Abstract
Mitochondria DNA (mtDNA) has distinct features from nuclear DNA. It has a circular DNA and coding its own genome. mtDNA consists of two regions, control region and coding region. Control region has start site for replication and transcription start sites. Coding regions have rRNAs and protein coding genes. Only the mtDNA in an oocyte is transmitted to the offspring, therefore it is transmitted through female lineage only. Thousands of mtDNA copies are in a cell and this makes mtDNA extraction easier. The mutation rate of mtDNA is higher than nuclear DNA. Hyper Variable Regions (HVR) in the control region have even higher mutation rates. Because of these features, mtDNA is frequently used for forensic studies or ancient DNA studies. Closely related mtDNA sequences are grouped into haplogroups. The combination of mutation including recurrent mutations determines the haplogroup. Whole mtDNA sequences are ideal for determining haplogroup. Caution is needed when haplogroups are determined based on control region.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Anderson S, Bankier AT, Barrell BG, De Bruijn M (1981) Sequence and organization of the human mitochondrial genome. Nature 290:457–465
Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N (1999) Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet 23:147
Awadalla P, Eyre-Walker A, Smith JM (1999) Linkage disequilibrium and recombination in hominid mitochondrial DNA. Science 286:2524–2525
Behar DM, van Oven M, Rosset S, Metspalu M, Loogväli E-L, Silva NM, Kivisild T, Torroni A, Villems R (2012) A “Copernican” reassessment of the human mitochondrial DNA tree from its root. Am J Hum Genet 90:675–684
Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu C-H, Xie D, Suchard MA, Rambaut A, Drummond AJ (2014) BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol 10:e1003537
Brown DT, Samuels DC, Michael EM, Turnbull DM, Chinnery PF (2001) Random genetic drift determines the level of mutant mtDNA in human primary oocytes. Am J Hum Genet 68:533–536
Chatters JC, Kennett DJ, Asmerom Y, Kemp BM, Polyak V, Blank AN, Beddows PA, Reinhardt E, Arroyo-Cabrales J, Bolnick DA, Malhi RS, Culleton BJ, Erreguerena PL, Rissolo D, Morell-Hart S, Stafford TW Jr (2014) Late Pleistocene human skeleton and mtDNA link Paleoamericans and modern native Americans. Science 344:750–754
Chinnery PF, Elliott HR, Syed A, Rothwell PM, Oxford Vascular Study (2010) Mitochondrial DNA haplogroups and risk of transient ischaemic attack and ischaemic stroke: a genetic association study. Lancet Neurol 9:498–503. https://doi.org/10.1016/S1474-4422(10)70083-1
Dowling DK, Friberg U, Lindell J (2008) Evolutionary implications of non-neutral mitochondrial genetic variation. Trends Ecol Evol 23:546–554
Drummond AJ, Rambaut A, Shapiro B, Pybus OG (2005) Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol 22:1185–1192
Fagundes NJRN, Kanitz RR, Eckert RR, Valls ACSA, Bogo MRM, Salzano FMF, Smith DGD, Silva WAW, Zago MAM, Ribeiro-dos-Santos AKA, Santos SEBS, Petzl-Erler MLM, Bonatto SLS (2008) Mitochondrial population genomics supports a single pre-Clovis origin with a coastal route for the peopling of the Americas. Am J Hum Genet 82:583–592
Fenner JN (2005) Cross-cultural estimation of the human generation interval for use in genetics-based population divergence studies. Am J Phys Anthropol 128:415–423
Gaweda-Walerych K, Maruszak A, Safranow K, Bialecka M, Klodowska-Duda G, Czyzewski K, Slawek J, Rudzinska M, Styczynska M, Opala G, Drozdzik M, Canter JA, Barcikowska M, Zekanowski C (2008) Mitochondrial DNA haplogroups and subhaplogroups are associated with Parkinson's disease risk in a Polish PD cohort. J Neural Transm 115:1521–1526
