Extensive mitochondrial DNA transfer in a rapidly evolving rodent has been mediated by independent insertion events and by duplications

Abstract

Mitochondrial DNA translocations to the nucleus (numt pseudogenes) are pervasive among eukaryotes, but copy number within the nuclear genome varies widely among taxa. As an increasing number of genomes are sequenced in their entirety, the origins, transfer mechanisms and insertion sites of numts are slowly being characterized. We investigated mitochondrial transfers within a genetically diverse rodent lineage and here report 15 numts totaling 21.8 kb that are harbored within the nuclear genome of the vole Microtus rossiaemeridionalis. The 15 numts total 21.8 kb and range from 0.39 to over 3.0 kb in length. Phylogenetic analyses revealed that these numts resulted from three independent insertions to the nucleus, two of which were followed by subsequent nuclear duplication events. The dates of the two translocations that led to subsequent duplications were estimated at 1.97 and 1.19 MYA, which coincide with the origin and radiation of the genus Microtus. Numt sequence data from five Microtus species were used to estimate an average rate of nucleotide substitution as 2.6x10(-8) subs/site/yr. This substitution rate is higher than in many other mammals, but is concordant with the elevated rate of mtDNA substitution in this lineage. Our data suggest that numt translocation in Microtus is more extensive than in either Mus or in Rattus, consistent with the elevated rate of speciation, karyotypic rearrangement, and mitochondrial DNA evolution in Microtus.