doi:

DOI: 10.3724/SP.J.1141.2012.06566

Zoological Research (动物学研究) 2012/33:6 PP.566-573

Review of mtDNA in molecular evolution studies


Abstract:
Mitochondria are old organelles found in most eukaryotic cells. Due to its rapid mutation ratio, mitochondrial DNA (mtDNA) has been widely used as a DNA marker in molecular studies and has long been suggested to undergo neutral evolution or purifying selection. Mitochondria produces 95% of the adenosine triphosphate (ATP) needed for locomotion, and heat for thermoregulation. Recent studies had found that mitochondria play critical roles in energy metabolism, and proved that functional constraints acting on mitochondria, due to energy metabolism and/or thermoregulation, influence the evolution of mtDNA. This review summarizes mitochondrial genome composition, evolution, and its applications in molecular evolution studies (reconstruction of species phylogenesis, the relationship between biological energy metabolism and mtDNA evolution, and the mtDNA codon reassignment influences the adaptation in different creatures).

Key words:mtDNA genome,Adaptive evolution,Natural selection

ReleaseDate:2014-07-21 16:32:47



Aleixo A. 2004. Historical diversification of a terra-firme forest bird superspecies: a phylogeographic perspective on the role of different hypotheses of Amazonian diversification[J]. Evolution, 58(6): 1303-1317.

Allen JF. 2003. The function of genomes in bioenergetic organelles[J]. Phil Trans R Soc B, 358(1429): 19-38.

Andersson SG, Kurland CG. 1990. Codon preferences in free-living microorganisms[J]. Microbiol Rev, 54(2): 198-210.

Andersson SG, Zomorodipour A, Andersson1 JO, Sicheritz-Pontén T, Alsmark UC, Podowski1 RM, Näslund AK, Eriksson AS, Winkler HH, Kurland CG. 1998. The genome sequence of Rickettsia prowazekii and the origin of mitochondria[J]. Nature, 396(6707): 133-140.

Andolfatto P. 2005. Adaptive evolution of non-coding DNA in Drosophila [J]. Nature, 437(7062): 1149-1152.

Avise JC. 2000. Phylogeography: The History and Formation of Species[M]. Cambridge: Harvard University Press.

Björnerfeldt S, Webster MT, Vilà C. 2006. Relaxation of selective constraint on dog mitochondrial DNA following domestication[J]. Genome Res, 16(8): 990-994.

Bond J, Roberts E, Mochida GH, Hampshire DJ, Scott S, Askham JM, Springell K, Mahadevan M, Crow YJ, Markham AF, Walsh CA, Woods CG. 2002. ASPM is a major determinant of cerebral cortical size[J]. Nat Genet, 32(2): 316-320.

Bonen L, Cunningham RS, Gray MW, Doolittle WF. 1977. Wheat embryo mitochondrial 18S ribosomal RNA: evidence for its prokaryotic nature[J]. Nucleic Acids Res, 4(3): 663-671.

Bourgeron T, Rustin P, Chretien D, Birch-Machin M, Bourgeois M, Viegas-Péquignot E, Munnich A, Rötig A. 1995. Mutation of a nuclear succinate dehydrogenase gene results in mitochondrial respiratory chain deficiency[J]. Nat Genet, 11(2): 144-149.

Brown WM, George M Jr, Wilson AC. 1979. Rapid evolution of animal mitochondrial DNA[J]. Proc Natl Acad Sci USA, 76(4): 1967-1971.

Castresana J, Feldmaier-Fuchs G, Pääbo S. 1998. Codon reassignment and amino acid composition in hemichordate mitochondria[J]. Proc Natl Acad Sci USA, 95(7): 3703-3707.

Coleman AW, Thompson WF, Goff LJ. 1991. Identification of the mitochondrial genome in the chrysophyte alga Ochromonas danica [J]. J Eukaryot Microbiol, 38(2): 129-135.

