Assessing Substitution Variation Across Sites in Grass Chloroplast DNA |
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Authors: | Tian Zheng Tomoyuki Ichiba Brian R Morton |
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Affiliation: | (1) Department of Statistics, Columbia University, New York, NY 10027, USA;(2) Department of Biological Sciences, Barnard College, Columbia University, 3009 Broadway, New York, NY 10027, USA |
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Abstract: | We assess the similarity of base substitution processes, described by empirically derived 4 × 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.
Reviewing Editor: Dr. Martin Kreitman] |
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Keywords: | Mutation Nucleotide substitution Context dependency Markov process Chloroplast genome Substitution matrix Substitution rate |
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