Pervasive multinucleotide mutational events in eukaryotes

Many aspects of mutational processes are nonrandom, from the preponderance of transitions relative to transversions to the higher rate of mutation at CpG dinucleotides [1]. However, it is still often assumed that single-nucleotide mutations are independent of one another, each being caused by separate mutational events. The occurrence of multiple, closely spaced substitutions appears to violate assumptions of independence and is often interpreted as evidence for the action of adaptive natural selection [2, 3], balancing selection [4], or compensatory evolution [5, 6]. Here we provide evidence of a frequent, widespread multinucleotide mutational process active throughout eukaryotes. Genomic data from mutation-accumulation experiments, parent-offspring trios, and human polymorphisms all show that simultaneous nucleotide substitutions occur within short stretches of DNA. Regardless of species, such multinucleotide mutations (MNMs) consistently comprise ~3% of the total number of nucleotide substitutions. These results imply that previous adaptive interpretations of multiple, closely spaced substitutions may have been unwarranted and that MNMs must be considered when interpreting sequence data.