Mitonuclear discordance

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.


Andersen MJ, McCullough JM, Gyllenhaal EF, Mapel XM, Haryoko T, Jonsson KA, and Joseph L (2021), Complex histories of gene flow and a mitochondrial capture event in a nonsister pair of birds, Mol. Ecol. 30, 2078-2103. (pdf)

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Bonnet T, Leblois R, Rousset F, and Crochet PA (2017), A reassessmant of explanations for discordant introgressions of mitochondrial and nuclear genomes, Evolution 712140-58. (abstract)

Burton RS (2022), The role of mitonuclear incompatibilities in allopatric speciation, Cell. Mol. Life Sci. 79, e:103. (abstract)

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)

Denton RD, Kenyon LJ, Greenwald KR, and Gibbs HL (2014), Evolutionary basis of mitonuclear discordance between sister species in mole salamanders (Ambystoma sp.), MolEcol. 23, 2811-24. (abstract)

DeRaad DA, McCullough JM, DeCicco LH, Hime PM, Joseph L, Andersen MJ, and Moyle RG (2023), Mitonuclear discordance results from incomplete lineage sorting, with no detectable evidence for gene flow, in a rapid radiation of Todiramphus kingfishers, Mol. Ecol. 32, 4844-62. (abstract) 

Després L (2019), One, two or more species? Mitonuclear discordance and species delimitation, MolEcol. 28, 3845-47. (pdf)

Dias C, de Araújo Lima K, Araripe J, Aleixo A, Vallinoto M, Sampaio I, Schneider H, and Sena do Rêgo P (2018), Mitochondrial introgression obscures phylogenetic relationships among manakins of the genus Lepidothrix (Aves: Pipridae), MolPhylogenetEvol. 126, 314-320. (abstract)

Fedorov VB, Trucchi E, Goropashnaya AV, and Stenseth NC (2022), Conflicting nuclear and mitogenome phylogenies reveal ancient mitochondrial replacement between two North American species of collared lemmings (Dicrostonyx groenlandicus, D. hudsonius), Mol. Phylogenet. Evol. 168, e:107399. (abstract)

Gonzalez JCT, Sheldon BC, Collar NJ, and Tobias JA (2013), A comprehensive molecular phylogeny for the hornbills (Aves: Bucerotidae), Mol. Phylogenet. Evol. 67, 468-483. (abstract)

Hill GE (2015), Mitonuclear ecology, MolBiolEvol. 32, 1917-27. (free pdf)

Hill GE (2019), Reconciling the mitonuclear compatibility species concept with rampant mitochondrial introgression, IntegrCompBiol. 59, 912-924. (free pdf)

Kimball RT, Guido M, Hosner PA, and Braun EL (2021), When good mitochondria go bad: cyto-nuclear discordance in landfowl (Aves: Galliformes), Gene 801, e:145841. (abstract) 

Kryukov AP, Goroshko OA, Arkhipov VY, Red’kin YA, Lee SI, Dorda BA, Kryukov KA, Kapun M, and Haring E (2022), Introgression at the emerging secondary contact zone of magpie Pica pica subspecies (Aves: Corvidae): integrating data on nuclear and mitochondrial markers, vocalizations, and field observations, Org. Divers. Evol. 22, 1037-64. (pdf)

Mackiewicz P, Urantówka AD, Kroczak A, and Mackiewicz D (2019), Resolving phylogenetic relationships within Passeriformes based on mitochondrial genes and inferring the evolution of their mitogenomes in terms of duplications, Genome BiolEvol. 11, 2824-49. (free pdf)

McElroy K, Black A, Dolman G, Horton P, Pedler L, Campbell CD, and Joseph L (2020), Robbery in progress: historical museum collections bring to light a mitochondrial capture within a bird species widespread across southern Australia, the Copperback Quail-thrush Cinclosoma clarum, Ecol. Evol. 10, 6785-93. (pdf)