Covello PS, Gray MW. 1992. Silent mitochondrial and active nuclear genes for subunit 2 of cytochrome c oxidase (cox2) in soybean: evidence for RNA-mediated gene transfer[J]. EMBO J, 11(1): 3815-3820.

Cummings DJ. 1992. Mitochondrial genomes of the ciliates[J]. Int Rev Cytol, 141: 1-64.

Eduardo RP, Mishmar D, Brandon M, Procaccio V, Wallace DC. 2004. Effects of Purifying and Adaptive Selection on Regional Variation in Human mtDNA[J]. Science, 303(5655): 223-226.

Evans PD, Anderson JR, Vallender EJ, Gilbert SL, Malcom CM, Dorus S, Lahn BT. 2004. Adaptive evolution of ASPM, a major determinant of cerebral cortical size in humans[J]. Hum Mol Gen, 13(5): 489-494.

Feagin JE, Abraham JM, Stuart K. 1988. Extensive editing of the cytochrome c oxidase III transcript in Trypanosoma brucei[J]. Cell, 53(3): 413-422.

Fraser CM, Casjens S, Huang WM, Sutton GG, Clayton R, Lathigra R, White O, Ketchum KA, Dodson R, Hickey EK, Gwinn M, Dougherty B, Tomb JF, Fleischmann RD, Richardson D, Peterson J, Kerlavage AR, Quackenbush J, Salzberg S, Hanson M, van Vugt R, Palmer N, Adams MD, Gocayne J, Weidman J, Utterback T, Watthey L, McDonald L, Artiach P, Bowman C, Garland S, Fuji C, Cotton MD, Horst K, Roberts K, Hatch B, Smith HO, Venter JC. 1997. Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi[J]. Nature, 390(6660): 580-600.

Fraser CM, Gocayne JD, White O, Adams MD, Clayton RA, Fleischmann RD, Bult CJ, Kerlavage AR, Sutton G, Kelley JM, Fritchman RD, Weidman JF, Small KV, Sandusky M, Fuhrmann J, Nguyen D, Utterback TR, Saudek DM, Phillips CA, Merrick JM, Tomb JF, Dougherty BA, Bott KF, Hu PC, Lucier TS, Peterson SN, Smith HO, Hutchison CA 3rd, Venter JC. 1995. The minimal gene complement of Mycoplasma genitalium [J]. Science, 270(5235): 397-403.

Fraser CM, Norris SJ, Weinstock GM, White O, Sutton GG, Dodson R, Gwinn M, Hickey EK, Clayton R, Ketchum KA, Sodergren E, Hardham JM, McLeod MP, Salzberg S, Peterson J, Khalak H, Richardson D, Howell JK, Chidambaram M, Utterback T, McDonald L, Artiach P, Bowman C, Cotton MD, Fujii C, Garland S, Hatch B, Horst K, Roberts K, Sandusky M, Weidman J, Smith HO, Venter JC. 1998. Complete genome sequence of Treponema pallidum, the syphilis spirochete[J]. Science, 281(5375): 375-388.

Gray MW, Doolittle WF. 1982. Has the endosymbiont hypothesis been proven?[J]. Microbiol Rev, 46(1): 1-42.

Gray MW, Gertraud B, Lang BF. 1999. Mitochondrial evolution[J]. Science, 283(5407): 1476-1481.

Gray MW, Cedergren R, Abel Y, Sankoff D. 1989. On the evolutionary origin of the plant mitochondrion and its genome[J]. Proc Natl Acad Sci USA, 86(7): 2267-2271.

Gray MW, Lang BF, Cedergren R, Golding GB, Lemieux C, Sankoff D, Turmel M, Brossard N, Delage E, Littlejohn TG, Plante I, Rioux P, Saint-Louis D, Zhu Y, Burger G. 1998. Genome structure and gene content in protist mitochondrial DNAs[J]. Nucleic Acids Res, 26(4): 865-878.

