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.