Mitochondrial DNA (mtDNA)


Eukaryotic cells typically contain several mitochondria, each containing several double-stranded circular DNA molecules. In vertebrate mitochondria, gene content, genome architecture, and gene strand asymmetry are almost invariant (Gissi et al., 2008). 

Critical comments

In mitogenomics, there is a lack of basic conventions: 

(I) there is no unequivocal assignment of strands. Historically, the strand with the lower G+T content was referred to as (L)-strand (Anderson et al., 1981). However, present-day strand assignments in vertebrates do not comply with the original definition (Lima & Prosdocimi, 2017). Recommendation: to avoid confusion, the strands should be distinguished by the relative number of genes contained, with the (+)-strand being the one containing more genes than the (–)-strand (Taanman 1999, fig.1; Gissi et al., 2008; Lima & Prosdocimi, 2017). 

(II) annotations may be based on either (+)- or (–)- strand. Recommendation: annotations should always be based on the (+)-strand. 

(III) annotations may start with any gene or the control region; they can even start within the control region. Recommendation: vertebrate annotations should start with gene F (Montaña-Lozano et al., 2022, Fig. 3) and  have the control region at the end. 

(IV) circular maps may be oriented with genes and the control region arranged either clockwise or counter-clockwise. Recommendation: circular maps should always be displayed in clockwise orientation. 

(V) circular maps may display any gene or the control region at the 12 o’clock position. Recommendation: circular maps should always display gene F (the DNA template for tRNA Phe) at the top center, and the control region immediately left of it. 

Mitogenome composition

In the avian ground pattern, the mitochondrial genome (mitogenome) contains 2 rRNA genes, 22 tRNA genes, 13 protein-coding genes, an non-coding control region, and possibly an extended tandem duplication. Compared to other vertebrates, in avian mitogenomes the positions of the gene clusters CYB:T:P and ND6:E are interchanged. The derived gene order CYB:T:P:ND6:E thus represents an avian ground-pattern autapomorphy (Montaña-Lozano et al., 2022). 

Circular map depicting the putative ancestral avian mitogenome organisation (not to scale). The tandem duplication (TD), which extends between the non-coding control region (CR) and F, is shown separately as it is absent in many bird taxa. When fully developed, it contains a pseudogene Ψ (a degenerate copy of CYB), four functional genes, and an extended control region (Urantówka et al., 2020). Transfer RNA genes are depicted by their one-letter amino-acid code [with L1 = trnL (CUN), L2 = trnL(UUR), S1 = trnS(AGN), and S2 = trnS(UCN)]. 

Avian tandem duplication

Most avian mitogenomes are distinguished from typical vertebrate mitogenomes by the presence of a large tandem duplication comprising several genes and the control region (Urantówka et al., 2018, 2020, 2021; Mackiewicz et al., 2019). Dating back to Haring et al. (1999) this region is also referred to as “pseudo-control region”. Duplicated genes are often (largely) identical to their counterpart, a phenomenon referred to as “concerted evolution” (Urantówka et al., 2021). The molecular mechanism underlying this phenomenon is unknown. In Galloanserae, tandem duplications are entirely absent, and it is unclear whether the lack is primary or secondary. Although representing a putative ground-pattern trait of most avian orders (Mackiewicz et al., 2019), there is a considerable amount of homoplasy in the observed configurations: 

Schematic map of the multigene tandem duplication (type 0) and variously derived configurations (types 1-7). The CR copy 1 was lost in moa (Dinornithiformes), recently extinct palaeognaths from New Zealand (type 7). 

Annotation of mitogenomes

After sequencing, DNA strands have to be analysed in order to identify individual tRNA-, rRNA-, and protein-coding genes, the extended non-coding region commonly referred to as control region, as well as intergenic spacers and overlaps. For protein-coding genes, putative start and stop codons need to be determined. Process and outcome of this procedure are referred to as "annotation". It should be noted, however, that the exact limits of genes are often not recognisable with certainty (Slack et al., 2003). 

Summary of avian mitochondrial annotations. Duplicated regions are not considered. Partial stop codons (TA and T) are completed to UAA by posttranscriptional polyadenylation. 


The protein-coding gene ND3 is peculiar in having an extra nucleotide (mostly cytosine) at position 174. Its presence probably pertains to the avian ground pattern, but it has been lost many times during avian evolution (Jing et al., 2020, suppl. 12). The extra base, however, appears not to be processed during translation, as the downstream reading frame and amino-acid sequence are conserved due to a translational +1 frameshift (Mindell et al., 1998b; Al-Arab et al., 2017; Andreu-Sánchez et al., 2020). 

Control region

The control region (CR), which typically has a length of about 1,150 bp, is the only extended non-coding region of the mitogenome. This region is also referred to as ‘D-loop’, although the true D-loop does neither span the entire control region nor is it found in all mtDNA molecules at any given time (Pereira et al., 2008; Nicholls & Minczuk, 2014). 

For descriptive purposes, Brown et al. (1986) first divided the control region into three domains, with a central conserved domain that is flanked by highly variable domains. However, exact boundaries to delimit the domains have not been defined. 

Variation in the length of the CR, due to repeated terminal sequences, accounts for much mtDNA size variability. 

Both mitochondrial DNA strands are transcribed as long polycistronic molecules, with transcription initiated from the heavy-strand promoter (HSP) and light-strand promoter (LSP), respectively. 

Comparative mitogenomics

Before phylogenetic analyses can be performed, annotated mtDNA sequences have to be aligned, i.e. homologous nucleotide positions (orthologs, “sites”) need to be determined (Cucini et al, 2021). This process relies on the identification of conserved blocks (Castresana, 2000). 

Phylogenetic studies based on mitogenomes

For decades, some of the coding genes (e.g. CO1, CYB, ND2) have routinely been used in phylogenetic studies. While individual gene trees derived from the coding genes and 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 between 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). Since protein-coding mtDNA has a higher mutation rate than protein-coding nuclear DNA, mitochondrial genes are particularly suitable for studying shallow (intra- and interspecific) phylogenetic relationships. 

It may be helpful to partition the mitogenome into various subsets (e.g. according to codon position, RNA secondary structure pairing, and the coding/non-coding distinction) to accommodate data heterogeneity (Powell et al., 2012; de Panis et al., 2021). 

COI barcoding

DNA barcoding is a method of species identification by comparing DNA sequences of an unknown sample with DNA sequences of known species via public online reference databases. For animal species, the sequence used for DNA barcoding is a 648-bp fragment of the mitochondrial CO1 gene. The length of the fragment is determined by the limits of Sanger sequencing. 

COI-barcoding has been chosen, because it turned out that most animal species (except cnidarians) are separated from congeneric species by CO1 sequence divergences higher than 2%, while sequence divergences among conspecifics are usually less than 2% (Hebert et al., 2003). This observation is referred to as the “barcode gap” (Meyer & Paulay, 2005). More than 94% of morphologically defined bird species have been confirmed with COI as a species-level marker gene (Wang et al., 2020). 

In a comparative avian mitogenomic study, the CO1 gene proved to be the one with the least amount of rate heterogeneity across avian orders, thus being closest to a “molecular clock” (Pacheco et al., 2011). This explains its suitability as a reasonable indicator of species limits. 


