In most cases, phylogenetic assumptions based on mitogenomes perfectly match those based on nuclear/genomic analyses. Sometimes, however, the resulting phylogenies differ with respect to the placement of some taxa. The topological discordance between phylogenies based on mitogenomes vs. nuclear genes is referred to as mitonuclear discordance. The underlying reasons are thought to be incomplete lineage sorting (ILS) and introgressive hybridisation.

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