Fig. 1

Evolution of mtRNAs and mtRNA insertions in the nuclear genome. The gray outline shows the phylogenetic relationship of five species A, B, C, D, and E as a dated tree, i.e., the “y-axis” corresponds to time before the present. Mitochondrial DNA, usually transmitted through the maternal lineages, faithfully follows the species tree (red tree); its leaves are the extant mtRNAs. Insertions of mitochondrial material occur at random time points independently in the different lineages (red circles). Following an insertion, the inserted material (numtDNA) evolves independently, as shown by blue trees within the species trees. Blue bullets denote the MTLs, and dashed lines indicate MTLs that have been removed by genomic events or that have mutated beyond the detection threshold. Each species contains MTLs that have been inserted at different times. Orthologous MTLs derive from the same insertion event (here denoted by the same blue numbers). Sequence comparison between MTLs or MTLs and mtRNAs shows the substitutions accumulated along the path between them. Orthologous MTLs are connected by blue path only, along which only selective pressures in the nuclear genome have left their traces. Comparisons between MTLs and mtRNAs in the same species almost always trace back to the insertion event. Their sequence differences thus record both the selective pressures acting on mtRNAs (red part of the path) and those acting on the inserted MTL (blue part of the path). Rare exceptions are duplications of MTLs after their insertion (yellow ball on the right). A comparison of arbitrary pairs of MTLs from different species in general corresponds to MTLs deriving from distinct insertion events. Their common history is a mixture of red paths (between the two insertion events) and blue paths (following the insertion events) and thus a mixture of selective pressures on mtRNA and MTL. These cannot be disentangled without exact dating of the insertion events