Fig. 2: Expression evolution in a complex history of gene family evolution.

a Modeling expression evolution with multi-optima Ornstein–Uhlenbeck process. A phylogenetic simulation is shown. Colors show branches belonging to different regimes. Regime shifts (change of color) appear as a substantial change in optimal trait values. b Nodes and branches of gene family phylogeny were categorized into S, D, or R based on the branching events, i.e., speciation, DNA-based duplication, or retrotransposition, respectively. c Venn diagrams of expression regime shifts. Circles represent the sets of branches where regime shifts were detected with SVA-log-TMM-FPKM or SVA-log-TPM. d The gene tree of phosphoglycerol kinases (orthogroup ID: OG0002332) is shown as an example. This orthogroup shows ortholog-specific expression patterns as well as regime shifts after speciation and lineage-specific gene duplication. Tips correspond to genes. The colors of branches and tip labels indicate expression regimes. Node colors match to the categorization in b. The heatmap shows expression levels and among-organ expression patterns are shown as a pie chart for each regime. To the right, the number of introns and located chromosomes (A, autosome; X, X chromosome; Y, Y chromosome) are indicated. For full information including complete tip labels and bootstrap branch supports, see Supplementary Dataset https://doi.org/10.17632/3vcstwdbrn.1.