Human mitochondrial DNA haplogroup



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.

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.

Phylogeny


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


 * L (Mitochondrial Eve)
 * L0
 * L1-6
 * L1
 * L2-6
 * L5
 * L2'3'4'6
 * L2
 * L3'4'6
 * L6
 * L3'4
 * L4
 * L3
 * N
 * N1: I
 * N2: W
 * N9: Y
 * A
 * S
 * X
 * R
 * R0 (FMKA pre-HV)
 * HV: (H, V)
 * pre-JT or R2'JT
 * JT: (J, T)
 * R9: F
 * R11'B: B
 * P
 * U (formerly UK)
 * U8: K
 * O
 * M
 * M9: E
 * M12'G: G
 * M29'Q: Q
 * D
 * M8: CZ (C, Z)

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.
 * Haplogroup L0
 * L1-7
 * Haplogroup L1
 * L2-7
 * L3'4'6
 * Haplogroup L2
 * L346
 * L34
 * Haplogroup L3
 * Haplogroup L4
 * Haplogroup L6
 * L5'7
 * Haplogroup L5
 * Haplogroup L7

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

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.

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)<!--
 * copyedit
 * move to Indigenous_Australians

M sub groups that are currently identified as specific to Australia are M42a, M42c, M14 and M15. Also Q1, Q1b, Q3a1 in northern Australia (Q is a major sub division of M also found in New Guinea.

N sub-groups are S, O (Australia).

R (itself derived from N) : P N: S & O. S: Haplogroup S has a wide distribution in Australia and has several major subclades, S1, S1a, S1b, S1b1, S1b2, S1b3, S2, S2a, S2b, S3, S4. The ancient matriline, called S1a has been characterised by complete and partial mt genomes in New South Wales, central, western, south Australia, Northern  Territory (Refs)and in Tasmania by partial sequences (ref 8) O haplogroup: O1, O2 identified by complete mt genome have  been identified in southern, northern and western Australia.

P haplogroup:

 Widespread in PNG, Timor (Ref 7), northern and eastern Australia. The Darling River region of NSW has a distinctive sub-clade called

P4b (now called P11), further diversified by into several distinct but culturally connected family lineages (van Holst Pellekaan 2011) and 2013.

