Recombination of human mitochondrial DNA.

Human mitochondrial DNA (mtDNA) is a 16.5-kb, circular genome essential for the maintenance of mitochondrial function and is present in multiple copies in most cell types. High sequence divergence and maternal inheritance make mtDNA useful in tracing human lineages. Whether recombination occurs between mitochondrial genomes is a longstanding question in mitochondrial biology, human evolution, and population studies (1). MtDNA recombination occurs in yeast, and recombinant mtDNA has been found in several animal species (2); however, the evidence for recombination between heterologous mtDNA in humans is controversial (1). We searched for mtDNA recombinants in muscle tissue of an individual with paternal inheritance of the mitochondrial genome (3), where heterologous (paternal and maternal) mtDNAs are mixed and thus may have an opportunity to recombine. DNA was cleaved (4) by a paternal-specific restriction endonuclease at position 14,793 (fig. S1) to exclude a 10:1 excess of paternal mtDNA. It was then subjected to single-molecule polymerase chain reaction (PCR), which avoids in vitro recombination and has been successfully used to isolate nuclear DNA recombinants (5). In singlemolecule PCR, each PCR product is a clone of identical molecules that originate from a single template. We recovered 450 PCR clones containing a maternal sequence at position 14,793 and screened them for paternal sequences at position 73 (fig. S1). We found 33 such clones. Their sequences revealed alternating maternal and paternal segments, a hallmark of recombination (Fig. 1). Multiple lines of evidence, including a control experiment with a reconstructed 10:1 mixture of paternal and maternal DNA, support an in vivo origin of these recombinants (supporting online text). The recombinants fall into two structural classes (Fig. 1): class 1, with a short paternal sequence inserted into a mostly maternal molecule, and class 2, with a maternal sequence flanked by paternal sequences. Furthermore,