Assessing substitution variation across sites in grass chloroplast DNA

We assess the similarity of base substitution processes, described by empirically derived 4 x 4 matrices, using chi-square homogeneity tests. Such significance analyses allow us to assess variation in sequence evolution across sites and we apply them to matrices derived from noncoding sites in different contexts in grass chloroplast DNA. We show that there is statistically significant variation in rates and patterns of mutation among noncoding sites in different contexts and then demonstrate a similar and significant influence of context on substitutions at fourfold degenerate sites of coding regions from grass chloroplast DNA. These results show that context has the same general effect on substitution bias in coding and noncoding DNA: the A+T content of flanking bases is correlated with rate of substitution, transition bias, and GC --> AT pressure, while the number of flanking pyrimidines on a single strand is correlated with a mutational bias, or skew, toward pyrimidines. Despite the similarity in general trends, however, when we compare coding and noncoding matrices we find that there is a statistically significant difference between them even when we control for context. Most noticeably, fourfold degenerate sites in coding sequences are undergoing substitution at a higher rate and there are also significant differences in the relationship between pyrimidines skew and the number of flanking pyrimidines. Possible reasons for the differences between coding and noncoding sites are discussed. Furthermore, our analysis illustrates a simple statistical way for comparing substitution processes across sites allowing us to better study variation in evolutionary processes across a genome.