Abbott CL, Double MC, Trueman JWH, Robinson A, and Cockburn A (2005), An unusual source of apparent mitochondrial heteroplasmy: duplicate mitochondrial control regions in Thalassarche albatrosses, Mol. Ecol. 14, 3605-13. (abstract)

Adawaren EO, Du Plessis M, Suleman E, Kindler D, Oosthuizen AO, Mukandiwa L, and Naidoo V (2020), The complete mitochondrial genome of Gyps coprotheres (Aves, Accipitridae, Accipitriformes): phylogenetic analysis of mitogenome among raptors, PeerJ 8, e:10034. (pdf)

Akiyama T, Nishida C, Momose K, Onuma M, Takami K, and masuda R (2017), Gene duplication and concerted evolution of mitochondrial DNA in crane species, Mol. Phylogenet. Evol. 106, 158-263. (abstract)

Al-Arab M, Höner zu Siederdissen C, Tout K, and Sahyoun AH (2017), Accurate annotation of protein-coding genes in mitochondrial genomes, Mol. Phylogenet. Evol. 106, 209-216. (abstract)

Aleix-Mata G, Ruiz-Ruano FJ, Perez JM, Sarasa M, and Sanchez A (2019), Complete mitochondrial genomes of the Western Capercaillie Tetrao urogallus (Phasianidae, Tetraoninae), Zootaxa 4550, 585-593. (pdf)

Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, and Sanger F (1981), Sequence and organization of  the human mitochondrial genome, Nature 290, 457-465. (abstract)

Andreu-Sánchez S, Chen W, Stiller J, and Zhang G (2020), Multiple origins of a frame shift insertion in a mitochondrial gene in birds and turtles, GigaScience 10, 1-11. (free pdf)

Anmarkrud JA, and Lifjeld JT (2017), Complete mitochondrial genomes of eleven extinct or possibly extinct bird species, Mol. Ecol. Res. 17, 334-341. (abstract)

Baba Y, Fujimaki Y, Yoshii R, and Koike H (2001), Genetic variability in the mitochondrial control region of the Japanese Rock Ptarmigan Lagopus mutus japonicus, Jpn. J. Ornithol. 50, 53-64. (free pdf)

Baker AJ, and Marshall HD (1997), Mitochondrial control-region sequences as tools for understanding the evolution of avian taxa, In: “Avian molecular systematics and evolution” (Mindell DP, ed.), pp. 49-80, Academic Press, NY. (link)

Barker FK, Benesh MK, Vandergon AJ, and Lanyon Sam (2012), Contrasting evolutionary dynamics and information content of the avian mitochondrial control region and ND2 gene, PLOS ONE 7, e:46403. (pdf)

Barreira AS, Lijtmaer DA, and Tubaro PL (2016), The multiple applications of DNA barcodes in avian evolutionary studies, Genome 59, 899-911. (free pdf)

Bensch S, and Härlid A (2000), Mitochondrial genomic rearrangements in songbirds, Mol. Biol. Evol. 17, 107-113. (free pdf)

Berg T, Moum T, and Johansen S (1995), Variable numbers of simple tandem repeats make birds of the order Ciconiiformes heteroplasmic in their mitochondrial genomes, Curr. Genet. 27, 257-262. (abstract)

Bi D, Ding H, Wang Q, Jiang L, Lu W, Zhu R, Zeng J, Zhou S, Yang X, and Kan X (2019), Two new mitogenomes of Picidae (Aves, Piciformes): sequence, structure and phylogenetic analyses, Int. J. Biol. Macromol. 133, 683-692. (abstract)

Brown GG, Gadeleta G, Pepe G, Saccone C, and Sbisá E (1986), Structural conservation and variation in the D-loop containing region of vertebrate mitochondrial DNA, J. Mol. Biol. 192, 503-511. (abstract)

Bruxaux J, Gabrielli M, Ashari H, Prys-Jones R, Joseph L, Milá B, Besnard G, and Thébaud C (2018), Recovering the evolutionary history of crowned pigeons (Columbidae: Goura): implications for the biogeography and conservation of New Guinean lowland birds, Mol. Phylogenet. Evol. 120, 248-258. (abstract)

Buehler DM, and Baker AJ (2003), Characterization of the red knot (Calidris canutus) mitochondrial control region, Genome 46, 565-572. (abstract)

Cadahía L, Pinsker W, Negro JJ, Pavlicev M, Urios V, and Haring E (2009), Repeated sequence homogenisation between the control and pseudo-control regions in the mitochondrial genomes of the subfamily Aquilinae, J. Exp. Zool. 312B, 171-185. (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)

Caparroz R, Rocha AV, Cabanne GS, Tubaro P, Aleixo A, Lemmon EM, and Lemmon AR (2018), Mitogenomes of two neotropical bird species and the multiple independent origin of mitochondrial gene orders in Passeriformes, Mol. Biol. Rep. 45, 279-285. (abstract)

Castresana J (2000), Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis, Mol. Biol. Evol. 17, 540-552. (free pdf)

Chen DS, Qian CJ, Ren QQ, Wang P, Yuan J, Jiang L, Bi D, Zhang Q, Wang Y, and Kan XZ (2015), Complete mitochondrial genome of the Chinese Hwamei Garrulax canorus (Aves: Passeriformes): the first representative of the Leiotrichidae family with a duplicated control region, Genet. Mol. Res. 14, 8964-76. (pdf)

Chen P, Han Y, Zhu C, Gao B, and Ruan L (2017), Complete mitochondrial genome of Porzana fusca and Porzana pusilla and phylogenetic relationship of 16 Rallidae species, Genetica 145, 559-573. (abstract)

Chen P, Huang Z, Zhu C, Han Y, Xu Z, Sun G, Zhang Z, Zhao D, Ge G, and Luzhang R (2020), Complete mitochondrial genome and phylogenetic analysis of Gruiformes and Charadriiformes, Pakistan J. Zool. 52, 425-439. (free pdf)

Chen W, Miao K, Wang J, Wang H, Sun W, Yuan S, Luo S, Zhu C, and Chang Q (2022), Five new mitogenomes sequences of Calidrine sandpipers (Aves: Charadriiformes) and comparative mitogenomics of genus Calidris, PeerJ 10, e:13268. (pdf)

Chen Y, Li F, Zhang Q, and Wang Q (2019), Complete mitochondrial genome of the Himalayan Monal Lophophorus impejanus (Phasianidae), with phylogenetic implication, Conserv. Genet. Resour. 10, 877-880. (abstract)

Cho HJ, Eda M, Nishida S, Yasukochi Y, Chong JR, and Koike H (2009), Tandem duplication of mitochondrial DNA in the black-faced spoonbill, Platalea minor, Genes Genet. Syst. 84, 297-305. (pdf)

Clayton DA (1992), Transcription and replication of animal mitochondrial DNAs, Int. Rev. Cyt. 141, 217-232. (abstract)

Cobb LJ, Lee C, Xiao J, Yen K, Wong RG, Nakamura HK, Mehta HH, Gao Q, Ashur C, Huffman DM, Wan J, Muzumdar R, Barzilai N, and Cohen P (2016), Naturally occurring mitochondrial-derived peptides are age-dependent regulators of apoptosis, insulin sensitivity, and inflammatory markers, AGING 8, 796-809. (pdf)

Colihueque N, Gants A, and Parraguez M (2021), Revealing the diversity of Chilean birds through the COI barcode approach, ZooKeys 1016, 143-161. (free pdf)

Cooper A, Lalueza-Fox C, Anderson S, Rambaut A, Austin J, and Ward R (2001), Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution, Nature 409, 704-707. (abstract)

Crochet PA, and Desmarais E (2000), Slow rate of evolution of the mitochondrial control region of gulls (Aves: Laridae), Mol. Biol. Evol. 17, 1797-806. (free pdf)

