Fig. 1

Expression level evolution following WGD. a Phylogenetic tree of the species included in the study, with the estimated time of the salmonid-specific whole genome duplication (Ss4R) indicated. b Conceptual illustration of the expression level evolution tests. c Proportion of complete singleton (top) and ohnolog (bottom) gene trees with significant shifts in expression level in a salmonid ancestor. d, e Heatmaps show tissue expression, from an independent tissue atlas in Atlantic salmon, of ohnolog pairs where one copy has shifted up (d) or down (e) in liver. Barplots show the distribution of the number of tissues where the shifted copy has lower or higher expression than the conserved copy. Only ohnologs from complete orthogroups (panel c) are included in the heatmap. Each ohnolog pair (row) is scaled so that red signifies the highest expression across the two copies and blue the lowest. The color bar indicates the number of tissues that are experiencing a shift in expression in the same direction as that of liver (down (d), up (e)) between the shifted and conserved copy. f Proportion of partial gene trees (i.e., trees with some gene loss) with significant shifts in expression level in a salmonid ancestor. The shadings indicate that we report here up/down shifts for the complete salmonid clade and the partial salmonid clade separately, which is in contrast to panel c where both salmonid clades are complete and therefore indistinguishable. g Cumulative proportion of dN/dS for ohnologs with one copy shifted down, versus their conserved counterpart. Results are shown for all ohnologs with one copy shifted down (down-shift) and for the subset that is down-shifted in all tissues in the tissue atlas (down-shift all tissues affected). h Cumulative proportion of TE content in promoters of ohnologs with one copy shifted down