Species tree topology used for evolutionary analyses (A), and branch specific Ka/Ks ratios obtained from different data sets (B?D). Each of the three electric fish clades was labeled as follows: a-Mormyroidea, b-Malapterurus electricus, and c-Gymnotiformes; and nonelectric taxa used for comparisons are labeled as follows: d-Asian arowana, e-Channel catfish, and f-Cave fish. Images of representative electric fishes are provided (A). The Ka/Ks ratios for each terminal branch were calculated from all 4,657 orthologs (B), concatenated all orthologs (C), and 1,000 concatenated alignments constructed from ten randomly chosen orthologs (D).

(A) UpSet plot of PSGs identified in three electric fish lineages. (B) UpSet plots of the PSGs identified in corresponding nonelectric fish lineages. The plot in the left corner indicates total number of PSGs. The main plot shows the number of unique PSGs and the connected dots show the PSG intersections/overlaps between species.

(A) UpSet plot of convergent genes identified between pairs of electric fish lineages. The plot in the left corner indicates total numbers of convergent genes. The main plot indicates the number of unique convergent genes and the connected dots indicate the convergent intersections between branch pairs. (B) UpSet plot of convergent genes identified between pairs of nonelectric fish lineages. (C) Comparison of shared convergent amino acid replacements in scn4aa, parp1, and scamp2 among nine electric fish species and four nonelectric fish species.

Statistics of adaptively convergent genes and functional enrichment. (A) The intersections of convergent genes and PSGs that occurred along the branches of at least two electric fish lineages. Convergent genes that occurred in PSGs are shaded red. (B) Functional enrichment of adaptively convergent genes.