Ghezzi D, Marelli C, Achilli A, Goldwurm S, Pezzoli G, Barone P, Pellecchia MT, Stanzione P, Brusa L, Bentivoglio AR, Bonuccelli U, Petrozzi L, Abbruzzese G, Marchese R, Cortelli P, Grimaldi D, Martinelli P, Ferrarese C, Garavaglia B, Sangiorgi S, Carelli V, Torroni A, Albanese A, Zeviani M (2005) Mitochondrial DNA haplogroup K is associated with a lower risk of Parkinson’s disease in Italians. Eur J Hum Genet 13:748–752
Green RE, Malaspinas A-S, Krause J, Briggs AW, Johnson PLF, Uhler C, Meyer M, Good JM, Maricic T, Stenzel U, Prüfer K, Siebauer M, Burbano HA, Ronan M, Rothberg JM, Egholm M, Rudan P, Brajkovic D, Kucan Z, Gusic I, Wikström M, Laakkonen L, Kelso J, Slatkin M, Pääbo S (2008) A complete neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell 134:416–426
Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MHY, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, Alkan C, Prufer K, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Hober B, Hoffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, Novod N, Affourtit J, Egholm M, Verna C, Rudan P, Brajkovic D, Kucan Z, Gusic I, Doronichev VB, Golovanova LV, Lalueza-Fox C, la Rasilla de M, Fortea J, Rosas A, Schmitz RW, Johnson PLF, Eichler EE, Falush D, Birney E, Mullikin JC, Slatkin M, Nielsen R, Kelso J, Lachmann M, Reich D, Pääbo S (2010) A draft sequence of the neandertal genome. Science 328:710–722
Greenberg JH, Turner CG, Zegura SL, Campbell L (1986) The settlement of the Americas: a comparison of the linguistic, dental, and genetic evidence. Curr Anthropol 27:477–497
Haas RH (2010) Autism and mitochondrial disease. Dev Disabil Res Rev 16:144–153
Hagen CM, Aidt FH, Hedley PL, Jensen MK, Havndrup O, Kanters JK, Moolman-Smook JC, Larsen SO, Bundgaard H, Christiansen M (2013) Mitochondrial haplogroups modify the risk of developing hypertrophic cardiomyopathy in a Danish population. PLoS ONE 8:e71904
Howell N, Bindoff LA, McCullough DA, Kubacka I, Poulton J, Mackey D, Taylor L, Turnbull DM (1991) Leber hereditary optic neuropathy: identification of the same mitochondrial ND1 mutation in six pedigrees. Am J Hum Genet 49:939–950
Howell N, Smejkal CB, Mackey DA, Chinnery PF, Turnbull DM, Herrnstadt C (2003) The pedigree rate of sequence divergence in the human mitochondrial genome: there is a difference between phylogenetic and pedigree rates. Am J Hum Genet 72:659–670
Hudson G, Sims R, Harold D, Chapman J, Hollingworth P, Gerrish A, Russo G, Hamshere M, Moskvina V, Jones N, Thomas C, Stretton A, Holmans PA, O’Donovan MC, Owen MJ, Williams J, Chinnery PF, GERAD1 Consortium (2012) No consistent evidence for association between mtDNA variants and Alzheimer disease. Neurology 78:1038–1042
Hudson G, Gomez-Duran A, Wilson IJ, Chinnery PF (2014) Recent mitochondrial DNA mutations increase the risk of developing common late-onset human diseases. PLoS Genet 10:e1004369
Ingman M, Kaessmann H, Pääbo S, Gyllensten U (2000) Mitochondrial genome variation and the origin of modern humans. Nature 408:708–713
Innan H, Nordborg M (2002) Recombination or mutational hot spots in human mtDNA? Mol Biol Evol 19:1122–1127
Jobling MA, Hollox E, Hurles M, Kivisild T, Tyler-Smith C (2014) Human evolutionary genetics. Garland Science, New York
Johns DR, Neufeld MJ, Park RD (1992) An ND-6 mitochondrial DNA mutation associated with leber hereditary optic neuropathy. Biochem Biophys Res Commun 187:1551–1557
Jorde LB, Bamshad M (2000) Questioning evidence for recombination in human mitochondrial DNA. Science 288:1931
Kivisild T, Villems R (2000) Questioning evidence for recombination in human mitochondrial DNA. Science 288:1931
Kraytsberg Y, Schwartz M, Brown TA, Ebralidse K, Kunz WS, Clayton DA, Vissing J, Khrapko K (2004) Recombination of human mitochondrial DNA. Science 304:981
Krings M, Stone A, Schmitz RW, Krainitzki H, Stoneking M, Pääbo S (1997) Neandertal DNA sequences and the origin of modern humans. Cell 90:19–30
