Fig. 2: Gene duplication and evolution.

a The Ka/Ks ratio distributions of gene pairs derived from different modes of duplication. WGD whole-genome duplication, TD tandem duplication, PD proximal duplication, TRD transposed duplication, DSD dispersed duplication. In the boxplot representations, points are outliers; the center line is the median; the lower and upper hinges correspond to the first and third quartiles (25th and 75th percentiles); whiskers extend to the minimum (left whiskers) and maximum (right whiskers) estimates located within the 1.5× interquartile range (IQR) of the first and third quartiles, respectively. Gaussian kernel estimates of Ka/Ks of different duplicated groups are shown as violins; 6056 WGD, 4746 TD, 3732 PD, 6399 TRD, and 8463 DSD duplicates were incorporated in the statistics. b Venn diagram shows the possible logical relations between members of expanded gene family and modes of duplication (WGD, TD, PD, TRD, and DSD). TDp: tandem duplication experienced positive selection, PDp: proximal duplication experienced positive selection, DSDp: dispersed duplication experienced positive selection, EGFs: expanded gene families. c Functional enrichment analysis of genes overlapping between expanded gene families (EGFs) and five modes of duplication (WGD, TD, PD, TRD, and DSD). The enriched GO terms with corrected P value <0.001 are presented. The color of circles represents the statistical significance of enriched GO terms. The size of the circles represents the number of genes in a GO term. For all annotated genes their GO terms are provided as background information. ‘P adjust’ is the Benjamini–Hochberg false discovery rate (FDR) adjusted P value. d The numbers of genes from different families and gene duplications are provided. SL singletons.