Human mitochondrial DNA haplogroup

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Contemporary human mtDNA haplogroup distribution, based on analysis of 2,054 individuals from 26 populations. (a) Pie charts on the map. (b) Counts of haplogroups in table format. For populations details, see 1000 Genomes Project#Human genome samples. MtDNA haplogroup distribution among 2,054 individuals across 26 populations from the 1000 Genomes Project.png
Contemporary human mtDNA haplogroup distribution, based on analysis of 2,054 individuals from 26 populations. (a) Pie charts on the map. (b) Counts of haplogroups in table format. For populations details, see 1000 Genomes Project#Human genome samples.

In human genetics, a human mitochondrial DNA haplogroup is a haplogroup defined by differences in human mitochondrial DNA. Haplogroups are used to represent the major branch points on the mitochondrial phylogenetic tree. Understanding the evolutionary path of the female lineage has helped population geneticists trace the matrilineal inheritance of modern humans back to human origins in Africa and the subsequent spread around the globe.

Contents

The letter names of the haplogroups (not just mitochondrial DNA haplogroups) run from A to Z. As haplogroups were named in the order of their discovery, the alphabetical ordering does not have any meaning in terms of actual genetic relationships.

The hypothetical woman at the root of all these groups (meaning just the mitochondrial DNA haplogroups) is the matrilineal most recent common ancestor (MRCA) for all currently living humans. She is commonly called Mitochondrial Eve.

The rate at which mitochondrial DNA mutates is known as the mitochondrial molecular clock. It is an area of ongoing research with one study reporting one mutation per 8000 years. [2]

Phylogeny

mtDNA haplogroup tree and distribution map. The numbers are haplogroup labels, reported according to the http://www.phylotree.org/ nomenclature, and give the location of one of the mutations leading to the derived haplotype. (Only a single branch defining marker, preferably from the coding region, is shown.) The main geographic features of haplogroup distribution are highlighted with colour. MtDNA haplogroup tree and distribution map.gif
mtDNA haplogroup tree and distribution map. The numbers are haplogroup labels, reported according to the http://www.phylotree.org/ nomenclature, and give the location of one of the mutations leading to the derived haplotype. (Only a single branch defining marker, preferably from the coding region, is shown.) The main geographic features of haplogroup distribution are highlighted with colour.
Dispersal route of human mtDNA haplogroups Migration route of Human mtDNA haplogroups.png
Dispersal route of human mtDNA haplogroups

This phylogenetic tree is based Van Oven (2009). [4] In June 2022, an alternative phylogeny for haplogroup L was suggested [5]

Major mtDNA Haplogroups

Estimated world map of human migrations based on mtDNA haplogroups. Human migrations and mitochondrial haplogroups.PNG
Estimated world map of human migrations based on mtDNA haplogroups.

Macro-haplogroup L

Macro-haplogroup L is the most basal of human mtDNA haplogroups, from which all other haplogroups descend (specifically, from haplogroup L3). It is found mostly in Africa.

Macro-haplogroup M

Macro-haplogroup M is found mostly in Asia and the Americas. Its descendants are haplogroup M, haplogroup C, haplogroup Z, haplogroup D, haplogroup E, haplogroup G and haplogroup Q.

Macro-haplogroup N

Macro-haplogroup N is found mostly in Australia, the Americas and parts of Asia. Its descendants are haplogroup N, haplogroup O, haplogroup A, haplogroup S, haplogroup I, haplogroup W, haplogroup X and haplogroup Y, as well as macro-haplogroup R.

