Transition-Transversion Bias Is Not Universal: A Counter Example from Grasshopper Pseudogenes

Abstract

Comparisons of the DNA sequences of metazoa show an excess of transitional over transversional substitutions. Part of this bias is due to the relatively high rate of mutation of methylated cytosines to thymine. Postmutation processes also introduce a bias, particularly selection for codon-usage bias in coding regions. It is generally assumed, however, that there is a universal bias in favour of transitions over transversions, possibly as a result of the underlying chemistry of mutation. Surprisingly, this underlying trend has been evaluated only in two types of metazoan, namely Drosophila and the Mammalia. Here, we investigate a third group, and find no such bias. We characterize the point substitution spectrum in Podisma pedestris, a grasshopper species with a very large genome. The accumulation of mutations was surveyed in two pseudogene families, nuclear mitochondrial and ribosomal DNA sequences. The cytosine-guanine (CpG) dinucleotides exhibit the high transition frequencies expected of methylated sites. The transition rate at other cytosine residues is significantly lower. After accounting for this methylation effect, there is no significant difference between transition and transversion rates. These results contrast with reports from other taxa and lead us to reject the hypothesis of a universal transition/transversion bias. Instead we suggest fundamental interspecific differences in point substitution processes. Some mutations occur more frequently than others. We need to understand these biases if we are to interpret the differences that have accumulated between species and individuals. Applications include estimating the time since evolutionary lineages diverged and detecting the signature of natural selection in DNA sequences. However, mutational biases have been obscured because, since mutations arose, natural selection has eliminated some whilst allowing others to persist to the present. We therefore study mutations that have accumulated in regions of the genome that are free from selection in a grasshopper with a gigantic genome. All other animal studies using this approach find an excess of mutations between DNA bases having similar biochemical properties (transitions rather than transversions). This bias has been widely interpreted as a consequence of the fundamental biochemical basis of mutation. However, once we exclude mutations associated with DNA methylation, we find no evidence of a transition bias, unlike the few comparable animal studies that make the same correction. We propose that this result indicates previously unanticipated differences between species in the selection on or mutation of their DNA.