Mitonuclear discordance

Phylogenetic assumptions based on mitogenomes in most cases are congruent with those based on genomic and transcriptomic analyses. However, sometimes the resulting phylogenies differ with respect to the placement of individual taxa. The topological discordance between trees based on mitogenomes vs nuclear genes is referred to as mitonuclear discordance. The underlying reasons for this phenomenon are unknown. 


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)

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)

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)

Hinojosa JC, Koubínová D, Szenteczki MA, Pitteloud C, Dincā V, Alvarez N, and Vila R (2019), A mirage of cryptic species: genomics uncover striking mitonuclear discordance in the butterfly Thymelicus sylvestris, MolEcol. 28, 3857-68. (abstract)

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)

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)

McGuire JA, Linkem CW, Koo MS, Hutchison DW, Lappin AK, Orange DI, Lemos-Espinal J, Riddle BR, and Jaeger JR (2007), Mitochondrial introgression and incomplete lineage sorting through space and time: phylogenetics of crotaphytid lizards, Evolution 61, 2879-97. (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 (2021), Mitonuclear co-introgression opposes genetic differentiation between phenotypically divergent songbirds, bioRxiv (pdf)

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) 

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)

Sloan DB, Havird JC, and Sharbrough J (2016), The on-again, off-again relationship between mitochondrial genomes and species boundaries, Mol. Ecol. 26, 2212-36. (pdf)

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) 

Thanou E, Kornilios P, Lamberakis P, and Leaché AD (2020), Genomic and mitochondrial evidence of ancient isolations and extreme introgression in the four-lined snake, CurrZool. 66, 99-111. (free pdf)

Thielsch A, Knell A, Mohammadyari A, Petrusek A, and Schwenk K (2017), Divergent clades or cryptic species? Mito-nuclear discordance in a Daphnia species complex, BMC EcolEvol. 17, e:227. (pdf)

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