  Despite the greater functional importance of protein levels, our knowledge of
gene expression evolution is based almost entirely on studies of mRNA levels.
In contrast, our understanding of how translational regulation evolves has
lagged far behind. Here we have applied ribosome profiling - which measures
both global mRNA levels and their translation rates - to two species of
Saccharomyces yeast and their interspecific hybrid in order to assess the
relative contributions of changes in mRNA abundance and translation to
regulatory evolution. We report that both cis and trans-acting regulatory
divergence in translation are abundant, affecting at least 35% of genes. The
majority of translational divergence acts to buffer changes in mRNA abundance,
suggesting a widespread role for stabilizing selection acting across regulatory
levels. Nevertheless, we observe evidence of lineage-specific selection acting
on a number of yeast functional modules, including instances of reinforcing
selection acting at both levels of regulation. Finally, we also uncover
multiple instances of stop-codon readthrough that are conserved between
species. Our analysis reveals the under-appreciated complexity of
post-transcriptional regulatory divergence and indicates that partitioning the
search for the locus of selection into the binary categories of 'coding' vs.
'regulatory' may overlook a significant source of selection, acting at multiple
regulatory levels along the path from genotype to phenotype.