Cucini C, Leo C, Iannoti N, Boschi S, Brunetti C, Pons J, Fanciulli PP, Frati F, Carapelli A, and Nardi F (2021), EZmito: a simple and fast tool for multiple mitogenome analyses, Mitochondrial DNA B 6, 1101-9. (pdf)

Cui B, Ma F, Wang X, Sun Y, Yu L, Li-Ling J, and Li Q (2006), Phylogenetic analyses of Fringillidae (Aves: Passeriformes) using mitochondrial tRNA gene sequences and secondary structure, J. Biol. Syst. 14, 413-424.(abstract)

Del-Rio G, Rego MA, Whitney BM, Schunck F, Silveira LF, Faircloth BC, and Brumfield RT (2021), Displaced clines in an avian hybrid zone (Thamnophilidae: Rhegmatorhina) within an Amazonian Interfluve, Evolution (abstract)

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)

Desjardins P, and Morais R (1999), Sequence and gene organization of the chicken mitochondrial genome: a novel gene order in higher vertebrates, J. Mol. Biol. 212, 599-634. (abstract)

Dey P, Sharma SK, Sarkar I, Ray SD, Pramod P, Kochiganti VHS, Quadros G, Rathore SS, Singh V, and Singh RP (2021), Complete mitogenome of endemic plum-headed parakeet Psittacula cyanocephala – characterization and phylogenetic analysis, PLOS ONE 16, e:0241098. (free pdf)

Dey P, Sarkar I, Ray SD, Pramod P, Natarajan J, and Singh RP (2022), Genome survey sequencing, microsatellite motif identification and complete mitogenome of Turnix suscitator – novel implications for Charadriiformes phylogeny, Helyon (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)

Donath A, Jühling F, Al-Arab M, Bernhart SH, Reinhardt F, Stadler PF, Middendorf M, and Bernt M (2019), Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes, Nucleic Acids Res. 47, 10543-52. (free pdf)

Du C, Zhang L, Lu T, MA J, Zeng C, Yue B, and Zhang ax (2017), Mitochondrial genomes of blister beetles (Coleoptera, Meloidae) and two large inter genie spacers in Hycleus genera, BMC Genomics 18, e:698. (pdf)

Du C, Liu Y, and Fu Z (2020), The complete mitochondrial genome of the Eurasian wryneck Jynx torquilla (Aves: Piciformes: Picidae) and its phylogenetic inference, Zootaxa 4810, 351-360. (abstract)

Eberhard JR, and Wright TF (2016), Rearrangement and evolution of mitochondrial genomes in parrots, Mol. Phylogenet. Evol. 94, 34-46. (abstract) 

Eberhard JR, Wright TF, and Bermingham E (2001), Duplication and concerted evolution of the mitochondrial control region in the parrot genus Amazona, Mol. Biol. Evol. 18, 1330-1342. (free pdf) 

Falkenberg M, and Gustafsson CM (2020), Mammalian mitochondrial DNA replication and mechanisms of deletion formation, Crit. Rev. Biochem. Mol. Biol. 55, 509-524. (pdf)

Formenti G, Rhie A, Balacco J, Haase B, Mountcastle J, Fedrigo O, Brown S, Capodiferro MR, Al-Ajli FO, Ambrosini R, Houde P, Koren S, Oliver K, Smith M, Skelton J, Betteridge E, Dolucan J, Corton C, Bista I, Torrance J, Tracey A, Wood J, Uliano-Silva M, Howe K, McCarthy S, Winkler S, Kwak W, Korlach J, Fungtammasan A, Fordham D, Costa V, Mayes S, Chiara M, Horner DS, Myers E, Durbin R, Achilli A, Braun EL, Phillippy AM, and Jarvis ED (2021), Complete vertebrate mitogenomes reveal widespread repeats and gene duplications, Genome Biol. 22, e:120. (pdf)

Galtier N, Nabholz B, Glémin S, and Hurst GDD (2009), Mitochondrial DNA as a marker of molecular diversity: a reappraisal, Mol. Ecol. 18, 4541-50. (free pdf)

Gao J, Wang G, Zhou C, Price M, Ma J, Sun X, Chen B, Zhang X, and Yue B (2021), Complete mitochondrial genome of Fulvetta cinereiceps (Sylviidae: Passeriformes) and consideration of its phylogeny within babblers, Pakistan J. Zool. 53, 2091-2104. (pdf)

Gibb GC, England R, Hartwig G, McLenachan PA, Smith BLT, McComish BJ, Cooper A, and Penny D (2015), New Zealand passerines help clarify the diversification of major songbird lineages during the Oligocene, Genome Biol. Evol. 7, 2983-95. (free pdf)

Gissi C, Ianneli F, and Pesole G and (2008), Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species, Heredity 101, 301-320. (pdf)

Gong J, Zhao R, Huang Q, Sun X, Huang L, and Jing M (2017), Two mitogenomes of Gruiformes (Amaurornis akool/A. phoenicurus) and the phylogenetic placement of Rallidae, Genes Genom. 39, 987-995. (abstract)

Gordon EL, Kimball RT, and Braun EL (2021), Protein structure, models of sequence evolution, and data type effects in phylogenetic analyses of mitochondrial data: a case study in birds, Diversity 13, e:555. (pdf)

Guan X, Silva P, Gyenai KB, Xu J, Geng T, Tu Z, Samuels DC and Smith EJ (2009), The mitochondrial genome sequence and molecular phylogeny of the turkey, Meleagris gallopavo, Animal Genet. 40, 134-141. (pdf)

Guan X, Xu J, and Smith EJ (2016), The complete mitochondrial genome sequence of the budgerigar, Melopsittacus undulatus, Mitochondrial DNA A 27, 401-402. (abstract)

Guo ZL, Zhang Y, Yang H, Wang TS, Wang WW, Zeng SS, Guo Y, Ye L, Du A, Wang ZW, Zeng SM, Tuan J, and Wang L (2022), Sequencing and structural characteristic analysis of mitochondrial genome in Zhijin White Goose (Anser cygnoides), Res. Square (pdf)

Gutell RR, Lee JC, & Cannone JJ (2002), The accuracy the ribosomal RNA comparative structure models, Curr. Opin. Struct. Biol. 12, 301-310. (abstract)

Härlid A, Janke A, and Arnason U (1997), The mtDNA sequence of the ostrich and the divergence between paleognathous and neognathous birds, Mol. Biol. Evol. 14, 754-761. (free pdf)

Härlid A, Janke A, and Arnason U (1998), The complete mitochondrial genome of Rhea americana and early avian divergences, J. Mol. Evol. 46, 669-679. (abstract)

Halley YA, Oldeschulte DL, Bhattarai EK, Hill J, Metz RP, Johnson CD, Presley SM, Ruzicka RE, Rollins D, Peterson MJ, Murphy WJ, and Seabury CM (2015), Northern Bobwhite (Colinus virginianus) mitochondrial population genomics reveals structure, divergence, and evidence for heteroplasmy, PLoS ONE 10, e:0144913. (pdf)

Hanna ZR, Henderson JB, Sellas AB, Fuchs J, Bowie RCK, and Dumbacher JP (2017), Complete mitochondrial genome sequences of the northern spotted owl (Strix occidentalis caurina) and the barred owl (Strix varia; Aves: Strigiformes: Strigidae) confirm the presence of a duplicated control region, PeerJ 5, e:3901. (pdf)

Hansen CCR, Baleka S, Gudjónsdottir SM, Rasmussen JA, Ballesteros JAC, Hallgrimsson GT, Stefansson RA, von Schmalensee M, Skarphédinsson KH, Labansen AL, Leivits M, Skelmose, Sonne C, Dietz R, Boertmann D, Eulaers I, Martín MD, and Pálsson S (2022), Distinctive mitogenomic lineages within populations of White-Teiles Eagles, Ornithology 139, (abstract)