Hasegawa M, Cao Y, Yang Z. 1998. Preponderance of slightly deleterious polymorphism in mitochondrial DNA: nonsynonymous/synonymous rate ratio is much higher within species than between species[J]. Mol Biol Evol, 15(11): 1499-1505.

Hebert PDN, Ratnasingham S, de Waard JR. 2003. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species[J]. Proc R Soc Lond B, 270(S1): 96-99.

Henn BM, Gignoux CR, Feldman MW, Mountain JL. 2009. Characterizing the time dependency of human mitochondrial DNA mutation rate estimates[J]. Mol Biol Evol, 26(1): 217-230.

Himmelreich R, Plagens H, Hilbert H, Reiner B, Herrmann R. 1996. Comparative analysis of the genomes of the bacteria Mycoplasma pneumoniae and Mycoplasma genitalium [J]. Nucleic Acids Res, 25(4): 701-712.

Kayal E, Bentlage B, Collins AG, Kayal M, Pirro S, Lavrov DV. 2012. Evolution of linear mitochondrial genomes in medusozoan cnidarians[J]. Genome Biol Evol, 4(1): 1-12.

Keita SOY, Kittles RA, Royal CDM, Bonney GE, Furbert-Harris P, Dunston GM, Rotimi CN. 2004. Conceptualizing human variation[J]. Nat Genet, 36(11): S17-S20.

Mekel-Bobrov N, Gilbert SL, Evans PD, Vallender EJ, Anderson JR, Hudson RR, Tishkoff SA, Lahn BT.2005.Ongoing Adaptive Evolution of ASPM, a Brain Size Determinant in Homosapiens[J]. Science, 309(5471): 1720- 1722.

Kimura M. 1968. Evolutionary rate at the molecular level[J]. Nature, 217(5129): 624-6-626.

Kimura M. 1985. The role of compensatory neutral mutations in molecular evolution[J]. J Genet, 64(1): 7-19.

Kimura M. 1968. Evolutionary rate at the molecular level[J]. Nature, 217(5129): 624-626.

Klicka J, Zink RM. 1997. The importance of recent ice ages in speciation: a failed paradigm[J]. Science, 277(5332): 1666-1669.

Knight RD, Freeland SJ, Landweber LF. 2001. Rewiring the keyboard: evolvability of the genetic code[J]. Nat Rev Genet, 2(1): 49-58.

Kouprina N, Pavlicek A, Mochida GH, Solomon G, Gersch W, Yoon YH, Collura R, Ruvolo M, Barrett JC, Woods CG, Walsh CA, Jurka J, Larionov V. 2004. Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion[J]. PLoS Biol, 2(5): E126.

Lang BF, Gray MW, Burger G. 1999. Mitochondrial genome evolution and the origin of eukaryotes[J]. Annu Rev Genet, 33: 351-357.

Li N.2005.Evolution biology[M]. //Higher Education press,15-30.

MacDermot KD, Bonora E, Sykes N, Coupe AM, Lai CSL, Vernes SC, Vargha-Khadem F, McKenzie F, Smith RL, Monaco AP, Fisher SE. 2005. Identification of FOXP2 truncation as a novel cause of developmental speech and language deficits[J]. Am J Hum Gene, 76(6): 1074-1080.

Maina JN. 2000. What it takes to fly: the structural and functional respiratory refinements in birds and bats[J]. J Exp Biol, 203: 3045-3064.

Margulis L. 1970. Origin of Eukaryotic Cells: Evidence and Research Implications for A Theory of the Origin and Evolution of Microbial, Plant, and Animal Cells on the Precambrian Earth[M]. New Haven: Yale University Press.

McDonald R, Lerman K, Pereira F. 2006. Multilingual dependency analysis with a two-stage discriminative parser[C]. // Proceedings of the Tenth Conference on Computational Natural Language Learning. Stroudsburg: Association for Computational Linguistics, 65: 216-220.

