Cytonuclear discordance

Cytonuclear discordance describes the discrepancy in phylogenetic relationships using mitochondrial DNA (mtDNA) versus nuclear genes (or nuclear DNA, nDNA). In other words, mitochondrial and nuclear gene sequences may lead to different, if not contradictory conclusions with respect to the relationships among species. In theory, nuclear DNA and mt DNA sequences should lead to similar phylogenetic relationships among species but this is often not the case.

An example are Australian rock-wallabies (Petrogale) in which several species form a monophyletic group with nDNA genes, but not with mtDNA. This cytonuclear discordance involves at least four operational taxonomic units (OTUs) across four species.

Many other taxonomic groups display cytonuclear discordance, e.g. Burmese pythons or vipers of the genus Cerastes.