Summary
In many taxa of bilaterian animals, there is little diversity in mitochondrial genotype within a species but substantial variation between species. This pattern is the basis for mt DNA barcoding as a means for identifying species. Despite the failure of neutral theory to explain this pattern of mt DNA sequence variation, most of the variation in the nucleotide sequence of barcode genes is neutral with respect to function. In other words, changes to the nucleotide sequence of mt DNA are evolving in a non-neutral manner despite the fact that they have no functional consequences. A solution to this paradox is that directional selection on any gene in the mitochondrial genome, including genes that code for rRNA and tRNA, can lead to selective sweeps that eliminate genetic diversity and fix neutral or slightly deleterious alleles in other parts of the mt genome. It is proposed that genetic hitchhiking by neutral elements in the DNA barcoding region explains how the DNA barcode gap evolves. This hypothesis proposes that mt DNA barcodes will only be effective when there is little or no recombination of mt genes, potentially explaining why DNA barcoding fails for some groups of eukaryotes.