Extended Data Fig. 2: Divergence times and introgression among Gadinae.
a Distribution ranges of species in the genera Gadus, Arctogadus and Boreogadus. Partially overlapping distribution ranges are shown in dark grey, with outline shades indicating the species (all distributions are shown separately in Supplementary Figure 7). b Species tree of the six species and three outgroups (P. virens, M. aeglefinus and M. merlangus; outgroups shown in beige), estimated under the isolation-with-migration model from 109 alignments with a total length 383,727 bp. The Bayesian analysis assigned 99.7% of the posterior probability to two tree topologies that differ in the position of Arctic cod and were supported with Bayesian posterior probabilities (BPP) of 0.763 and 0.234, respectively. Rates of introgression estimated in the Bayesian analysis are marked with arrows. Thin grey and beige lines show individual trees sampled from the posterior distribution; the black line indicates the maximum-clade-credibility summary tree, separately calculated for each of the two topologies. Of Atlantic cod, both migratory and stationary individuals were included. c Pairwise introgression among species of the genera Gadus, Arctogadus and Boreogadus. Introgression was quantified with the D-statistic. The heatmap shows two versions of the D-statistic, DBBAA and Dfix, above and below the diagonal, respectively. d Introgression across the genome. The fdM-statistic103 is shown for sliding windows in comparisons of three species. The top and bottom rows show support for introgression between polar cod and Arctic cod and between Atlantic cod and Greenland cod, respectively. Results are shown separately for the stationary and migratory Atlantic cod genomes. The mean D-statistic across the genome is marked with a thin solid line. See Supplementary Notes 3 and 4 for details and a discussion of these results. Fish drawings by Alexandra Viertler.