Meijaard E, Groves CP. 2004. The biogeographical evolution and phylogeny of the genus Presbytis[J]. Primate Rep, 68: 71-90.

Meiklejohn CD, Montooth KL, Rand DM. 2007. Positive and negative selection on the mitochondrial genome[J]. Trends Genet, 23(6): 259-263.

Meyer D, Rinaldi ID, Ramlee H, Perwitasari-Farajallah D, Hodges JK, Roos C. 2011. Mitochondrial phylogeny of leaf monkeys (genus Presbytis, Eschscholtz, 1821) with implications for taxonomy and conservation[J]. Mol Phylogenet Evol, 59(2): 311-319.

Nachman MW. 1998. Deleterious mutations in animal mitochondrial DNA[J]. Genetics, 103(1-6): 61-69.

Nosek J, Tomáška L, Fukuhara H, Suyama Y, Kováč L. 1998. Linear mitochondrial genomes: 30 years down the line[J]. Trends Genet, 14(5): 184-188.

Oldenburg DJ, Bendich AJ. 1998. The structure of mitochondrial DNA from the liverwort, Marchantia polymorpha [J]. J Mol Biol, 276(4): 745-758.

Osada N, Akashi H. 2012. Mitochondrial-nuclear interactions and accelerated compensatory evolution: evidence from the primate cytochrome C oxidase complex[J]. Mol Biol Evol, 29(1): 337-346.

Osawa S, Jukes TH. 1989. Codon reassignment (codon capture) in evolution[J]. J Mol Evol, 28(4): 271-278.

Osawa S, Jukes TH. 1995. On codon reassignment[J]. J Mol Evol, 41(2): 241-249.

Pagliarini DJ, Calvo SE, Chang B, Sheth SA, Vafai SB, Ong SE, Walford GA, Sugiana C, Boneh A, Chen WK, Hill DE, Vida M, Evans JG, Thorburn DR, Carr SA, Mootha VK. 2008. A mitochondrial protein compendium elucidates complex I disease biology[J]. Cell, 134(1): 112-123.

Paquin B, Laforest MJ, Forget L, Roewer I, Wang Z, Longcore J, Lang BF. 1997. The fungal mitochondrial genome project: evolution of fungal mitochondrial genomes and their gene expression[J]. Curr Genet, 31(5): 380-395.

Pereira L, Freitas F, Fernandes V, Pereira JB, Costa MD, Costa S, Máximo V, Macaulay V, Rocha R, Samuels DC. 2009. The diversity present in 5140 human mitochondrial genomes[J]. Am J Hum Genet, 84(5): 628-640.

Pereira SL, Baker AJ. 2006. A mitogenomic timescale for birds detects variable phylogenetic rates of molecular evolution and refutes the standard molecular clock[J]. Mol Biol Evol, 23(9): 1731-1740.

Puerta MVS, Bachvaroff TR, Delwiche CF. 2004. The complete mitochondrial genome sequence of the Haptophyte Emiliania huxleyi and its relation to Heterokonts[J]. DNA Res, 11(1): 1-10.

Rand DM. 2001. The units of selection on mitochondrial DNA[J]. Annu Rev Ecol Syst, 32: 415-448.

Rand DM, Kann LM. 1996. Excess amino acid polymorphism in mitochondrial DNA: contrasts among genes from Drosophila, mice, and humans[J]. Mol Biol Evol, 13(6): 735-748.

Rivera MC, Jain R, Moore JE, Lake JA. 1998. Genomic evidence for two functionally distinct gene classes[J]. Proc Natl Acad Sci USA, 95(11): 6239-6244.

Schindel DE, Miller SE. 2005. DNA barcoding a useful tool for taxonomists[J]. Nature, 435(7038): 17-19.

Schultz DW, Yarus M. 1994. Transfer RNA mutation and the malleability of the genetic code[J]. J Mol Biol, 235(5): 1377-1380.

Shen YY. 2010. The Genetic Basis of Adaption Evolution in Vertebrate Energy Metabolism [D]. Ph. D. thesis, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology.