Haring E, Kruckenhauser L, Gamauf A, Riesling MJ, and Pinsker W (2001), The complete sequence of the mitochondrial genome of Buteo buteo (Aves, Accipitridae) indicates an early split in the phylogeny of raptors, Mol. Biol. Evol. 18, 1892-1904. (free pdf)

Harrison GL, McLenachan PA, Phillips MJ, Slack KE, Cooper A, and Penny D (2004), Four new avian mitochondrial genomes help get to basic evolutionary questions in the Late Cretaceous, Mol. Biol. Evol. 21, 974-983. (free 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)

He L, Dai B, Zeng B, Zhang X, Chen B, Yue B, and Li J (2009), The complete mitochondrial genome of the Sichuan Hill Partridge (Arborophila rufipectus) and a phylogenetic analysis with related species, Gene 435, 23-28. (abstract)

He XL, Ding CQ, and Han JL (2013), Lack of structural variation but extensive length polymorphisms and heteroplasmic length variations in the mitochondrial DNA control region of highly inbred Crested Ibis, Nipponia nippon, PLOS ONE 8, e:66324. (pdf)

Hebert PDN, Ratnasingham S, and deWaard JR (2003), Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species, Proc. R. Soc. Lond. B (Suppl.) 270, S96-99. (pdf)

Hebert PDN, Stoeckle MY, Zemlak TS, and Francis CM (2004), Identification of birds through DNA barcodes, PLoS Biol. 2, 1657-63. (pdf) 

Hosner PA, Zhao M, Kimball RT, Braun EL, and Burleigh JG (2022), Reconciling GenBank names with standardized avian taxonomies to improve linkage between phylogeny and phenotype, bioRxiv, (pdf)

Hu C, Zhang C, Sun L, Zhang y, Xie W, Zhang B, and Chang Q (2017), The mitochondrial genome of pin-tailed snipe Gallinago stenura, and its implications for the phylogeny of Charadriiformes, PLOS ONE 12, e:0175244. (pdf)

Hu C, Xu X, Yao W, Liu W, Tai D, Chen W, and Chang Q (2021), Complete mitochondrial genome of the Eurasian Oystercatcher Haematopus ostralegus and comparative genomic analyses of Charadriiformes, Pakistan J. Zool. 53, 2407-15. (free pdf)

Huang Z, Liu N, Xiao Y, Cheng Y, Mei W, and Wen L (2009), Phylogenetic relationships of four endemic genera of the Phasianidae in China based on mitochondrial DNA control region genes, Mol. Phylogenet. Evol. 53, 378-383. (abstract)

Huang Z, Liu N, Liang W, Zhang Y, Liao X, Ruan L, and Yang Z (2010), Phylogeography of Chinese bamboo partridge, Bambusicola thoracica thoracica (Aves: Galliformes) in south China: inference from mitochondrial DNA control-region sequences, Mol. Phylogenet. Evol. 56, 273-280. (abstract)

Huang Z, and Ke D (2014a), Structure and evolution of the Phasianidae mitochondrial control region, Mitochondrial DNA A 27, 350-354. (abstract)

Huang Z, and KE D (2014b), Structure and variation of the Anseriformes mitochondrial DNA control region, Mitochondrial DNA A 27, 2036-39. (abstract)

Huang Z, Tu F, and Murphy RW (2016), Analysis of the complete mitogenome of Oriental turtle dove (Streptopelia orientalis) and implications for species divergence, Biochem. Syst. Ecol. 65, 209-213. (abstract)

Huang Z, Li M, Ruan R, and Qin J (2017a), Organization and variation of the mitochondrial DNA control region in Ardeidae (Aves: Ciconiiformes) and their phylogenetic relationship, Pakistan J. Zool. 49, 1917-1920. (pdf, incl. Suppl. Mat.)

Huang Z, Shen Y, and Ma Y (2017b), Structure and variation of the Fringillidae (Aves: Passeriformes) mitochondrial DNA control region and their phylogenetic relationship, Mitochondrial DNA A 28, 867-871. (abstract)

Huang Z, and KE D (2017c), Organization and variation of the Tetraoninae (Aves: Galliformes) mitochondrial DNA control region, Mitochondrial DNA B 2, 568-570. (pdf)

Huang Z, Tu F, and Tang S (2018), Two new mitogenomes of Pellorneidae (Aves: Passeriformes) and a phylogeny of the superfamily Sylvioidea, Austr. J. Zool. 66, 167-173. (abstract)

Jemt E, Persson Ö, Shi Y, Mehmedovic M, Uhler JP, López MD, Freyer C, Gustafsson CM, Samuelsson T, and Falkenberg M (2015), Regulation of DNA replication at the end of the mitochondrial D-loop involves the helicase TWINKLE and a conserved sequence element, Nucleic Acid Res. 43, 9262-75. (pdf)

Jiang F, Miao Y, Liang W, Ye H, Liu H, and Liu B (2010), The complete mitochondrial genomes of the whistling duck (Dendrocygna javanica) and black swan (Cygnus atratus): dating evolutionary divergence in Gallianserae, Mol. Biol. Rep. 37, 3001-15. (abstract)

Jiang L, Wang G, Peng R, Peng Q, & Zou F (2014), Phylogenetic and molecular dating analysis of Taiwan Blue Pheasant (Lophura swinhoii), Gene 539, 21-29. (abstract)

Jiang L, Chen J, Wang P, Ren Q, Yuan J, Qian C, Hua X, Guo Z, Zhang L, Yang J, Wang Y, Zhang Q, Ding H, Bi D, Zhang Z, Wang Q, Chen D, and Kan X (2015), The mitochondrial genomes of Aquila fasciata and Buteo lagopus (Aves, Accipitriformes): sequence, structure and phylogenetic analyses, PLoS ONE 10, e:0136297. (pdf)

Jiang L, Peng L, Tang M, You Z, Zhang M, West A, Ruan Q, Chen W, and Merilä J (2019), Complete mitochondrial genome sequence of the Himalayan Griffon, Gyps himalayensis (Accipitriformes: Accipitridae): sequence, structure, and phylogenetic analyses, Ecol. Evol. 9, 8813-28. (pdf)

Jin X, Cheng Z, Wang B, Yau T, Chen Z, Barker SC, Chen D, Bu W, Sun D, and Gao S (2020), Precise annotation of human, chimpanzee, rhesus macaque and mouse mitochondrial genomes leads to insight into mitochondrial transcription in mammals, RNA Biol. 17, 395-402. (pdf)

Jing M, Yang H, Li K, and Huang L (2020), Characterization of three new mitochondrial genomes of Coraciiformes (Megaceryle lugubris, Alcedo atthis, Halcyon smyrnensis) and insights into their phylogenetics, Genet. Mol. Biol. 43, e:20190392. (pdf)

Johnsen A, Kearns AM, Omland KE, and Anmarkrud JA (2017), Sequencing of the complete mitochondrial genome of the common raven Corvus corax (Aves: Corvidae) confirms mitogenome-wide deep lineages and a paraphyletic relationship with the Chihuahuan raven C. cryptoleucus, PLoS ONE 12, e:0187316. (pdf)

Jühling F, Pütz J, Bernt M, Donath A, Middendorf M, Florentz C, and Stadler PF (2012), Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements, Nucl. Acid Res. 40, 2833-45. (pdf) 

