How clonal are human mitochondria?

Phylogenetic trees constructed using human mitochondrial sequences contain a large number of homoplasies. These are due either to repeated mutation or to recombination between mitochondrial lineages. We show that a tree const ructed using synonymous Variation in the protein coding sequences of 29 lar gely complete human mitochondrial molecules contains 22 homoplasies at 32 p hylogenetically informative sites. This level of homoplasy is very unlikely if inheritance is clonal, even if we take into account base composition bi as. There must either be 'hypervariable' sites or recombination between mit ochondria. We present evidence which suggests that hypervariable sites do n ot exist in our data. It therefore seems likely that recombination has occu rred between mitochondrial lineages in humans.