Duplication and Concerted Evolution of the Mitochondrial Control Region in the Parrot Genus Amazona

We report a duplication and rearrangement of the mitochondrialgenome involving the control region of parrots in the genusAmazona. This rearrangement results in a gene order of cytochromeb/tRNA^Thr/pND6/pGlu/CR1/tRNA^Pro/NADH dehydrogenase 6/tRNA^Glu/CR2/tRNA^Phe/12srRNA, where CR1 and CR2 refer to duplicate control regions,and pND6 and pGlu indicate presumed pseudogenes. In contrastto previous reports of duplications involving the control regionsof birds, neither copy of the parrot control region shows anyindications of degeneration. Rather, both copies contain manyof the conserved sequence features typically found in aviancontrol regions, including the goose hairpin, TASs, the F, C,and D boxes, conserved sequence box 1 (CSB1), and an apparenthomolog to the mammalian CSB3. We conducted a phylogenetic analysisof homologous portions of the duplicate control regions from21 individuals representing four species of Amazona (A. ochrocephala,A. autumnalis, A. farinosa, and A. amazonica) and Pionus chalcopterus.This analysis revealed that an individual's two control regioncopies (i.e., the paralogous copies) were typically more closelyrelated to one another than to corresponding segments of otherindividuals (i.e., the orthologous copies). The average sequencedivergence of the paralogous control region copies within anindividual was 1.4%, versus a mean value of 4.1% between controlregion orthologs representing nearest phylogenetic neighbors.No differences were found between the paralogous copies in eitherthe rate or the pattern in which the two copies accumulatedbase pair changes. This pattern suggests concerted evolutionof the two control regions, perhaps through occasional geneconversion events. We estimated that gene conversion eventsoccurred on average every 34,670 ± 18,400 years basedon pairwise distances between the paralogous control regionsequences of each individual. Our results add to the growingbody of work indicating that under some circumstances duplicatedmitochondrial control regions are retained through evolutionarytime rather than degenerating and being lost, presumably dueto selection for a small mitochondrial genome.