Shen YY, Shi P, Sun YB, Zhang YP. 2009. Relaxation of selective constraints on avian mitochondrial DNA following the degeneration of flight ability[J]. Genome Res, 19(10): 1760-1765.

Shen YY, Liang L, Zhu ZH, Zhou WP, Irwin DM, Zhang YP. 2010. Adaptive evolution of energy metabolism genes and the origin of flight in bats[J]. Proc Natl Acad Sci USA, 107(19): 8666-8671.

Sengupta S, Higgs PG. 2005. A unified model of codon reassignment in alternative genetic codes[J]. Genetics, 170(2): 831-840.

Shields GF, Wilson AC. 1987. Calibration of mitochondrial DNA evolution in genes[J]. J Mol Evol, 24(3): 212-217.

Stewart JB, Freyer C, Elson JL, Wredenberg A, Cansu Z, Trifunovic A, Larsson NG. 2008. Strong purifying selection in transmission of mammalian mitochondrial DNA[J]. PLoS Biol, 6: e10.

Sun YB, Shen YY, Irwin DM, Zhang YP. 2011. Evaluating the roles of energetic functional constraints on teleost mitochondrial-encoded protein evolution[J]. Mol Biol Evol, 28(1): 39-44.

Swanson WJ, Vacquier VD. 2002. The rapid evolution of reproductive proteins[J]. Nat Rev Genet, 3(2): 137-144.

Thomas SP, Suthers RA. 1972. The physiology and energetics of bat flight[J]. J Exp Biol, 57: 317-335.

Ting N. 2008. Mitochondrial relationships and divergence dates of the African colobines: evidence of Miocene origins for the living colobus monkeys[J]. J Hum Evol, 55(2): 312-325.

Torroni A, Achilli A, Macaulay V, Richards M, Bandelt HJ. 2006. Harvesting the fruit of the human mtDNA tree[J]. Trends Genet, 22(6): 339-345.

Tzagoloff A, Myers AM. 1986. Genetics of mitochondrial biogenesis[J]. Annu Rev Biochem 55: 249-285.

Underhill PA, Kivisild T. 2007. Use of Y chromosome and mitochondrial DNA population structure in tracing human migrations[J]. Annu Rev Genet, 41: 539-564.

Unseld M, Marienfeld JR, Brandt P, Brennicke A. 1997. The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366, 924 nucleotides[J]. Nature Genet, 15(1): 57-61.

Wallace DC. 2010. Mitochondrial DNA mutations in disease and aging[J]. Environ Mol Mutagen, 51(5): 440-450.

Wang XP, Yu L, Roos C, Ting N, Chen CP, Wang J, Zhang YP. 2012. Phylogenetic relationships among the colobine monkeys revisited: new insights from analyses of complete mt genomes and 44 nuclear non-coding markers[J]. PLoS ONE, 7(4): e36274.

Wilson AC, Cann RL, Carr SM, George M, Gyllensten UB, Helm-bychowski KM, Higuchi RG, Palumbi SR, Prager EM, Sage RD, Stoneking M. 1985. Mitochondrial DNA and two perspectives on evolutionary genetics[J]. Biol J Linn Soc, 26(4): 375-400.

Yang D, Oyaizu Y, Oyaizu H, Olsen GJ, Woese CR. 1985. Mitochondrial origins[J]. Proc Nat Acad Sci USA, 82(13): 4443-4447.

Yokobori S, Suzuki T, Watanabe K. 2001. Genetic code variations in mitochondria: tRNA as a major determinant of genetic code plasticity[J]. J Mol Evol, 53(4-5): 314-326.

Zhang J. 2003. Evolution of the human ASPM gene, a major determinant of brain size[J]. Genetics, 165(4): 2063-2070.

Zuckerkandl E, Pauling L. 1965. Molecules as documents of evolutionary history[J]. J Theor Biol, 8(2): 357-366.

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