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). 

References/Literature

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, 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)