Patterns of genetic diversification within the Adh gene family in the grasses (Poaceae)

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.