Kan XZ, Li XF, Lei ZP, Wang M, Chen L, Gao H, and Yang ZY (2010a), Complete mitochondrial genome of Cabot‘s tragopan, Tragopan caboti  (Galliformes: Phasianidae), Genet. Mol. Res. 9, 1204-1216. (pdf)

Kan XZ, Li XF, Zhang LQ, Chen L, Qian CJ, Zhang XW, and Wang L (2010b), Characterization of the complete mitochondrial genome of the rock pigeon, Columba livia (Columbiformes, Columbidae), Genet. Mol. Res. 9, 1234-49. (pdf)

Kan X, Yuan J, Zhang L, Li X, Yu L, Chen L, Guo Z, and Yang J (2013), Complete mitochondrial genome of the Tristram’s Bunting, Emberiza  tristrami (Aves: Passeriformes): the first representative of the family Emberizidae with six boxes in the central conserved domain II of control region, Mitochondrial DNA 24, 648-650. (abstract)

Kang H, Li B, Ma X, and a Xu at (2018), Evolutionary progression of mitochondrial gene rearrangements and phylogenetic relationships in Strigidae (Strigiformes), Gene 674, 8-14. (abstract)

Ke Y, Huang Y, and Lei FM (2008), [Sequencing and analysis of the complete mitochondrial genome of Podoces hendersoni (Aves, Corvidae)], Yi Chuan. 32, 951-960. (Chinese) (abstract)

Kim JI, Do TD, Choi Y, Yeo Y, and Kim CB (2021), Characterization and comparative analysis of complete mitogenomes of three Cacatua parrots (Psittaciformes: Cacatuidae), Genes 12, e:209. (pdf)

Kim JI, Do TD, Yeo Y, and Kum CB ((2022), Comparative analysis of complete mitochondrial genomes of three Trichoglossus species (Psittaciformes: Psittacidae), Mol. Biol. Rep. (abstract)

Kumazawa Y, and Nishida M (1993), Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics, J. Mol. Evol. 37, 380-398. (abstract)

Kundu S, Alam I, Maheswaran G, Tyagi K, and Kumar (2021), Complete mitochondrial genome of Great Frigatebird (Fregata minor): phylogenetic position and gene rearrangement, Biochem. Genet. 60, 1177-1188.bu (abstract)

Kuro-o M, Yonekawa H, Saito S, Eda M, Higuchi H, Koike H, and Hasegawa H (2010), Unexpectedly high genetic diversity of mtDNA control region through severe bottleneck in vulnerable albatross Phoebastria albatrus, Conserv. Genet. 11, 127-137. (abstract)

L‘Abbe D, Duhaime JF, Lang BF, and Morais R (1991), The transcription of DNA in chicken mitochondria initiates from one major bidirectional promoter, J. Biol. Chem. 266, 10844-50. (free pdf)

Lai WN, Yan SQ, Jiao SY, Yao JY, and Li YM (2019), Complete mitochondrial genome of Dendrocopos canicapillus (Piciformes: Picidae), Mitochondrial DNA B 4, 141-142. (abstract)

Li JY, Li WX, Wang AT, and Zhang Y (2021), MitoFlex: an efficient, high-performance toolkit for animal mitogenome assembly, annotation and visualization, Bioinformatics 37, 3001-3. (abstract)

Li X, Huang Y, and Lei F (2015), Comparative mitochondrial genomics and phylogenetic relationships of Crossoptilon species (Phasianidae, Galliformes), BMC Genomics 16, e:42. (pdf)

Lima NCB, and Prosdocimi F (2017), The heavy strand dilemma of vertebrate mitochondria on genome sequencing age: number of encoded genes or G+T content?, Mitochondrial DNA A 29, 300-302. (abstract)

Lima NCB (2018), Comparative mitogenomic analyses of Amazona parrots and Psittaciformes, Gen. Mol. Biol. 41, 593-604. (free pdf)

Liu F, Ma L, Yang C, Tu F, Xu Y, Ran J, Yue B, and Zhang X (2014), Taxonomic status of Tetraophasis obscurus and Tetraophasis szechenyii (Aves: Galliformes: Phasianidae) based on the complete mitochondrial genome, Zool. Sci. 31, 160-167. (abstract)

Liu G, Zhou LZ, and Gu CM (2012), Complete sequence and gene organization of the mitochondrial genome of scaly-sided merganser (Mergus  squamatus) and phylogeny of some Anatidae species, Mol. Biol. Rep. 39, 2139-45. (abstract)

Liu G, Zhang Z, Luo L, and Xu W (2013), The complete mitochondrial genome of bean goose (Anser fabalis) and implications for Anseriformes taxonomy, PLoS ONE 8, e:63334. (pdf)

Liu G, Zhou L, Li B, and Zhang L (2014), The complete mitochondrial genome of Aix galericulata and Tadorna ferruginea: bearings on their phylogenetic position in the Anseriformes, PLoS ONE 9, e:109701. (pdf)

Liu G, Li C, Du Y, and Liu X (2017), The complete mitochondrial genome of Japanese sparrowhawk (Accipiter gularis) and the phylogenetic relationships among some predatory birds, Biochem. Syst. Ecol. 70, 116-125. (abstract)

Liu W, Hu C, Xie W, Chen P, Zhang Y, Yao R, , (2018), The mitochondrial genome of red-necked phalarope Phalaropus lobatus (Charadriiformes: Scolopacidae) and phylogeny analysis among Scolopacidae, Genes Genomics 40, 455-462. (abstract)

Lubbe P, Rawlence NJ, Kardailsky O, Robertson BC, Day R, Knapp M, and Dussex N (2022), Mitogenomes resolve the phylogeography and divergence times within the endemic New Zealand (Callaeidae: Passerida), Zool. J. Linn. Soc. (free pdf)

Lucchini V, Höglund J, Klaus S, Swenson J, and Randi E (2001), Historical biogeography and a mitochondrial DNA phylogeny of grouse and phylogenetic ptarmigan, Mol. Phylogenet. Evol. 20, 149-162. (abstract)

Ma YG, Huang Y, and Lei FM (2014), Sequencing and phylogenetic analysis of the Pyrgilauda ruficollis (Aves, Passeridae) complete mitochondrial genome, Zool. Res.  35, 81-91. (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)

Marshall HD, and Baker AJ (1997), Structural conservation and variation in the mitochondrial control region of fringilline finches (Fringilla spp.) and the Greenfinch (Carduelis chloris), Mol. Biol. Evol. 14, 173-184. (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)

Meyer CP, and Paulay G (2005), DNA barcoding: error rates based on comprehensive sampling, PLoS Biol. 3, e:422. (pdf)

Miller HC, Lambert DM (2006), A molecular phylogeny of New Zealand’s Petroica (Aves: Petroicidae) species based on mitochondrial DNA sequences, Mol. Phylogenet. Evol. 40, 844-855. (abstract)

Mindell DP, Sorenson MD, and Dimcheff DE (1998a), Multiple independent origins of mitochondrial gene order in birds, Proc. Natl. Acad. Sci. USA 95, 10693-97. (pdf)

Mindell DP, Sorenson MD, and Dimcheff DE (1998b), An extra nucleotide is not translated in mitochondrial ND3 of some birds and turtles, Mol. Biol. Evol. 15, 1568-71. (free pdf)

Mindell DP, Sorenson MD, Dimcheff DE, Hasegawa M, Ast JC, and Yuri (1999), Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes, Syst. Biol. 48, 138-152. (free pdf)

Mitchell KJ, Wood JR, Scofield RP, Llamas B, and Cooper A (2013), Ancient mitochondrial genome reveals unsuspected taxonomic affinity of the extinct Chatham duck (Pachyanas chathamica) and resolves divergence times for New Zealand and sub-Antarctic brown teals, Mol. Phylogenet. Evol. 70, 420-428. (abstract)

