Local introgression at two spatial scales in mosaic hybrid zones of mussels

JEB-2019-00404

The manuscript comparatively analysis 6 secondary contact zones between species of the Mytilus edulis species complex (M. edulis, M. trossulus, M. galloprovinacialis) in the northern hemisphere. The aim is to contrast ongoing introgression with past introgression using a genome wide assay (212 SNP) and different methods to estimate the admixture proportion as well as introgression rates based on genomic clines. The authors successfully established an ancestry diagnostic SNP-marker-set, show that introgression between the three Mytilus species is widespread while genomic clines are largely concordant, and provide insight into ongoing vs. past introgression by comparing hybrid populations with central/peripheral parental populations. The study addresses a timely question related to the evolution of the Mytilus edulis species complex and uses State-of-the-art methods in genome and data analyses. Thus, I believe that the manuscript is interesting for the readers of JEB (particularly for those interested in marine sessile invertebrates and hybridization) and I can recommend publication after minor revision.

My suggestions for changes are mainly motivated by the fact that the massive amount of information and data make the ms difficult to read. This is always the fact if large datasets are analysed and presented but few changes may help the reader to get an easier overview:

1) Please express the major aims of the ms clearly in the last paragraph of the introduction. The current phrasing (lines 82 to 94) appear like a summary not like aims and objectives and the clearest outline of the motivation is currently presented in the abstract (lines 6-10).
2) I suggest providing the population ID in table 1 (e.g., which populations are considered edu_eu_north etc.). This could be done instead or in addition by adding these population codes in table S1.
3) I feel that a brief explanation of the molecular basic principles behind the GoldenGate Genotyping assay may particularly help those JEB-readers who are not primarily working with genomic tools (liens 103-105; e.g. saying that the method targets SNP at particular loci based on Primer extension and PCR etc.).
4) Please provide the citation and software version for i) ADMIXTURE (line 155) and ii) STRUCTURE (line 189).
5) Table 3: The column “species” for the Hybrid zone “Öresund” gives edu_am/tros_am (=American populations). I would have expected to read edu_eu-North and tros_eu-baltic (=European populations) ? I also think that table captions should be self explaining and suggest encoding P1/P2 as Parental populations 1/2. and referring to tables S1
6) Figure 2: The top panel (PCA) is easy to understand but the STRUCTURE Plot below is extremely difficult to link to the panel above. Why not labelling the origin of the populations and a respective hybrid zones with the names according to table 3 and/or sorting the populations according to the PCA clusters while using the same labelling (origin code like edu-am and Letters A-E). (Might also apply to Figure S3)
7) Figure 4 panel B: What population is tros_eu_north? Cannot find this in table 1!
8) Figure 5: indicate the abbreviation “h” as Hybrid Index