Extended Data Fig. 1: Relationships among gene concordance factor (gCF) values, site concordance factor values (sCF) and branch lengths (substitutions per sequence site) along all branches of the acanthomorph phylogeny represented in Supplementary Figs. 1–25.

Note that unlike gCF values, site concordance and discordance values sum to 100% because their calculations allow for only three possible resolutions of a branch. Branch lengths have a positive, logarithmic correlation with gCF and sCF. A one percent increase in branch lengths leads to a 0.1413 increase in the natural log of gCF (Standard Error = 0.2925, y-intercept = 108.3323, R-squared = 0.6791) and a 0.0905 change in the natural log of sCF (Standard Error = 0.3416, y-intercept = 109.851, R-squared = 0.3889). These correlation analyses were performed using base R functions after log-transforming branch lengths; all branches were included in these calculations. a, Relationship between gCF and sCF, with points colored by branch lengths. The dashed black line with a slope of 1 demonstrates dissimilar levels of conflict among loci and sites, suggesting that the low gCF values are not just caused by genuine discordance in the gene trees. Eleven gray points reflect extremely long branches with lengths greater than 0.1 nucleotide substitutions per site (greater than the upper 99th percentile). b, Logarithmic relationship between branch lengths and gCF. c, Relationship between branch lengths and sCF values, with points colored by gCF values. Not shown are three points with very long branches (0.176-0.328 substitutions per sequence sites), all of which have sCF and gCF values >94%.