Montaña-Lozano P, Moreno-Carmona M, Ochoa-Capera M, Medina NS, Boore JL, and Prada CF (2022), Comparative genomic analysis of vertebrate mitochondria reveals a differential of rearrangement rate between taxonomic class, Sci. Rep. 12, e:5479. (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)

Morinha F, Clemente C, Cabral JA, Lewicka MM, Travassos P, Carvalho D, Dávila JA, Santos M, Blanco G, and Bastos E (2016), Next-generation sequencing and comparative analysis of Pyrrhoxorax pyrrhoxorax and Pyrrhoxorax graculus (Passeriformes:Corvidae) mitochondrial genomes, Mitochondrial DNA 27, 2278-81. (abstract)

Morris-Pocock JA, Taylor SA, Birt TP, and Friesen VL (2010), Concerted evolution of duplicated mitochondrial control regions in three related seabird species, BMC Evol. Biol. 10, e:14. (pdf)

Moum T, and Bakke I (2001), Mitochondrial control region structure and single site heteroplasmy in the razorbill (Alca torda; Aves), Curr. Genet. 39, 198-203. (abstract)

Mu CY, Huang ZY, Chen Y, Wang B, Su YH, Li Y, Sun ZM, Xu Q, Zhao WM, and Chen GH (2014), Completely sequencing and gene organization of the Anser cygnoides mitochondrial genome, J. Agric. Biotechnol22, 1482-93. (abstract)

Nabholz B, Jarvis E, and Ellegren H (2010), Obtaining mtDNA genomes from next-generation transcriptome sequencing: a case study on the basal Passerida (Aves: Passeriformes) phylogeny, Mol. Phylogenet. Evol. 57, 466-470. (abstract)

Nicholls TJ, and Minczuk M (2014), In D-loop: 40 years of mitochondrial 7S DNA, Exp. Geront. 56, 175-181. (abstract)

Nishibori M, Hayashi T, Tsudzuki M, Yamamoto Y, and Yasue H (2001), Complete sequence of the Japanese quail (Coturnix japonica) mitochondrial genome and its genetic relationship with related species, Animal Genet. 32, 380-385. (abstract)

Nishibori M, Tsudzuki M, Hayashi T, Yamamoto Y, and Yasue H (2002), Complete nucleotide sequence of the Coturnix chinensis (Blue-breasted Quail) mitochondrial genome and phylogenetic analysis with related species, J. Hered. 93, 439-444. (free pdf)

Nishibori M, Hayashi T, and Yasue H (2004), Complete nucleotide sequence of Numida meleagris (Helmeted guineafowl) mitochondrial genome, J. Poultry Sci. 41, 259-268. (pdf)

Omote K, Nishida C, Dick MH, and Masuda R (2013), Limited phylogenetic distribution of a long tandem-repeat cluster in the mitochondrial control region in Bubo (Aves, Strigidae) and cluster variation in Blakiston’s fish owl (Bubo blakistoni), Mol. Phylogenet. Evol. 66, 889-897. (abstract)

Pacheco MA, Battistuzzi FU, Lentino M, Aguilar RF, Kumar S, and Escalante AA (2011), Evolution of modern birds revealed by mitogenomics: timing the radiation and origin of major orders, Mol. Biol. Evol. 28, 1927-42. (free pdf)

Peng C, Li J, Lu H, Liu W, and Zhang J (2022), Characterization of the complete mitochondrial genome of the Sea Duck Mergus serrator and comparison with other Anseriformes species, Res. Square (pdf) 

Pereira F, Soares P, Carneiro J, Pereira L, Richards MB, Samuels DC, and Amorim A (2008), Evidence for variable selective pressures at a large secondary structure of the hunan mitochondrial DNA control region, Mol. Biol. Evol. 25, 2759-70. (free pdf)

Pereira SL, Grau ET, and Wayntal A and (2004), Molecular architecture and rates of DNA substitutions of the mitochondrial control region of cracid birds, Genome 47, 535-545. (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)

Qian C, Ren Q, Kan X, Guo Z, Yang J, Li X, Yuan J, Qian M, Zhu Q, and Zhang L (2012), Complete mitochondrial genome of the Red-billed Starling, Sturnus sericeus (Aves: Passeriformes): the first representative of the family Sturnidae with a single control region, Mitochondrial DNA 24, 129-131. (abstract)

Quinn TW, and Wilson AC (1993), Sequence evolution in and around the mitochondrial control region in birds, J. Mol. Evol. 37, 417-425. (abstract)

Ramirez V, Savoie P, and Morais R (1993), Molecular characterization and evolution of a duck mitochondrial genome, J. Mol. Evol. 37, 296-310. (abstract)

Randi E, and Lucchini V (1998), Organization and evolution of the mitochondrial DNA control region in the avian genus Alectoris, J. Mol. Evol. 47, 449-462. (abstract)

Ratnasingham S, and Hebert PDN (2013), A DNA-based registry for all animal species: the Barcode Index Number (BIN) system, PLOS ONE 8, e:66213. (pdf)

Ren Q, Qian C, Yuan J, Li X, Yang J, Wang P, Jiang L, Zhang Q, Wang Y, and Kan X (2014a), Complete mitochondrial genome of the Black-capped Bulbul, Pycnonotus melanicterus (Passeriformes: Pycnonotidae), Mitochondrial DNA A 27, 1378-80. (abstract)

Ren Q, Yuan J, Ren L, Zhang L, Zhang L, Jiang L, Chen D, Kan X, and Zhang B (2014b), The complete mitochondrial genome of the yellow-browed bunting, Emberiza chrysophrys (Passeriformes: Emberizidae), and phylogenetic relationships within the genus Emberiza, J. Genet. 93, 699-707. (abstract)

Roques S, Godoy A, Negro JJ, and Hiraldo F (2004), Organization and variation of the mitochondrial control region in two vulture species, Gypaetus barbatus and Neophron percnopterus, J. Hered. 95, 332-337. (free pdf)

Ruokonen M, Kvist L, and Lumme J (2000), Close relatedness between mitochondrial DNA from seven Anser goose species, J. Evol. Biol. 13, 532-540. (pdf)

Ruokonen M, and Kvist L (2002), Structure and evolution of the avian mitochondrial control region, Mol. Phylogenet. Evol. 23, 422-432. (abstract)

Ryu SH, and Hwang UW (2012), Complete mitochondrial genome of Saunders’s gull Chroicocephalus saundersi  (Charadriiformes, Laridae), Mitochondrial DNA 23, 134-136. (abstract)

Saccone C, Pesole G, and Sbisá E (1991), The main regulatory region of the mammalian mitochondrial DNA: structure-function model and evolutionary pattern, J. Mol. Evol. 33, 83-91. (abstract)

Sammler S, Bleidorn C, and Tiedemann R (2011), Full mitochondrial genome sequences of two endemic Philippine hornbill species (Aves: Bucerotidae) provide evidence for pervasive mitochondrial DNA recombination, BMC Genomics 12, e:35. (pdf)

Sammler S, Keramiker V, Havenstein K, Krause U, Curio E, and Tiedemann R (2012), Mitochondrial control region I and microsatellite analyses of endangered Philippine hornbill species (Aves; Bucerotidae) detect gene flow between island populations and genetic diversity loss, BMC Evol. Biol. 203, e:203. (pdf)

