RNA editing and phylogenetic reconstruction in two monocot mitochondrial genes

The mitochondrial genome of land plants has a high level of evolutionary plasticity that may impair its use in phylogenetic analyses. Among the most challenging properties are RNA editing and retroprocessing of edited mRNA into the mitochondrial and/or nuclear genome as processed paralogs. Using mtDNA sequence data encoding for apocytochrome B ( cob ) and the alpha subunit of F1‐ATP synthase ( atp1 ) across the monocots, and in two subclades, alismatids and Agavaceae, it is shown that edited sites, despite being more homoplasious than non‐edited sites, perform well on the trees, and that they are not randomly distributed among taxa but have a clade specific distribution. Indirect evidence for the presence of processed paralogs is presented and their likely evolutionary fate discussed.