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). 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. Likewise, AMOVA was not conducted using Dest for either loci. 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. 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. The revised manuscript is well written and well structured, and figures/tables are clear and appropriate. Also, what are the circles in the figure? I'm assuming they mean non-significant, but that does not show in the legend, which mentions asterisks. Line 381: add (LGM) after last glaciation maximumįigure 5: Not sure why it says GST, when it should be FST and phiST. Line 312: a nucleotide diversity of 0.18 is not low. Line 286: remove the extra sentence saying AMOVA results Line 277 (and 364): Isolation-by-distance Line 253: a nucleotide diversity of 0.036 is not low. Otherwise, the authors should have estimated BSP for both populations Line 226: it seems that BSP analysis was only conducted for the Atlantic samples, please specify this in the methods. Line 168: remove and, make it two sentences

Line 132: not necessary to show the primer sequences if they are described elsewhere Line 67: add a - between sargus and Bargelloni Therefore, I would recommend for the title to be changed to accommodate the new version. Title - the new version of the manuscript acknowledged the difficulty in attributing the observed phylogeographic pattern in Salaria pavo to a specific model. Therefore, I recommend the manuscript to be accepted pending minor (mainly editorial) revisions. I am particularly pleased with the thorough reply considering the IMA-2 and Migrate-N discussion, and I have no further comments on that part. The new version of the manuscript is much improved and provides a more balanced interpretation of the results. The authors of 'Isolation-by-distance and asymmetrical dispersal of an intertidal blenniid across the Atlantic-Mediterranean divide' are to be congratulated for their effort in answering all my comments and addressing my concerns. The new analyses done and the changes introduced in the manuscript make it more robust. Experimental designĮxperimental design is adequate and the new analyses done provide further support to the findings.

I would suggest changing the title to reflect this version, though.

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.

Samova genodive