For many years, individual mitochondrial elements (mostly CO1, CYB, ND2, and the control region) have been used in phylogenetic studies. It turned out, however, that gene trees that are derived from individual coding genes or the control region often differ from each other and from species trees based on nuclear DNA.

In contrast, phylogenies that are based on entire mitochondrial genomes (mitogenomes) are mostly concordant with nuclear DNA-based species trees. Because of the observed gene-tree discordance among individual mtDNA genes, phylogenetic studies should no longer rely on limited sets of mitochondrial genes but on mitogenomes (Meiklejohn et al., 2014; Havird & Santos, 2014; Campillo et al., 2019).

Sometimes, however, even mitogenomic and nuclear DNA differ in their phylogenetic signatures. This phenomenon is referred to as mitonuclear discordance. Ultimately, phylogenies should be based on either nuclear, or a combination of mitogenomic and nuclear DNA (e.g. Rubinoff & Holland, 2005).

References

Campillo LC, Burns KJ, Moyle RG, and Manthey JD (2019), Mitochondrial genomes of the bird genus Piranga: rates of sequence evolution, and discordance between mitochondrial and nuclear markers, Mitochondrial DNA B 4, 2566-69. (free pdf)

De Panis D, Lambertucci SA, Wiemeyer G, Dopazo H, Almeida FC, Mazzoni CJ, Gut M, Gut I, and Padró J (2021), Mitogenomic analysis of extant condor species provides insights into the molecular evolution of vultures, Sci. Rep. 11, e:17109. (pdf)

Havird JC, and Santos SR (2014), Performance of single and concatenated sets of mitochondrial genes at inferring metazoan relationships relative to full mitogenome data, PLoS ONE 9, e:84080. (pdf)

Meiklejohn KA, Danielson MJ, Faircloth BC, Glenn TC, Braun EL, and Kimball RT (2014), Incongruence among different mitochondrial regions: a case study using complete mitogenomes, Mol. Phylogenet. Evol. 78, 314-323. (abstract)

Powell AFLA, Barker FK, and Lanyon SM (2013), Empirical evaluation of partitioning schemes for phylogenetic analyses of mitogenomic data: an avian case study, Mol. Phylogenet. Evol. 66, 69-79. (abstract)

Rubinoff D, and Holland BS (2005), Between two extremes: mitochondrial DNA is neither the panacea nor the nemesis of phylogenetic and taxonomic inference, Syst. Biol. 54, 952-961. (free pdf)

van den Burg MP, and Vieites DR (2023), Bird genetic databases need improved curation and error reporting to NCBI, Ibis 165, 472-481. (pdf)