colors in Fig 1E were explained in the legend to the Figure   Fig S3: The chromosome comparisons seem to show more similarity than difference between the two populations. These data require a more detailed discussion and presentation. It would be appropriate to have quantitative figures on the indels similar to those for SNPs. Since these will come later, mention that fact here. Line 184: The computation of effective population size based on SNP data needs more explanation. Sure, the mutation rate and generation time were added.
Line 220: The computation and meaning of the fastsimcoal2 numbers in Table 1 requires explanation. We add more explanations just below the table Line 221: #14 should be #4.

Yes, corrected
Lines 221-233: The logic of this argument needs to be articulated more full, both for determining "best fit" and for the exclusion of allopatry.
We added more explanation on how to choose the best model and how to exclude the possibility of allopatry. Lines 277ff: The statistical analysis really adds no functional or ecological information and can be removed.

Although we don't know the functional or ecological information of the CNV, this is a description of CNV of the two populations and future work might illuminate it.
Lines 292-296: This is an important observation. It could be supported by citing one or more articles on the regulatory roles played by short and long non-coding RNAs in plants, particularly those affecting developmental timing.

Yes, add citation on long non-coding RNA.
Line 308: "Floristically" is not proper English usage. An equivalent formulation would be "With regard to flowering plants,"

Yes, corrected.
Lines 348-349: Are there direct measurements of flowering time to confirm this inference from the GA-related sequences? Not yet. They will be sought in future work.
Line 367: Is there genetic data (not geological) indicating the basalt population is younger than the chalk population? No.
Line 385 Line 428: "controversy" reads better as "debate" Yes, changed to CONTROVERSY Line 443: "Originated" a new species of WB may be an overinterpretation of the evidence presented here. "Initiated formation" of a new species would be better.

Yes, was changed to initiated formation of a new species
Line 459: It's questionable that "free breeding" is the right description for self-fertilizing plants such as WB. Thank you for submitting your revised manuscript entitled "Incipient sympatric speciation in wild barley caused by geological-edaphic divergence". We would be happy to publish your paper in Life Science Alliance pending final revisions necessary to meet our formatting guidelines.
Along with the changes listed below, please also make the following edits in the revised manuscript, Callouts ---Supplemental figure S6A and S6B are called out separately in the manuscript text, but the S6 figure and S6 figure legends do not include an A or B -please reconcile Author Contributions --There is an author Wang Y. that is listed in the 'Author Contributions' but is missing from the Author List, both in eJP and in the manuscript file --Cui X. and Li X. are listed on the author list, but not included in the Author contribution. Please clarify what their role was in this study.
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Thank you for this interesting contribution, we look forward to publishing your paper in Life Science Alliance.