Kumar S (2005) Molecular clocks: four decades of evolution. Nat Rev Genet 6:654–662
Kumar S, Hedrick P, Dowling T, Stoneking M (2000) Questioning evidence for recombination in human mitochondrial DNA. Science 288:1931
Li M, Schönberg A, Schaefer M, Schroeder R, Nasidze I, Stoneking M (2010) Detecting heteroplasmy from high-throughput sequencing of complete human mitochondrial DNA genomes. Am J Hum Genet 87:237–249
Man PYW, Griffiths PG, Brown DT, Howell N, Turnbull DM, Chinnery PF (2003) The epidemiology of Leber hereditary optic neuropathy in the North East of England. Am J Hum Genet 72:333–339
Mancuso M, Conforti FL, Rocchi A, Tessitore A, Muglia M, Tedeschi G, Panza D, Monsurrò M, Sola P, Mandrioli J, Choub A, DelCorona A, Manca ML, Mazzei R, Sprovieri T, Filosto M, Salviati A, Valentino P, Bono F, Caracciolo M, Simone IL, La Bella V, Majorana G, Siciliano G, Murri L, Quattrone A (2004) Could mitochondrial haplogroups play a role in sporadic amyotrophic lateral sclerosis? Neurosci Lett 371:158–162
Mancuso M, Nardini M, Micheli D, Rocchi A, Nesti C, Giglioli NJ, Petrozzi L, Rossi C, Ceravolo R, Bacci A, Choub A, Ricci G, Tognoni G, Manca ML, Siciliano G, Murri L (2007) Lack of association between mtDNA haplogroups and Alzheimer’s disease in Tuscany. Neurol Sci 28:142–147
Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A, Cho JH, Guttmacher AE, Kong A, Kruglyak L, Mardis E, Rotimi CN, Slatkin M, Valle D, Whittemore AS, Boehnke M, Clark AG, Eichler EE, Gibson G, Haines JL, Mackay TFC, McCarroll SA, Visscher PM (2009) Finding the missing heritability of complex diseases. Nature 461:747–753
Moraes CT, DiMauro S, Zeviani M, Lombes A, Shanske S, Miranda AF, Nakase H, Bonilla E, Werneck LC, Servidei S (1989) Mitochondrial DNA deletions in progressive external ophthalmoplegia and Kearns-Sayre syndrome. N Engl J Med 320:1293–1299
Osada N, Akashi H (2012) Mitochondrial-nuclear interactions and accelerated compensatory evolution: evidence from the primate cytochrome C oxidase complex. Mol Biol Evol 29:337–346
Pakendorf B, Stoneking M (2005) Mitochondrial DNA and human evolution. Annu Rev Genomics Hum Genet 6:165–183
Parsons TJ, Irwin JA (2000) Questioning evidence for recombination in human mitochondrial DNA. Science 288:1931
Patti ME, Corvera S (2010) The role of mitochondria in the pathogenesis of type 2 diabetes. Endocr Rev 31:364–395
Prezant TR, Agapian JV, Bohlman MC, Bu X, Öztas S, Qiu W-Q, Arnos KS, Cortopassi GA, Jaber L, Rotter JI, Shohat M, Fischel-Ghodsian N (1993) Mitochondrial ribosomal RNA mutation associated with both antibiotic-induced and non-syndromic deafness. Nat Genet 4:289–294
Ramos A, Santos C, Mateiu L, Gonzalez MDM, Alvarez L, Azevedo L, Amorim A, Aluja MP (2013) Frequency and pattern of heteroplasmy in the complete human mitochondrial genome. PLoS ONE 8:e74636
Reich D, Patterson N, Campbell D, Tandon A, Mazieres S, Ray N, Parra MV, Rojas W, Duque C, Mesa N, García LF, Triana O, Blair S, Maestre A, Dib JC, Bravi CM, Bailliet G, Corach D, Hünemeier T, Bortolini MC, Salzano FM, Petzl-Erler ML, Acuña-Alonzo V, Aguilar-Salinas C, Canizales-Quinteros S, Tusié-Luna T, Riba L, Rodríguez-Cruz M, Lopez-Alarcón M, Coral-Vazquez R, Canto-Cetina T, Silva-Zolezzi I, Fernandez-Lopez JC, Contreras AV, Jimenez-Sanchez G, Gómez-Vázquez MJ, Molina J, Carracedo A, Salas A, Gallo C, Poletti G, Witonsky DB, Alkorta-Aranburu G, Sukernik RI, Osipova L, Fedorova SA, Vasquez R, Villena M, Moreau C, Barrantes R, Pauls D, Excoffier L, Bedoya G, Rothhammer F, Dugoujon J-M, Larrouy G, Klitz W, Labuda D, Kidd J, Kidd K, Di Rienzo A, Freimer NB, Price AL, Ruiz-Linares A (2012) Reconstructing native American population history. Nature 488:370–374
Richards MB, Macaulay VA, Bandelt H-J, Sykes BC (1998) Phylogeography of mitochondrial DNA in western Europe. Ann Hum Genet 62:241–260
