Stabilizing and directional selection shape the genetic variation of gene expression in the transcriptome of Chlamydomonas

Gene expression has proven to be a source of evolutionary novelty and is important to phenotypic evolution. However, we still have a poor understanding of the degree to which mutation contributes to variation in segregating and diverging populations. Here, we aim to investigate the evolutionary forces that shape the transcriptome in 24 wild strains of the green alga Chlamydomonas reinhardtii, originating from two subpopulations and four closely related species. We employ a comparative analysis of expression variation in the presence (i.e., genetic variance, VG) and absence (i.e., mutational variance, VM) of selection, in conjunction with the phylogenetic comparative model Expression Variance Evolution (EVE), to identify the selective forces that may be shaping variation. We found that gene expression displays moderate heritability, with genetic changes accounting for 17% of the differences in expression. The transcriptome evolved under the dominant influence of stabilizing selection, with a minor role of directional selection, which was present in 14% of genes, supporting the strong conservation of expression across species that had diverged over 10 MYA. Indeed, we found that genes with high within-species variation also displayed high expression differences between species.