Sammler S, Keramiker V, Havenstein K, and Tiedemann R (2013), Intraspecific rearrangement of duplicated mitochondrial control regions in the Luzon Tarictic Hornbill Penelopides manillae (Aves: Bucerotidae), J. Mol. Evol. 77, 199-205. (abstract)

Sangster G, and Luksenburg JA (2021), Sharp increase of problematic mitogenomes of birds: causes, consequences and remedies, Genome Biol. Evol. 13, e:evab210. (free pdf)

Sarkar I, Dey P, Sharma SK, Ray SD, Kochiganti VHS, Singh R, Pramod P, and Singh RP (2020), Turdoides affinis mitogenome reveals the translational efficiency and importance of NADH dehydrogenase complex-I in the Leiotrichidae family, Sci. Rep. 10, e:16202. (pdf)

Saunders MA, and Edwards SV (2000), Dynamics and phylogenetic implications of mtDNA control region sequences in New World jays (Aves: Corvidae), J. Mol. Evol. 51, 97-109. (abstract)

Sbisà E, Tanzariello F, Reyes A, Pesole G, and Saccone C (1997), Mammalian mitochondrial D-loop region structural analysis: identification of new conserved sequences and their functional and evolutionary implications, Gene 205, 125-140. (abstract)

Schirtzinger EE, Tavares ES, Gonzales LA, Eberhard JR, Miyaki CY, Sanchez JJ, Hernandez A, Müeller H, Graves GR, Fleischer RC, and Wright T (2012), Multiple independent origins of mitochondrial control region duplications in the order Psittaciformes, Mol. Phylogenet. Evol. 64, 342-356. (pdf)

Seligmann H, and Labra A (2014), The relation between harpin formation by mitochondrial WANCY tRNAs and the occurrence of the light strand replication origin in Lepidosauria, Gene 542, 248-257. (abstract)

Shuangye W, Yunlin Z, Zhenggang X, Tian H, Guiyan Y, and Zhiyuan H (2021), The complete mitochondrial genome comparison between Pelecanus occidentalis and Pelecanus crispus, Russ. JGenet. 57, 1073-81. (abstract)

Singh TR, Shneor O, and Huchon D (2008), Bird mitochondrial gene order: insight from 3 warbler mitochondrial genomes, Mol. Biol. Evol. 25, 475-477. (free pdf)

Slack KE, Janke A, Penny D, and Arnason U (2003), Two new avian mitochondrial genomes (penguin and goose) and a summary of bird and reptile mitogenomic features, Gene 302, 43-52. (abstract)

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)

Soares AER, Novak BJ, Haile J, Heupink TH, Fjeldså J, Gilbert MTP, Poinar H, Church GM, and Shapiro B (2016), Complete mitochondrial genomes of living and extinct pigeons revise the timing of the columbiform radiation, BMC Evol. Biol. 16, e:230. (pdf)

Song X, Huang J, Yan C, Xu G, Zhang X, and Yue B (2015), The complete mitochondrial genome of Accipiter virgatus and evolutionary history of the pseudo-control regions in Falconiformes, Biochem. Syst. Ecol. 58, 75-84. (abstract)

Spiridonova LN, and Surmach SG (2018), Whole mitochondrial genome of Blakiston’s fish owl Bubo (Ketupa) blakistoni suggests its redesription in the genus Ketupa, Russ. J. Genet. 54, 369-373. (abstract)

Sun CH, Liu HY, Min X and Lu CH (2020), Mitogenome of the little owl Athene noctua and phylogenetic analysis of Strigidae, Int. J. Biol. Macromol. 151, 924-931. (abstract)

Sun G, Zhao C, Xia T, Wei Q, Yang X, Feng S, Sha W, and Zhang H (2020), Sequence and organisation of the mitochondrial genome of Japanese Grosbeak (Eophona personata), and the phylogenetic relationships of Fringillidae, ZooKeys 995, 67-80. (free pdf)

Sun X, Zhou W, Sun Z, Qian L, Zhang Y, Pan T, and Zhang B (2016), The complete mitochondrial genome of Glaucidium brodiei (Strigiformes: Strigidae), Mitochondrial DNA A 27, 2508-2509. (abstract)

Sun X, Zhao R, Zhang T, Gong J, Jung M, and Huang L (2017), Two mitochondrial genomes in Alcedinidae (Ceryle rudis/Halcyon pileata) and the phylogenetic placement of Coraciiformes, Genetica 145, 431-440. (abstract)

Sveinsdóttir M, Gudmundsdóttir L, and Magnússon KO (2016), Complete mitochondrial genome of the gyrfalcon Falco rusticolus (Aves, Falconiformes, Falconidae), Mitochondrial DNA A 28, 370-371. (abstract)

Taanman JW (1999), The mitochondrial genome: structure, transcription, translation and replication, Biochim. Biophys. Acta 1410, 103-123. (free reading)

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

Urantówka AD, Kroczak A, Silva T, Padrón RZ, Gallardo NF, Blanch J, Blanch B, and Mackiewicz P (2018), New insight into parrot’s mitogenomes indicates that their ancestor contained a duplicated region, MolBiolEvol. 35, 2989-3008. (free pdf)

Urantówka AD, Kroczak A, and Mackiewicz P (2020), New view on the organization and evolution of Palaeognathae mitogenomes poses the question on the ancestral rearrangement in Aves, BMC Genomics 21, e:874. (pdf)

Urantówka AD, Kroczak A, Strzala T, Zaniewicz G, Kurkowski M, and Mackiewicz P (2021), Mitogenomes of Accipitriformes and Cathartiformes were subjected to ancestral and recent duplications followed by gradual degradation, Genome BiolEvol. 13, e:evab193. (pdf) 

Ushida A, Murugesapillai D, Kastner M, Wang Y, Lodeiro MF, Prabhakar S, Oliver GV, Arnold JJ, Maher LJ, Williams MC, and Cameron CE (2017), Unexpected sequences and structures of mtDNA required for efficient transcription from the first heavy-strand promoter, eLife 6, e:27283. (pdf)

Väli Ü, Treinys R, Bergmanis U, Daroczi S, Demerdzhiev D, Donbrovski V, Dravecky M, Ivanovski V, Kicko J, Langgemach T, Lontkowski J, Maciorowski G, Poirazidis K, Rodziewicz M, and Meyburg BU (2022), Contrasting patterns of genetic diversity and lack of population structure in the lesser spotted eagle Clanga pomarina (Aves: Accipitriformes) across its breeding range, Biol. J. Linn. Soc. (abstract)

Valverde JR, Marco R, and Garesse R (1994), A conserved heptamer motif for ribosomal RNA transcription termination in animal mitochondria, Proc. Natl. Acad. Sci. USA 91, 5368-71. (pdf)

Verkuil YI, Piersma T, and Baker AJ (2017), A novel mitochondrial gene order in shorebirds (Scolopacidae, Charadriiformes), Mol. Phylogenet. Evol. 57, 411-416. (abstract)

Wang E, Zhang D, Braun MS, Hotz-Wagenblatt A, Pärt T, Arlt D, Schmaljohann H, Bairlein F, Lei F, and Wink M (2020), Can mitogenomes of the Northern Wheatear (Oenanthe oenanthe) reconstruct its phylogeography and reveal the origin of migrant birds?, Sci. Rep. 10, e:9290. (pdf)

Wang J, Liu G, Zhou L, Quing H, Li L, Li B, and Zhang L (2014), Complete mitochondrial genome of Tundra swan Cygnus columbianus jankowskii (Anseriformes: Anatidae), Mitochondrial DNA 27, 90-91. (abstract)

