Polygenic and directional regulatory evolution across pathways in Saccharomyces

Abstract

The search to understand how genomes innovate in response to selection dominates the field of evolutionary biology. Powerful molecular evolution approaches have been developed to test individual loci for signatures of selection. In many cases, however, an organism's response to changes in selective pressure may be mediated by multiple genes, whose products function together in a cellular process or pathway. Here we assess the prevalence of polygenic evolution in pathways in the yeasts Saccharomyces cerevisiae and S. bayanus. We first established short-read sequencing methods to detect cis-regulatory variation in a diploid hybrid between the species. We then tested for the scenario in which selective pressure in one species to increase or decrease the activity of a pathway has driven the accumulation of cis-regulatory variants that act in the same direction on gene expression. Application of this test revealed a variety of yeast pathways with evidence for directional regulatory evolution. In parallel, we also used population genomic sequencing data to compare protein and cis-regulatory variation within and between species. We identified pathways with evidence for divergence within S. cerevisiae, and we detected signatures of positive selection between S. cerevisiae and S. bayanus. Our results point to polygenic, pathway-level change as a common evolutionary mechanism among yeasts. We suggest that pathway analyses, including our test for directional regulatory evolution, will prove to be a relevant and powerful strategy in many evolutionary genomic applications.

Fig. 1.

Schematic of RNA-seq method for inferring differential allele-specific expression in a hybrid diploid; resampling procedure for an example gene. (Left) Observed base-level read counts are displayed for the S. bayanus and S. cerevisiae orthologs, using color to represent the nucleotide at each base. The x axis gives the position of each base, and the y axis gives the number of allele-specific reads whose first nucleotide maps to a given position. Above each plot are the allele-specific marginal nucleotide frequencies π_b = [π_b(A),π_b(C),π_b(G),π_b(T)] and π_c = [π_c(A),π_c(C),π_c(G),π_c(T)], for S. bayanus and S. cerevisiae, respectively. (Center) For each ortholog, “null” counts are created by resampling base-level read counts according to the S. bayanus and S. cerevisiae nucleotide frequencies π_b and π_c, respectively. Null expression log-fold-changes are computed by averaging (across lanes for each of the two biological replicates) log-ratios of S. bayanus to S. cerevisiae null per-base read counts. The resampling procedure is repeated 10,000 times for each ortholog. (Right) Boxplots of the 10,000 null expression log-fold-changes for each ortholog. The observed log-fold-change from the original read counts is represented by dark red dashed lines and is compared with each null distribution to obtain two-sided P values, p_b and p_c. The significance of the observed allele-specific expression difference is summarized by the maximum P value, max(p_b, p_c).

Fig. 2.

Evidence for directional cis-regulatory evolution, for the example of the nuclear exosome. Shown is a schematic of the proteins in the Gene Ontology terms “nuclear exosome” and “colocalizes_with: nuclear exosome,” colored to reflect expression differences between S. cerevisiae and S. bayanus alleles in the interspecific hybrid. Blue, up-regulation of the S. bayanus allele; orange, up-regulation of the S. cerevisiae allele; gray, no measured expression effect. The complex in the center of the cartoon represents the exosome. The thick black line indicates RNA in the act of processing, the beige cylinder represents a nuclear pore, and the thin line represents the nuclear envelope. 1: CSL4; 2: RRP4; 3: RRP40; 4: RRP41; 5: RRP46; 6: MTR3; 7: RRP42; 8: RRP43; 9: RRP45; 10: RRP6; 11: RRP44; 12: MMP6; 13: LRP1; 14: NRD1; 15: KAP95; 16: SRP1.