A survey of the molecular evolutionary dynamics of twenty-five multigene families from four grass taxa

We surveyed the molecular evolutionary characteristics of 25 plant gene fam ilies, with the goal of better understanding general processes in plant gen e family evolution. The survey was based on 247 GenBank sequences represent ing four grass species (maize, rice, wheat, and barley). For each gene fami ly, orthology and paralogy relationships were uncertain. Recognizing this u ncertainty, we characterized the molecular evolution of each gene family in four ways. First, we calculated the ratio of nonsynonymous to synonymous s ubstitutions (d(N)/d(S)) both on branches of gene phylogenies and across co dons. Our results indicated that the cl,lds ratio was statistically heterog eneous across branches in 17 of 25 (68%) gene families. The vast majority o f d(N)/d(S) estimates were <<1.0, suggestive of selective constraint on ami no acid replacements, and no estimates were >1.0, either across phylogeneti c lineages or across codons. Second, we tested separately for nonsynonymous and synonymous molecular clocks. Sixty-eight percent of gene families reje cted a nonsynonymous molecular clock, and 52% of gene families rejected a s ynonymous molecular clock. Thus, most gene families in this study deviated from clock-like evolution at either synonymous or nonsynonymous sites. Thir d, we calculated the effective number of codons and the proportion of G+C s ynonymous sites for each sequence in each gene family. One or both quantiti es vary significantly within 18 of 25 gene families. Finally, we tested for gene conversion, and only six gene families provided evidence of gene conv ersion events. Altogether, evolution for these 25 gene families is marked b y selective constraint that varies among gene family members, a lack of mol ecular clock at both synonymous and nonsynonymous sites, and substantial va riation in codon usage.