Complex Pattern of Coalescence and Fast Evolution of a Mitochondrial rRNA Pseudogene in a Recent Radiation of Tiger Beetles

Abstract

Transposed copies of mitochondrial DNA into the nucleus (numts) are widespread, but to date they have not been described from the Coleoptera (beetles). Here we report the discovery of a numt derived from a mitochondrial ribosomal RNA gene in Australian tiger beetles (genus Rivacindela). The loss of function of the numt was confirmed by high proportion of transversions, numerous noncompensatory substitutions in stem regions, and large deletions in functionally important sequences. Phylogenetic analysis of orthologous numt sequences was performed together with the corresponding mtDNA lineage for a study of origination and establishment of the transposed copies in closely related populations and species. All numt sequences were strongly supported to be monophyletic, indicating a single origin of this element. However, populations were polymorphic for the presence of the numt, and phylogenetic trees based on the numt sequences showed inconsistencies with the corresponding mtDNA phylogeny, suggesting slower processes of fixation compared to the mtDNA sequences. In a side-by-side comparison with their mtDNA sister lineage, the nucleotide substitution rate of 1.66 x 10(-8) substitutions/site/year in the numts was approximately equal to the average rate of mtDNA in this group but substantially higher than previous estimates of neutral nuclear rates in vertebrates. The numt clade was affected by several deletions but no insertions, with estimates of nucleotide loss exceeding the rate of nucleotide substitutions by approximately five times. The young age of the Rivacindela numt clade, their absence in species outside of a narrow lineage of related individuals, and the high rate of deletions suggest that insertions do not persist in this group, which is consistent with the view that comparatively small genomes as those of Coleoptera harbor fewer mitochondrial and other nuclear pseudogenes.