Rs Salaria Data Structure Pdf 51
Theodora Glime
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This article is Accepted. In the previous review round, Reviewer 1 indicated they would be satisfied with the minor edits and would not need to see the manuscript again. This version has been re-reviewed by Reviewer 2 who now also finds it Acceptable.
I very much appreciate the author's effort to address my concerns regarding what I felt were some inconsistencies regarding Dloop and S7 analyses, and I apologize for recommending analyses that were at this point not possible. I was under the impression that AMOVA could be conducted using Jost Dest in Genodive; however, I was clearly mistaken.
As you can see, two of the original reviewers have re-reviewed your submission. Although the comments of Reviewer 1 are mostly 'editorial', Reviewer 2 still has a significant concern which (as they indicate) could be addressed via some additional analyses.
Please address all of the review comments in your revision.
The revised version of the manuscript "Isolation-by-distance and asymmetrical dispersal of an intertidal blenniid across the Atlantic-Mediterranean divide" is much improved, with better background and context provided, and a more balanced discussion.
I would suggest changing the title to reflect this version, though.
I appreciate the significant time and effort the authors put into revising the manuscript, including undertaking additional analyses of population structure and a more detailed assessment of the S7 data. That said, I do not see any indication of results for a pairwise analysis of population structure nor the related IBD analysis for the S7 data. Likewise, AMOVA was not conducted using Dest for either loci.
I feel this is a non-trivial point as the argument for IBD is based on a significant signal in the D-loop Dest data, yet IBD was not tested using the S7 data and AMOVA/SAMOVA were not run using Dest.
I recommend the authors look into Genodive (Meirmans and Van Tienderen 2004) which offers an ability to test for hierachical structure (AMOVA) using several standardized measures of differentiation (including Dest).
Meirmans, P.G., and P.H. Van Tienderen: (2004), GENOTYPE and GENODIVE: two
programs for the analysis of genetic diversity of asexual organisms, Molecular Ecology
Notes 4 p.792-794.
While I think the manuscript will be well received once published, I feel there is still some ambiguity regarding the importance of IBD versus regional population structure. As I've indicated above, I feel the manuscript would benefit from a few additional analyses. Since the conclusion of IBD was based in part on a significant IBD pattern in the d-loop Dest data set, I think it would be appropriate to test this same data set for hierarchical population structure (AMOVA) using Genodive. I as well think it would be informative to test pairwise population structure and IBD (mantel test) using the S7 dataset, both of which can be run in Arlequin.
The sampling scheme of the manuscript is accurate for the proposed study. However, the Migrate-N and BSP analyses need to be addressed.
I would strongly recommend for the authors to use IMA2 instead of Migrate-N, as well as other faster mutation rates (see comments below).
Sampling at several sites is insufficient (Formentera and Galacia) and these sites should therefore not be included in tests for population structure. As I note below, I recommend testing for population structure in the S7 locus or adding additional loci to corroborate dloop findings. I as well recommend hierachical analysis of population structure for Dloop (and S7) to test for regional and subpopulation structure (which is indicated in figures 2 and 3).
As a single locus study, I have a hard time definitively accepting the authors' conclusion of assymetrical IBD. Dloop is notoriously challenging to work with because of it's hypervariability, which bias Fst estimates and considerably reduce power. See my general comments to the authors for a more detailed description of my concerns and recommendations.
The manuscript is pretty clearly laid out. It has a good structure, providing a good background, and also has very nice and clear figures.
At the end of the Introduction the criterion for choosing the species should be more openly stated. The Discussion, on the other hand, over-emphasizes IbD (see further below).
The findings are generally valid and realistic, with the caveat that the authors over-emphasize the role of Isolation by Distance, while their main test to detect it (Mantel) actually fails to reject the null hypothesis.
I am attaching the pdf with a few comments throughout the text.
I recommedn the authors to do as follows:
1) try a Mantel test simply based on an Fst matrix, as opposed to a Phi-st, as that way, historical polymorphisms will not affect the wide intra-sample nucleotide variance. This way, using only frequency-based differentiation, it may help picking up some association between genetic and geographic matrices.
2) unless point 1 revolutionises the relationship, I would considerably tone down the role of IbD, because it is somewhat speculative/hazy.
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