Wang X, Liu N, Zhang H, Yang XY, Huang Y, and Lei F (2015), Extreme variation in patterns of tandem repeats in mitochondrial control region of yellow-browed tits (Sylviparus modestus, Paridae), Sci. Rep. 5, e:13227. (pdf)

Warzecha J, Fornal A, Oczkowicz M, and Bugno-Poniewierska M (2018), A molecular characteristic of the Anatidae mitochondrial control region – a review, Ann. Anim. Sci. 18, 3-15. (pdf) 

Watanabe M, Nikaido M, Tsuda TT, Kobayashi T, Mindell D, Cao Y, Okada N, and Hasegawa M (2006), New candidate species most closely related to penguins, Gene 378, 65-73. (abstract)

Wenink PW, Baker AJ, Tilanus MGJ (1994), Mitochondrial control-region sequences of two shorebird species, the turnstone and the Dunlin, and their utility in population genetic structures, Mol, Biol. Evol. 11, 22-31. (free pdf)

Xiao B, Ma F, Sun Y, and Li QW (2006), Comparative analysis of complete mitochondrial DNA control region of four species of Strigiformes, Acta Genet. Sin. 33, 965-974. (abstract)

Xu N, Ding J, Que Z, Xu W, Ye W, and Liu H (2021), The mitochondrial genome and phylogenetic characteristics of the Thick-billed Green-Pigeon, Treron curvirostra: the first sequence for the genus, ZooKeys 1041, 167-182. (pdf) 

Xu Z, Wu L, Chen J, Zhao Y, Han C, Huang T, and Yang G (2022), Insight into the characteristics of an important evolutionary model bird (Geospiza magnirostris) mitochondrial genome through comparison, Biocell 46, 1733-1746. (pdf)

Xue H, Zhang H, Li Y, Wu X, Yan P, and Wu XB (2014), The complete mitochondrial genome of Garrulax cineraceus (Aves, Passeriformes, Timaliidae), Mitochondrial DNA A 27, 147-148. (abstract)

Yamamoto Y, Murata K, Matsuda H, Hosoda T, Tamura K, and Furuyama JI (2000), Determination of the complete nucleotide sequence and haplotypes in the D-loop region of the mitochondrial genome in the oriental white stork, Ciconia boyciana, Genes Genet. Syst. 75, 25-32. (pdf)

Yan C, Mou B, Meng Y, Tu F, Fan Z, Price M, Yue B, and Zhang X (2017), A novel mitochondrial genome of Arborophila and new insight into Arborophila evolutionary history, PLoS ONE 12, e:0181649. (pdf)

Yang C, Lei FM, and Huang Y (2010), Sequencing and analysis of the complete mitochondrial genome of Pseudopodoces humilis (Aves, Paridae), Zool. Res. 31, 333-344. (free pdf)

Yang C, Lian T, Wang QX, Huang Y, and Xiao H (2015), Structural characteristics of the Relict Gull (Larus relictus) mitochondrial DNA control region and its comparison to other Laridae, Mitochondrial DNA 27,  2487-91. (abstract)

Yang C, Yang M, Wang Q, Lu Y, and Li X (2018), The complete mitogenome of Falco amurensis (Falconiformes, Falconidae), and a comparative analysis of genus Falco, Zool. Sci. 35, 367-372. (abstract)

Yang C, Zhao L, Wang Q, Yuan H, Li X, and Wang Y (2021), Mitogenome of Alaudala cheleensis (Passeriformes: Alaudidae) and comparative analyses of Sylvioidea mitogenomes, Zootaxa 4952, 331-353. (abstract)

Yang C, Du X, Liu Y, Yuan H, Wang Q, Hou X, Gong H, Wang Y, Huang Y, Li X, and Ye H (2022), Comparative mitogenomics of the genus Motacilla (Aves, Passeriformes) and its phylogenetic implications, ZooKeys 1109, 49-65. (free pdf)

Yang R, Wu X, Yan P, Su X, and Yang B (2010), Complete mitochondrial genome of Otis tarda (Gruiformes, Otididae) and phylogeny of Gruiformes inferred from mitochondrial DNA sequences, Mol. Biol. Rep. 37, 3057-3066. (abstract)

Yoon BK, Cho CU, and Park YC (2015), The mitochondrial genome of the Saunders’s gull Chroicocephalus saundersi (Charadriiformes: Laridae) and a higher phylogeny of shorebirds (Charadriiformes), Gene 572, 227-236. (abstract)

Yu J, Liu J, Li C, Wu W, Feng F, Wang Q, Ying X, Qi D, and Qi G (2021), Characterization of the complete mitochondrial genome of Otus lettia: exploring the mitochondrial evolution and phylogeny of owls (Strigiformes), Mitochondrial DNA B 6, 3443-51. (pdf)

Yuan QM, Luo X, Cao J, and Duan YB (2021), Complete mitochondrial genomes of three nuthatches from the genus Sitta (Aves: Passeriformes: Sittidae) and mitogenome-based phylogenetic analysis, Res. Square (pdf) 

Zhang H, Bai Y, Shi X, Wang Z, and Wu X (2018), The complete mitochondrial genomes of Tarsiger cyanurus and Phoenicurus auroreus: a phylogenetic analysis of Passeriformes, Genes Genomics 40, 151-165. (abstract)

Zhang L, Wang L, Gouda V, Wang M, Li X, and Kan X (2012), The mitochondrial genome of the Cinnamon Bittern, Ixobrychus cinnamomeus  (Pelecaniformes: Ardeidae): sequence, structure and phylogenetic analysis. Mol. Biol. Rep. 39, 8315-26. (abstract)

Zhang Y, Song T, Pan T, Sun X, Sun Z, Qian L, and Zhang B (2015), Complete sequence and gene organization of the mitochondrial genome of Asio flammeus (Strigiformes, Strigidae), Mitochondrial DNA 132, 1-5. (abstract)

Zhao Q, Xu HL, and Yao YF (2018), The complete mitochondrial genome and phylogeny of the Emei Shan liocichla (Liocichla omeiensis), Conservation Genet. Resour. 11, 303-407. (abstract)

Zhenggang X, Liang W, Sihan H, Chongxuan H, Tian H, and Yunlin Z (2021), Structural variation and phylogenetic relationship of Geospiza magnirostris based on mitochondrial control region, Biologia 76, 1367-73. (abstract)

Zhong Y, Zhou M, Ouyang B, Zeng C, Zhang M, and Yang J (2020), Complete mtDNA genome of Otus sunia (Aves, Strigidae) and the relaxation of selective constrains on Strigiformes mtDNA following evolution, Genomics 112, 3815-25. (pdf) 

Zhou C, Hao Y, Ma J, Zhang W, Chen Y, Chen B, Zhang X, and Yue B (2017), The first complete mitogenome of Picumnus innominatus (Aves, Piciformes, Picidae) and phylogenetic inference within the Picidae, Biochem. Syst. Ecol. 70, 274-282. (abstract)

Zhou T, Zhou F, Yao Y, Xie M, Ni Q, Zhang M, and Xu H (2022), Comparative analysis of the complete mitochondrial genomes of related species Chrysolophus amherstiae and Chrysolophus pictus, Mitochondrial DNA B 7, 144-152. (pdf)

Zhou X, Lin Q, Fang W, and Chen X (2014), The complete mitochondrial genomes of sixteen ardeid birds revealing the evolutionary process of the gene rearrangements, BMC Genomics 15, e:573. (pdf)

Zou Y, Jing MD, Bi XX, Zhang T, and Huang L (2015), The complete mitochondrial genome sequence of the little egret (Egretta garzeta), Genet. Mol. Biol. 38, 162-172. (pdf)