Data from: The structure of an ancient genotype-phenotype map shaped the functional evolution of a protein family

Mutation is more likely to produce some phenotypes than others, but the
causal role of these production propensities in the evolution of
phenotypic diversity remains unclear. There are two major challenges: it
is difficult to separate the effect of the genotype-phenotype (GP) map
from that of natural selection when analyzing natural diversity, and most
extant phenotypes evolved long ago in species whose GP maps cannot be
recovered. Using reconstructed ancestral transcription factors, we created
libraries containing all possible amino acid combinations at historically
variable sites in the proteins’ DNA binding interface (the genotypes) and
measured their capacity to specifically bind DNA elements containing all
possible combinations of nucleotides at historically variable sites (the
phenotypes). The two ancestral GP maps were strongly anisotropic (the
distribution of phenotypes encoded by genotypes is highly nonuniform) and
heterogeneous (the phenotypes accessible around each genotype vary
dramatically among genotypes), but the extent and direction of these
properties differed dramatically between the maps. In both cases, these
properties steered evolution toward the lineage-specific phenotypes that
evolved during history. Our findings establish that ancient properties of
the GP relationship were causal factors in the evolutionary process that
produced present-day patterns of functional conservation and diversity.