Figure 1.
The red box in the inset shows the location of the depth transect along the slope, rise, and abyssal plain of the Northwest Atlantic, with station names and depths indicated. Stations are color-coded according to a genetic separation between shallow (red) and deep (blue; see Results).
Figure 2.
Structure analysis for all loci and just nuclear loci.
A, Mean likelihood scores and standard deviations from 20 replicate runs at each K from Structure analysis of all 5 loci. B, Plot of Delta K model scores using the Evanno et al. method (2005); “Pr” indicates the probability for the best model (K=3) according to the method of Pritchard et al. (2000) and for the Evanno-selected K=2. C, Admixture proportions for the most likely grouping (K=2). D–F, the same analyses and measures for Structure analysis on nuclear loci only.
Figure 3.
Branch lengths are proportional to substitutions per site, combined across loci. Bayesian posterior clade probabilities are shown if >0.75, and population assignments are colored as in Figure 1.
Figure 4.
Population demographic history and migration estimates from IM for all loci.
The gray box indicates the estimated effective population size (Ne) of the ancestral population. Estimated splitting time is indicated by the horizontal line. Descendant shallow and deep populations are represented above the line by polygons whose starting width is the estimated Ne just after the split and whose upper width is the estimated contemporary Ne. Curved dotted arrows represent estimated migration rates per generation, forward in time from source to destination. Demographic history estimation from starBEAST is shown in the inset, with branch thickness proportional to estimated population size. Coloring of shallow and deep is as in Figure 1.
Figure 5.
Extended Bayesian Skyline Plot of population size through time for the shallow population.
Median (line) and 95% HPD (red shading) population size are shown.