Macro-haplogroup R

Macro-haplogroup R is found mostly in Europe, Northern Africa, the Pacific and parts of Asia and the Americas. Its descendants are haplogroup R, haplogroup B, haplogroup F, haplogroup H, haplogroup V, haplogroup J, haplogroup T, haplogroup U and haplogroup K

Chronology

HaplogroupEst. time of origin (kya) [6] Possible place of originHighest frequencies
L200 Africa
L1-6170East Africa
L2-6150East Africa
L0150East Africa
L1140Central Africa
L3-6130
L5120
L290
L370East Africa
N70 East Africa or West Asia
M60 East Africa, West Asia or South Asia
R60 South Asia or Southeast Asia
U55North-East Africa or India (South Asia)
RT'JT55Middle East
JT50Middle East
U850Western Asia
R947
B444
F43
U4'942Central Asia
U535Western Asia
U635North Africa
J35
X30
K30
U5a27
HV27Near East
J1a27Near East
T27Mesopotamia
K127
I26
J124Near East
W20
U420Central Asia
X220
H20Western Asia
U5a118Europe
J1b11
V14
X2a13North America
H112
H312
X110

Geographical distribution

A 2004 paper suggested that the haplogroups most common in modern West Asian, North African and European populations were: H, J, K, N1, T, U4, U5, V, X and W. [7]

African haplogroups: L0, L1, L2, L3, L4, L5, L6, T, U5a

Australian haplogroups: M42a, M42c, M14, M15, Q, S, O, N, P. (Refs 1, 2, 3, 4, 5, 6)

Asian haplogroups: F, C, W, M, D, N, K, U, T, A, B, C, Z, U many number variants to each section

