We investigated the evolutionary dynamics of the Adh gene family within the
grasses (Poaceae), with the goal of using molecular evolutionary tools to
understand the process of gene family diversification. We analyzed 21 Adh s
equences representing a broad array of grasses. Phylogenetic analyses sugge
sted that Adh duplicated into Adh1 and Adh2 before the radiation of the gra
sses roughly 65 MYA. Gene structure, including intron length, has varied li
ttle over this period. Conservation of intron length prompted investigation
into the dynamics of intron evolution, particularly the ability of intron
sequences to form secondary structures. Intron sequences did not have an ex
tremely high or low minimum free energy of folding relative to permuted seq
uences, suggesting that individual Adh introns do not evolve under secondar
y structural constraints. For coding sequences, the diversification of Adh1
and Adh2 was marked by a shift in third- position G+C content. This shift
may reflect differential selection for codon use. Diversification between A
dh1 and Adh2 was also typified by a shift in nonsynonymous nucleotide subst
itution rates, but there was no evidence that relatively fast nonsynonymous
nucleotide substitution rates in the Adh2 clade were a product of diversif
ying selection. Gene conversion may have played a role in retarding diversi
fication of Adh1 and Adh2 in rice, but there is no evidence of gene convers
ion between paralogs in other taxa. Although the reasons for retention of t
wo functional Adh genes remain obscure, we propose that a shift in gene exp
ression was important for the retention of the two Adh gene copies within t
he grasses.