Shared mutations: Common descent or common mechanism?

Mutations are a fact of life. Darwin gave mutations, which he called natural variation between individuals, a key role to explain the origin of species. The origin and nature of mutations is one of the most fundamental questions of biology, and are a hot topic in origin debates. If mutations are merely a matter of chance, then the alignment of mutations in distinct species that do not reproduce together qualifies as independent molecular evidence of common descent. We know now, however, that mutations are not utterly chance driven phenomena as the DNA context may determine to a considerable extent where mutations occur. If mutations are modulated because of biophysical mechanisms the question is not whether rules and laws determine where mutations are introduced, but rather – do non-random mutations affect phylogenetic analysis? The DNA analysis of the 1G5 gene in Drosophila melanogaster demonstrates that over 70 percent of the mutations that are shared between subpopulations of species that do not interbreed are independent of common descent. Likewise, over 50 percent of the mutations in the GULO pseudogene that are shared between humans and the great apes are mutational hot spots also found in guinea pigs – they exactly match the mutations that set humans and primates apart from the rat and line up independent of common ancestry. This paper advances a new hypothesis to understand alignment of mutations in homologous DNA sequences of separated species as the result of a common mechanism operating in similar genomes, and provides the first biological evidence that the location where a mutation will occur and the type of mutation (transition or transversion) are largely predetermined. The consequence is that we may not be able to discriminate between common descent and this common mechanism.