Research software

Assignment

Dating

Phylogeny

Maps

Ancient

Modern

Databases

Ancient

Modern

See also

References

  1. ↑ Rishishwar L, Jordan IK (2017). "Implications of human evolution and admixture for mitochondrial replacement therapy". BMC Genomics. 18 (1): 140. doi: 10.1186/s12864-017-3539-3 . PMC   5299762 . PMID   28178941.
  2. ↑ Loogvali, Eva-Liis; Kivisild, Toomas; Margus, Tõnu; Villems, Richard (2009), O'Rourke, Dennis (ed.), "Explaining the Imperfection of the Molecular Clock of Hominid Mitochondria", PLOS ONE, 4 (12): e8260, Bibcode:2009PLoSO...4.8260L, doi: 10.1371/journal.pone.0008260 , PMC   2794369 , PMID   20041137
  3. ↑ Kivisild T (2015). "Maternal ancestry and population history from whole mitochondrial genomes". Investig Genet. 6: 3. doi: 10.1186/s13323-015-0022-2 . PMC   4367903 . PMID   25798216.
  4. 1 2 van Oven M, Kayser M (February 2009). "Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation". Human Mutation. 30 (2): E386–94. doi: 10.1002/humu.20921 . PMID   18853457. S2CID   27566749.
  5. ↑ Maier P, Runfeldt G, Estes R, Vilar M (2022). "African mitochondrial haplogroup L7: a 100,000-year-old maternal human lineage discovered through reassessment and new sequencing". Nature. 12 (1): 10747. Bibcode:2022NatSR..1210747M. doi: 10.1038/s41598-022-13856-0 . PMC   9232647 . PMID   35750688. S2CID   250021505.
  6. ↑ "Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock Supplementary" (PDF). Cell: 82–83 [89]. 2009. Archived from the original (PDF) on 2009-12-29.
  7. ↑ Villems, Richard; Usanga, Esien; Mikerezi, Ilia; Gölge, Mukaddes; Claustres, Mireille; Michalodimitrakis, Emmanuel N.; Pappa, Kalliopi I.; Anagnou, Nicholas P.; Chaventré, André; Moisan, Jean-Paul; Richard, Christelle; Grechanina, Elena; Balanovska, Elena V.; Rudan, Pavao; Puzyrev, Valery; Stepanov, Vadim; Khusnutdinova, Elsa K.; Gusar, Vladislava; Balanovsky, Oleg P.; Peričić, Marijana; Barać, Lovorka; Golubenko, Maria; Lunkina, Arina; Laos, Sirle; Pennarun, Erwan; Parik, Jüri; Tolk, Helle-Viivi; Reidla, Maere; Tambets, Kristiina; Metspalu, Ene; Kivisild, Toomas; Derenko, Miroslava V.; Malyarchuk, Boris A.; Roostalu, Urmas; Loogväli, Eva-Liis (November 1, 2004). "Disuniting Uniformity: A Pied Cladistic Canvas of mtDNA Haplogroup H in Eurasia". Molecular Biology and Evolution. 21 (11): 2012–2021. doi: 10.1093/molbev/msh209 . PMID   15254257 – via academic.oup.com.
  8. ↑ Capri, Miriam; Castellani, Gastone; Franceschi, Claudio; Lomartire, Laura; Sevini, Federica; Vianello, Dario (2013-06-12). "HAPLOFIND: a new method for high-throughput mtDNA haplogroup assignment". Human Mutation. 34 (9): 1189–1194. doi: 10.1002/humu.22356 . eISSN   1098-1004.
  9. ↑ Binna, Robert; Kloss-Brandstätter, Anita; Kronenberg, Florian; Pacher, Dominic; Schönherr, Sebastian; Specht, Günther; Weissensteiner, Hansi (2010-10-19). "HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups". Human Mutaton: Variation, Informatics, and Disease. 32 (1): 25–32. doi: 10.1002/humu.21382 . eISSN   1098-1004.
  10. ↑ Kronenberg, Florian; Forer, Lukas; Schönherr, Sebastian; Weissensteiner, Hansi (2023-04-23). "Haplogrep 3 - an interactive haplogroup classification and analysis platform". Nucleic Acids Research. 51 (1): 263–268. doi:10.1093/nar/gkad284. eISSN   1362-4962. PMC   10320078 . PMID   37070190.
  11. ↑ García-Olivares, Victor; et al. (2021-10-15) [received 2021-08-04]. "A benchmarking of human mitochondrial DNA haplogroup classifiers from whole-genome and whole-exome sequence data". Scientific Reports. 11 (20510): 20510. doi:10.1038/s41598-021-99895-5. eISSN   2045-2322. PMC   8519921 . PMID   34654896.
  12. ↑ Kim, Dong-han; Kim, Kijeong; Kim, Kyung-yong; Kim, Yoonyeong; Kwon, Chulhwan (2020-04-23). "Haplotracker: a web application for simple and accurate mitochondrial haplogrouping using short DNA fragments". bioRxiv   10.1101/2020.04.23.057646v1 .
  13. ↑ Kayser, Manfred; van Oven, Mannis (2008-10-13). "Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation". Human Mutation. 30 (2): 386–394. doi: 10.1002/humu.20921 . eISSN   1098-1004. PMID   18853457.
  14. ↑ Various (2017-05-30). "Rosenblatt's ancient DNA map". Anthrogenica.
  15. ↑ Chyleński, Maciej; Ehler, Edvard; Juras, Anna; Moravčík, Ondřej; Novotný, Jiří; Pačes, Jan (2018-09-24). "AmtDB: a database of ancient human mitochondrial genomes". Nucleic Acids Research. 47 (D1): 29–32. doi:10.1093/nar/gky843. eISSN   1362-4962.
  16. ↑ Brown, Michael D.; Kogelnik, Andreas M.; Lott, Marie T.; Navathe, Shamkant B.; Wallace, Douglas C. (1996-01-01). "MITOMAP: A Human Mitochondrial Genome Database". Nucleic Acids Research. 24 (1): 177–179. doi:10.1093/nar/24.1.177. eISSN   1362-4962. PMC   145607 .

Phylogenetic tree of human mitochondrial DNA (mtDNA) haplogroups

  Mitochondrial Eve (L)  
L0 L1–6 
L1 L2   L3    L4 L5 L6
M N  
CZ D E G Q   O A S R   I W X Y
C Z B F R0   pre-JT   P   U
HV JT K
H V J T
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