Ruiz-Pesini E, Lapeña AC, Díez-Sánchez C, Pérez-Martos A, Montoya J, Alvarez E, Díaz M, Urriés A, Montoro L, López-Pérez MJ, Enríquez JA (2000) Human mtDNA haplogroups associated with high or reduced spermatozoa motility. Am J Hum Genet 67:682–696
Santos C, Montiel R, Sierra B, Bettencourt C, Fernandez E, Alvarez L, Lima M, Abade A, Aluja MP (2005) Understanding differences between phylogenetic and pedigree-derived mtDNA mutation rate: a model using families from the Azores Islands (Portugal). Mol Biol Evol 22:1490–1505
Scally A, Durbin R (2012) Revising the human mutation rate: implications for understanding human evolution. Nat Rev Genet 13:745–753
Schurr TG, Ballinger SW, Gan YY, Hodge JA, Merriwether DA, Lawrence DN, Knowler WC, Weiss KM, Wallace DC (1990) Amerindian mitochondrial DNAs have rare Asian mutations at high frequencies, suggesting they derived from four primary maternal lineages. Am J Hum Genet 46:613–623
Smith DG, Malhi RS, Eshleman J, Lorenz JG, Kaestle FA (1999) Distribution of mtDNA haplogroup X among Native North Americans. Am J Phys Anthropol 110:271–284
Stanford D, Bradley B (2002) Ocean trails and prairie paths? Thoughts about Clovis origins. In: Jablonski N (ed) The First Americans: the Pleistocene colonization of the new world, vol 27. Memoirs of the California Academy of Sciences, San Francisco, pp 255–271
Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585–595
Takahata N (2007) Molecular clock: an anti-neo-Darwinian legacy. Genetics 176:1–6
Torroni A, Schurr TG, Cabell MF, Brown MD, Neel JV, Larsen M, Smith DG, Vullo CM, Wallace DC (1993) Asian affinities and continental radiation of the four founding Native American mtDNAs. Am J Hum Genet 53:563–590
van den Ouweland JMW, Lemkes HHPJ, Ruitenbeek W, Sandkuijl LA, de Vijlder MF, Struyvenberg PAA, van de Kamp JJP, Maassen JA (1992) Mutation in mitochondrial tRNALeu(UUR) gene in a large pedigree with maternally transmitted type II diabetes mellitus and deafness. Nat Genet 1:368–371
van der Walt JM, Dementieva YA, Martin ER, Scott WK, Nicodemus KK, Kroner CC, Welsh-Bohmer KA, Saunders AM, Roses AD, Small GW, Schmechel DE, Murali Doraiswamy P, Gilbert JR, Haines JL, Vance JM, Pericak-Vance MA (2004) Analysis of European mitochondrial haplogroups with Alzheimer disease risk. Neurosci Lett 365:28–32
van Oven M, Kayser M (2009) Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 30:E386–E394. https://doi.org/10.1002/humu.20921
Wallace DC (2012) Mitochondria and cancer. Nat Rev Cancer 12:685–698
Wallace DC, Singh G, Lott MT, Hodge JA, Schurr TG, Lezza AM, Nikoskelainen EK (1988) Mitochondrial DNA mutation associated with Leber’s hereditary optic neuropathy. Science 242:1427–1430
White DJ, Bryant D, Gemmell NJ (2013) How good are indirect tests at detecting recombination in human mtDNA? G3; genes|genomes|. Genetics 3:1095–1104
Williams RC, Steinberg AG, Gershowitz H, Bennett PH, Knowler WC, Pettitt DJ, Butler W, Baird R, Dowda-Rea L, Burch TA (1985) GM allotypes in native Americans: evidence for three distinct migrations across the Bering land bridge. Am J Phys Anthropol 66:1–19
Zsurka G, Kraytsberg Y, Kudina T, Kornblum C, Elger CE, Khrapko K, Kunz WS (2005) Recombination of mitochondrial DNA in skeletal muscle of individuals with multiple mitochondrial DNA heteroplasmy. Nat Genet 37:873–877
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2021 Springer Japan KK, part of Springer Nature
About this chapter
Cite this chapter
Gojobori, J. (2021). Mitochondrial DNA. In: Saitou, N. (eds) Evolution of the Human Genome II. Evolutionary Studies. Springer, Tokyo. https://doi.org/10.1007/978-4-431-56904-6_4
Download citation
DOI: https://doi.org/10.1007/978-4-431-56904-6_4
Published:
Publisher Name: Springer, Tokyo
Print ISBN: 978-4-431-56902-2
Online ISBN: 978-4-431-56904-6
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)