Recombination in animal mitochondrial DNA: evidence from published sequences.

The question of whether animal mitochondrial DNA (mtDNA) undergoes recombination has recently been the subject of intense debate. In a recent paper (Ladoukakis and Zouros 2001), we presented evidence for mtDNA recombination from direct recovery of recombinant molecules in the gonads of several males of the mussel Mytilus galloprovincialis. Because in this species there exist two lineages of mitochondrial genomes, each with a different mode of transmission (a phenomenon known as doubly uniparental inheritance [DUI] of mtDNA; Zouros et al. 1994), the possibility existed that mtDNA recombination was a peculiarity of DUI. Here, we present evidence for recombination in three different species with standard maternal mtDNA inheritance: a crustacean, an amphibian, and a mammal. Our initial objective was to apply the method of Awadalla, Eyre-Walker, and Maynard Smith (1999) to cases drawn from the literature. We used the study by Meyran, Gielly, and Taberlet (1998) of a segment of cytochrome oxidase I in Gammarus fossarum as one such case. In the process of analyzing these data, we realized that the signature of recombination was clearly preserved in the amino acid sequences. As a result, we turned our search to studies that reported coding mtDNA sequences with substantial differences at the amino acid level, even if the sequences were drawn from different species of a genus. We confined the search to within volume 16 (year 2000) of Molecular Phylogenetics and Evolution, from which we selected the study by Martin et al. (2000) on rodents of the genus Apodemus and the study by Sumida, Ogata, and Nishioka (2000) on frogs of the genus Rana. These two studies report only parts of the known sequences of the cytochrome b gene, but our analysis was based on the full DNA sequences, which we retrieved from GenBank (accession numbers and references in fig. 1). The protocol of the analysis was as follows: