Modern phylogenetics no longer relies on morphology, but on varying sets of mitochondrial and nuclear DNA sequences. In a few studies, RNA transcriptomes are evaluated. Molecular and morphological data are sometimes combined to propose “total evidence” phylogenies, but I will not take these hybrid studies into account. 


Somatic avian cells contain a single nucleus and numerous mitochondria, both organelles being provided with DNA. While nuclear DNA (nDNA) is distributed over several chromosomes that contain complex elements like microsatellites, transposable elements, introns, and numts, mitochondrial DNA (mtDNA) contains only a limited number of plain elements that are located on a single double-stranded circular molecule. Mitochondria are uniparentally inherited via egg cells, whereas nuclear DNA is biparentally inherited via sperm and egg cells. As a consequence, only nuclear DNA is diploid and subject to recombination (via meiotic chromosome segregation, meiotic crossing-over, and zygote formation). Since protein-coding mitochondrial DNA has a higher mutation rate than protein-coding nuclear DNA, mitochondrial genes are particularly suitable for studying shallow (intra- and interspecific) phylogenetic relationships. 

For many years, selected mitochondrial elements (mostly CO1, CYB, ND2, and the control region) have been used in phylogenetic studies. While individual gene trees derived from coding genes and the control region usually differ from each other and from species trees based on nuclear DNA, phylogenies that are based on entire 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 the mitogenome as a whole (Meiklejohn et al., 2014; Havird & Santos, 2014; Campillo et al., 2019). For drawing phylogenetic inferences it may, however, be useful to partition the mitogenome into subsets, e.g. rRNA genes, tRNA genes, selected codon positions of protein-coding genes, and control region (Powell et al., 2013; de Panis et al., 2021). 

In some cases, nDNA and mtDNA differ in their phylogenetic signatures. This phenomenon is referred to as cyto-nuclear discordance. As a consequence, integrated phylogenetics are based on a combination of mitochondrial and nuclear DNA sources (e.g. Rubinoff & Holland, 2005). 


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 insight into the molecular evolution of vultures, SciRep. 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, MolPhylogenetEvol. 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, MolPhylogenetEvol. 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, SystBiol. 54, 952-961. (free pdf)