Synonymous and Nonsynonymous Substitutions in Genes from Gramineae: Intragenic Correlations Fernando Alvarez-Valin, 1,3 Kamel Jabbari, 1 Nicolas Carels, 1,2 Giorgio Bernardi 1,2 1 Laboratoire de Ge ´ne ´tique Mole ´culaire, Institut Jacques Monod, 2 Place Jussieu, F-75005 Paris, France 2 Stazione Zoologica Anton Dohrn, Laboratorio de Evoluzione Molecolare, Villa Comunale I, 80121 Napoli, Italy 3 Seccio ´n Biomatema ´tica, Facultad de Ciencias, Universidad de la Repu ´blica, Montevideo, Uruguay Received: 2 July 1998 / Accepted: 18 April 1999 Abstract. In this work, we have investigated the rela- tionships between synonymous and nonsynonymous rates and base composition in coding sequences from Gramineae to analyze the factors underlying the varia- tion in substitutional rates. We have shown that in these genes the rates of nucleotide divergence, both synony- mous and nonsynonymous, are, to some extent, depen- dent on each other and on the base composition. In the first place, the variation in nonsynonymous rate is related to the GC level at the second codon position (the higher the GC 2 level, the higher the amino acid replacement rate). The correlation is especially strong with T 2 , the coefficients being significant in the three data sets ana- lyzed. This correlation between nonsynonymous rate and base composition at the second codon position is also detectable at the intragenic level, which implies that the factors that tend to increase the intergenic variance in nonsynonymous rates also affect the intragenic variance. On the other hand, we have shown that the synonymous rate is strongly correlated with the GC 3 level. This cor- relation is observed both across genes and at the intra- genic level. Similarly, the nonsynonymous rate is also affected at the intragenic level by GC 3 level, like the silent rate. In fact, synonymous and nonsynonymous rates exhibit a parallel behavior in relation to GC 3 level, indicating that the intragenic patterns of both silent and amino acid divergence rates are influenced in a similar way by the intragenic variation of GC 3 . This result, taken together with the fact that the number of genes display- ing intragenic correlation coefficients between synony- mous and nonsynonymous rates is not very high, but higher than random expectation (in the three data sets analyzed), strongly suggests that the processes of silent and amino acid replacement divergence are, at least in part, driven by common evolutionary forces in genes from Gramineae. Key words: Nucleotide substitutions — Nonsynony- mous substitutions — Monocots — Base composition Introduction Rates of synonymous and nonsynonymous substitutions have been shown to vary among genes of both animals and bacteria (Li et al. 1985; Wolfe and Sharp 1993; Bernardi et al. 1993). The variability in nonsynonymous rates has been attributed to different intensities of nega- tive selection acting towards maintaining amino acids. The larger the proportion of amino acids under func- tional constraint, the lower the substitution rate. On the other hand, several factors have been postulated to ex- plain the variation in synonymous rates: variation in the rate and pattern of mutation among different regions of the genome (Wolfe et al. 1989), base composition (Ticher and Graur 1989), and, in the case of enterobacterial genes, selection for codon usage (Sharp and Li 1987). Correspondence to: G. Bernardi at Stazione Zoologica Anton Dohrn; e-mail: bernardi@alpha.szn.it J Mol Evol (1999) 49:330–342 © Springer-Verlag New York Inc. 1999