Genomic structural variants involved in local adaptation of the European plaice
Evolution at two time-frames: ancient and common origin of two structural variants involved in local adaptation of the European plaice (Pleuronectes platessa)
Recommendation: posted 02 April 2020, validated 03 April 2020
Awareness has been growing that structural variants in the genome of species play a fundamental role in adaptive evolution and diversification . Here, Le Moan and co-authors  report empirical genomic-wide SNP data on the European plaice (Pleuronectes platessa) across a major environmental transmission zone, ranging from the North Sea to the Baltic Sea. Regions of high linkage disequilibrium suggest the presence of two structural variants that appear to have evolved 220 kya. These two putative structural variants show weak signatures of isolation by distance when contrasted against the rest of the genome, but the frequency of the different putative structural variants appears to co-vary in some parts of the studied range with the environment, indicating the involvement of both selective and neutral processes. This study adds to the mounting body of evidence that structural genomic variants harbour significant information that allows species to respond and adapt to the local environmental context.
 Wellenreuther, M., Mérot, C., Berdan, E., & Bernatchez, L. (2019). Going beyond SNPs: the role of structural genomic variants in adaptive evolution and species diversification. Molecular ecology, 28(6), 1203-1209. doi: 10.1111/mec.15066
 Le Moan, A. Bekkevold, D. & Hemmer-Hansen J. (2020). Evolution at two time-frames: ancient and common origin of two structural variants involved in local adaptation of the European plaice (Pleuronectes platessa). bioRxiv, 662577, ver. 5 peer-reviewed and recommended by PCI Evol Biol. doi: 10.1101/662577
Maren Wellenreuther (2020) Genomic structural variants involved in local adaptation of the European plaice. Peer Community in Evolutionary Biology, 100095. 10.24072/pci.evolbiol.100095
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article. The authors declared that they comply with the PCI rule of having no financial conflicts of interest in relation to the content of the article.
Evaluation round #2
DOI or URL of the preprint: https://doi.org/10.1101/662577
Version of the preprint: 1
Author's Reply, 01 Apr 2020
Decision by Maren Wellenreuther, posted 09 Mar 2020
Three referees evaluated your revised version and the responses provided. One of the referees made some suggestions for changes.
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Reviewed by anonymous reviewer 1, 27 Feb 2020
Reviewed by anonymous reviewer 3, 31 Jan 2020
Reviewed by anonymous reviewer 2, 21 Feb 2020
Evaluation round #1
DOI or URL of the preprint: https://doi.org/10.1101/662577
Author's Reply, 14 Jan 2020
Decision by Maren Wellenreuther, posted 28 Sep 2019
Evolution at two-time frames shape structural variants and population structure of European plaice (Pleuronectes platessa)
Alan Le Moan, Dorte Bekkevold & Jakob Hemmer-Hansen
https://doi.org/10.1101/662577 version 1
COMMENTS TO AUTHORS:
I now had three reviewers provide comments about the manuscript that has been submitted to PCI Evolutionary Biology entitled ‘Evolution at two-time frames shape structural variants and population structure of European plaice (Pleuronectes platessa)’. This manuscript explores the population structure and variation in two structural variants (SVs) in the European plaice in the North and Baltic Sea. Previous work identified these two SVs on chromosome 19 and 21 and this study further explores this variation by incorporating additional sampling locations and attempting to date the SVs. The paper also investigates whether the SVs could have been introduced through introgression from another species that is known to hybridize with plaice. Overall, I think the paper is interesting, and this was also shared by the reviewers. Given the increasing awareness about the importance of SVs to population structure, I think this paper would be of interest to many readers.
However the reviewers have also highlighted a number of issues that need attention and have provided detailed and constructive comments below on how the manuscript could be improved. The major areas in need of attention are:
1. The general framework needs to be broadened, particularly in the Introduction, to include general details about why the authors investigate the population structure of plaice. Right now, the authors mostly focus in SVs in their Introduction.
2. All of the reviewers found that the Methods lacked critical detail and explanations (e.g. lack of details about sampling and dataset sizes). Please go over the comments that the reviewers have made on a point by point basis and clarify this section.
3. Reviewer 3 added some thoughts about the dating of the SVs, and possible problems with it. Further, it would also be good for the context and interpretation if the authors could provide a bit more detail about the genes that are located in the SVs, and to qualify statements like ‘…many of these were involved in ion transport’ (how many?).
4. The reviewers felt that some of the statements were too vague, and were rather descriptive and lacked quantitative support, and I agree with that. I suggest the authors go over the manuscript again and qualify some of these (many-say how many, most of the times-how often?).
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