Table 1. Top-scoring fitted models of cis-regulatory evolution in yeast pathways from experimental expression measurements.

GO term	N	Model	wAIC	Constraint or shift parameter
34599	57	Ornstein-Uhlenbeck	0.899405768	49.97745883
6355	433	S. bayanus shift	0.837382338	0.230918849
6351	462	S. bayanus shift	0.849912647	0.258701476
1302	38	S. paradoxus shift	0.859866949	3.197059161
6897	73	S. paradoxus shift	0.965743399	4.292287639
6338	45	S. cerevisiae shift	0.840339574	0.037806902
42254	136	Ornstein-Uhlenbeck	0.924785133	3.733770466
6364	177	Ornstein-Uhlenbeck	0.902358815	3.079387696
44255	13	S. paradoxus shift	0.945799302	11.43989834
54	11	S. paradoxus shift	0.91523272	9.314688245
16310	188	S. bayanus shift	0.902247359	0.188381056
8152	243	S. bayanus shift	0.844716856	0.043114988
6629	136	S. bayanus shift	0.91650274	0.005082617
122	71	S. bayanus shift	0.819216472	0.040060263
30437	45	S. paradoxus shift	0.931136455	4.060128813

Each row reports the results of phylogenetic inference of the evolutionary history of gene regulation for one yeast Gene Ontology process term, from experimental measurements of cis-regulatory variation in interspecific yeast hybrids. , number of genes in the indicated GO term for which expression measurements were available in all species. Model, best-fit model from among the five possible Brownian motion models of evolutionary rate shift in lineages of the Saccharomyces phylogeny (see Figure 1a), the Ornstein-Uhlenbeck (OU) model of universal constraint, and the equal-rates model involving no lineage-specific differences in evolutionary rate. wAIC, Akaike Information Criterion weight of the indicated model. Constraint or shift parameter, fitted value of the strength of purifying selection or the shift in the rate of regulatory evolution on the indicated lineage, when the best-fit model was the OU model of constraint or a Brownian motion lineage-specific evolutionary rate model, respectively.