Morgan-Richards M, Bulgarella M, Sivyer L, Dowle EJ, Hale M, McKean NE, and Trewick SA (2017), Explaining large mitochondrial sequence differences within a population sample, R. Socopen sci. 4, e:170730. (pdf)

Nacer DF, and do Amaral FP (2017), Striking pseudogenization in avian phylogenetics: numts are large and common in falcons, MolPhylogenetEvol. 115, 1-6. (free pdf)

Nikelski E, Rubtsov AS, and Irwin D (2023), High heterogeneity in genomic differentiation between phenotypically divergent songbirds: a test of mitonuclear co-introgression, Heredity 130, 1-13. (abstract) 

Ostrow EN, Catanach TA, Bates JM, Aleixo A, and Weckstein JD (2023), Phylogenomic analysis confirms the relationships among toucans, toucan-barbets, and New World barbets but reveals paraphyly of Selenidera toucanets and evidence for mitonuclear discordance, Ornithology 140, e:ukad022. (abstract)

Ostrow EN, DeCicco LH, and Moyle RG (2023), Range-wide phylogenomics of the Great Horned Owl (Bubo virginianus) reveals deep north-south divergence in northern Peru, PeerJ 11, e:15787. (abstract)

Palacios C, Campagna L, Parra JL, and Cadena CD (2023), Mito-nuclear discordance in the phenotypically variable Andean hummingbirds Coeligena bonapartei and Coeligena helianthea (Trochilidae), Biol. J. Linn. Soc. 139, 145-157. (abstract)

Peters  JL, Bolender KA, and Pearce JM (2012), Behavioural vs. molecular sources of conflict between nuclear and mitochondrial DNA: the role of male-biased dispersal in a Holarctic sea duck, MolEcol. 21, 3562-75. (abstract)

Peters JL, Winker K, Millam KC, Lavretsky P, Kulikova I, Wilson RE, Zhuravlev YN, and McCracken KG (2014), Mito-nuclear discord in six congeneric lineages of Holarctic ducks (genus Anas), Mol. Ecol. 23, 2961-74. (abstract) 

Shen YY, Dai K, Cao C, Murphy RW, Shen XJ, and Zhang YP (2014), The updated phylogenies of the Phasianidae based on combined data of nuclear and mitochondrial DNA, PLoS ONE 9, e:95786. (pdf)

Shipham A, Schmidt DJ, Joseph L, and Hughes JM (2017), A genomic approach reinforces a hypothesis of mitochondrial capture in eastern Australian rosellas, Auk 134, 181-192. (free pdf)

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Spaulding F, McLaughlin JF, Cheek RG, McCracken KG, Glenn TC, and Winker K (2023), Population genomics indicate three different modes of divergence and speciation with gene flow in the green-winged teal duck complex, Mol. Phylogenet. Evol. 182, e:107733. (abstract)

Tamashiro RA, White ND, Braun MJ, Faircloth BC, Braun EL, and Kimball RT (2019), What are the roles of taxon sampling and model fit in tests of cyto-nuclear discordance using avian mitogenomic data?, Mol. Phylogenet. Evol. 130, 132-142. (open manuscript)

Taylor RS, Bramwell AC, Clemente-Carvalho R, Cairns NA, Bonier F, Dares K, and Lougheed C (2021), Cytonuclear discordance in crowned-sparrows, Zonotrichia atricapilla and Zonotrichia leucophrys, Mol. Phylogenet. Evol. 162, e:107216. (free pdf) 

Toews DPL, and Brelsford A (2012), The biogeography of mitochondrial and nuclear discordance in animals, Mol. Ecol. 21, 3907-30. (pdf) 

Zhang D, She H, Wang S, Wang H, Li S, Cheng Y, Song G, Jia C, Qu Y, Rheindt FE, Olsson U, Alström P, and Lei F (2023), Phylogenetic conflict between species tree and maternally inherited gene trees in a clade of Emberiza buntings (Aves: Emberizidae), Syst. Biol. (abstract)