Analysis of European mtDNAs for recombination

The standard paradigm postulates that the human mitochondrial genome (mtDNA ) is strictly maternally inherited and that, consequently, mtDNA lineages a re clonal. As a result of mtDNA clonality, phylogenetic and population gene tic analyses should therefore be free of the complexities imposed by bipare ntal recombination. The use of mtDNA in analyses of human molecular evoluti on is contingent, in fact, on clonality, which is also a condition that is critical both for forensic studies and for understanding the transmission o f pathogenic mtDNA mutations within families. This paradigm, however, has b een challenged recently by Eyre-Walker and colleagues. Using two different tests, they have concluded that recombination has contributed to the distri bution of mtDNA polymorphisms within the human population. We have assemble d a database that comprises the complete sequences of 64 European and 2 Afr ican mtDNAs. When this set of sequences was analyzed using any of three mea sures of linkage disequilibrium, one of the tests of Eyre-Walker and collea gues, there was no evidence for mtDNA recombination. When their test for ex cess homoplasies was applied to our set of sequences, only a slight excess of homoplasies was observed. We discuss possible reasons that our results d iffer from those of Eyre-Walker and colleagues. When we take the various re sults together, our conclusion is that mtDNA recombination has not been suf ficiently frequent during human evolution to overturn the standard paradigm .