References: -->
 * 1) van Holst Pellekaan, S.M., Ingman, M., Roberts-Thomson,     J., & Harding, R. M. 2006. Mitochondrial genomics identifies major     haplogroups in Aboriginal Australians. American J Physical Anthropology.     131:282-294.
 * 2) van Holst Pellekaan, S., 2011. Genetic evidence for the     colonization of Australia, Quaternary International.
 * 3) van Holst Pellekaan, Sheila M (March 2013) Origins of     the Australian and New Guinean Aborigines. In: eLS 2013, John Wiley &     Sons Ltd: Chichester http://www.els.net
 * 4) Nano Nagle1, Mannis van Oven2, Stephen Wilcox3, Sheila     van Holst Pellekaan4,5, Chris Tyler-Smith6, Yali Xue6, Kaye N.     Ballantyne2,7, Leah Wilcox1, Luka Papac1, Karen Cooke1, Roland A. H. van     Oorschot7, Peter McAllister8, Lesley Williams9, Manfred Kayser2, R. John     Mitchell1 & The Genographic Consortium#. Aboriginal Australian     mitochondrial genome variation – an increased understanding of population     antiquity and diversity. Scientific Reports | 7:43041 | DOI:     10.1038/srep43041
 * 5) Rasmussen, M., Guo, X., Wang, Y., Lohmueller, K. E.,     Rasmussen, S., Albrechtsen, A., Skotte, L., Lindgreen, S., Metspalu, M.,     Jombart, T., Kivisild, T., Zhai, W., Eriksson, A., Manica, A., Orlando,     L., De La Vega, F. M., Tridico, S., Metspalu, E., Nielsen, K.,     Avila-Arcos, M. C., Moreno-Mayar, J. V., Muller, C., Dortch, J., Gilbert,     M. T., Lund, O., Wesolowska, A., Karmin, M., Weinert, L. A., Wang, B., Li,     J., Tai, S., Xiao, F., Hanihara, T., Van Driem, G., Jha, A. R., Ricaut, F.     X., De Knijff, P., Migliano, A. B., Gallego Romero, I., Kristiansen, K., Lambert,     D. M., Brunak, S., Forster, P., Brinkmann, B., Nehlich, O., Bunce, M.,     Richards, M., Gupta, R., Bustamante, C. D., Krogh, A., Foley, R. A., Lahr,     M. M., Balloux, F., Sicheritz-Ponten, T., Villems, R., Nielsen, R., Wang,     J. & Willerslev, E. 2011. An Aboriginal Australian genome reveals     separate human dispersals into Asia. Science, 334, 94-8.
 * 6) Ray Tobler1*, Adam Rohrlach2,3*, Julien Soubrier1,4,     Pere Bover1, Bastien Llamas1, Jonathan Tuke2,3, Nigel Bean2,3, Ali     Abdullah-Highfold5, Shane Agius5, Amy O'Donoghue5, Isabel O'Loughlin5,     Peter Sutton5,6, Fran Zilio5, Keryn Walshe5, Alan N. Williams7, Chris S.M.     Turney7, Matthew Williams1,8, Stephen M. Richards1, Robert J. Mitchell9,     Emma Kowal10, John R. Stephen11, Lesley Williams12, Wolfgang Haak1,13§     & Alan Cooper1,14§ Aboriginal mitogenomes reveal 50,000 years of     regionalism in Australia
 * 7) Gomes, S. M., Bodner, M., Souto, L., Zimmermann, B.,     Huber, G., Strobl, C., Röck, A. W., Achilli, A., Olivieri, A., Torroni,     A., Côrte-Real, F. & Parson, W. 2015. Human settlement history between     Sunda and Sahul: a focus on East Timor (Timor-Leste) and the Pleistocenic     mtDNA diversity. BMC Genomics, 16.
 * 8) Ref: Presser JC, Deverell AJ, Redd A, and Stoneking M.     2002.Tasmanian Aborigines and DNA. Papers and Proceedings of the Royal     Society of Tasmania, 136:35-38).
 * 9) Hudjashov, G., Kivisild, T., Underhill, P. A.,     Endicott, P., Sanchez, J. J., Lin, A. A., Shen, P., Oefner, P., Renfrew,     C., Villems, R. & Forster, P. 2007. Revealing the prehistoric     settlement of Australia by Y chromosome and mtDNA analysis. Proc Natl Acad     Sci U S A, 104, 8726-30.

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

Assignment

 * mtHap: James Lick's tool (multiple input formats).
 * YSEQ mt Clade Finder: FASTA based haplogroup tool. Replaced HAPLOFIND.
 * HaploGrep: VCF based tool.
 * Haplocheck: Mitoverse's tool for both WGS and WES.
 * Haplotracker: A short fragment tool.
 * Haplogroup Finder: Ian Logan's SNP to haplogroup tool.

Dating

 * mtDNA Mutation Computer Model: Ian Logan's mutation calculator.

Phylogeny

 * FTDNA's mtDNA Haplotree: The largest mtDNA tree.
 * YFull's MTree: An mtDNA tree. Faster loading (simpler).
 * PhyloTreemt: A traditional mtDNA tree (last updated 2016-02-18).
 * HIP: Haplogroup trees.

Ancient

 * HIP Haplomap: Ancient uniparental map.
 * AH DNA: Nicky Rosenblatt's ancient uniparental map.
 * Ancient DNA: An aDNA map made with Map Maker.

Modern

 * HRAS mtDNA: A heatmap generator.

Ancient

 * AmtDB: An database of ancient mtDNA samples.
 * All Ancient DNA Dataset: Carlos Quiles' uniparental database (with BAM).

Modern

 * GenBank mtDNA Sequence Checker: Ian Logan's GenBank based accession matching tool.
 * mitoYDNA: A uniparental database.
 * MITOMAP: An mtDNA genome database.