Human mitochondrial DNA haplogroup

Phylogeny

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

Major 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). These haplogroups represent the majority of the typical sub-Saharan mtDNA variability. Approximately 65% of the European L lineages mostly likely arrived during the Arab conquest of Iberian Peninsula and Sicily and during the period of Atlantic slave trade. The remaining 35% of L mtDNAs form European-specific subclades, revealing that the gene flows from sub-Saharan Africa toward Europe from 11,000 years ago.

Macro-haplogroup H

Macro-haplogroup H is found mostly in European countries and forms ~40-45% of the European mitochondrial gene pool. Its focus has been an important aspect of human genetic diversity studies for more than a decade. It is estimated that the coalescence time for Hg H is ~21,000 years ago, which led to the proposal that the clade was involved in a post-glacial population re-expansion from southwestern Europe to the rest of the continent. Most of the population along the westernmost Mediterranean coasts, separated by a narrow body of water, shows the highest frequencies of mitochondrial haplogroup H. The most basal nodes of the most frequent H sub-haplogroup, H1 and H3, are found among many western Europeans origins (primarily in the Iberian and Maghrebian regions).

A 2017 study published in BMC Genomic Data analyzed mitochondrial DNA haplogroup H in 750 individuals from southern Spain, finding 337 carriers primarily from the Andalusian provinces of Huelva and Granada. The research revealed that both populations exhibited a predominantly western European genetic profile, though Granada showed additional affinities with eastern Mediterranean populations, suggesting historical gene flow. Sub-haplogroups H1 and H3 were the most common, with molecular dating indicating origins around 16,000 and 13,000 years ago, respectively, and shared ancestry between Iberian and North African groups. Significant haplotype sharing between Andalusia and Morocco pointed to the Strait of Gibraltar as a corridor for maternal gene exchange rather than a genetic barrier. Overall, haplogroup H frequencies of about 39% in Huelva and 48% in Granada highlighted local diversity shaped by post-glacial expansions and later trans-Mediterranean interactions.

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

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

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

Research software

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 discover tool for browsing their new mtDNA Haplotree. (Released 2025-02-25)
• FTDNA's mtDNA Haplotree: Mostly based on PhyloTree Build 17 but with the addition of haplogroup L7.
• FTDNA's Mitotree: "Classic" view of FTDNA's mtDNA tree.
• YFull's MTree: An mtDNA tree. Faster loading (simpler).
• PhyloTreemt: A traditional mtDNA tree (last updated 2016-02-18).
• HIP: Haplogroup trees.

Maps

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.

Databases

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.

References

References

1. Rishishwar L, Jordan IK. (2017). "Implications of human evolution and admixture for mitochondrial replacement therapy.". BMC Genomics.
2. (December 2017). "Implications of human evolution and admixture for mitochondrial replacement therapy". BMC Genomics.
3. (2011-11-25). "Degradation of Paternal Mitochondria by Fertilization-Triggered Autophagy in C. elegans Embryos". Science.
4. (2009). "Explaining the Imperfection of the Molecular Clock of Hominid Mitochondria". PLOS ONE.
5. (July 2025). "Inherited mitochondrial genetics as a predictor of immune checkpoint inhibition efficacy in melanoma". Nature Medicine.
6. Kivisild T. (2015). "Maternal ancestry and population history from whole mitochondrial genomes.". Investig Genet.
7. (February 2009). "Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation". Human Mutation.
8. (2022). "African mitochondrial haplogroup L7: a 100,000-year-old maternal human lineage discovered through reassessment and new sequencing". Nature.
9. (31 August 2004). "Most of the extant mtDNA boundaries in South and Southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans". BMC Genetics.
10. (May 2012). "Reconstructing ancient mitochondrial DNA links between Africa and Europe". Genome Research.
11. (2017-05-19). "The distribution of mitochondrial DNA haplogroup H in southern Iberia indicates ancient human genetic exchanges along the western edge of the Mediterranean". BMC Genetics.
12. (2009). "Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock Supplementary". Cell.
13. (November 1, 2004). "Disuniting Uniformity: A Pied Cladistic Canvas of mtDNA Haplogroup H in Eurasia". Molecular Biology and Evolution.
14. (2013-06-12). "HAPLOFIND: a new method for high-throughput mtDNA haplogroup assignment". Human Mutation.
15. (2010-10-19). "HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups". Human Mutation: Variation, Informatics, and Disease.
16. (2023-04-23). "Haplogrep 3 - an interactive haplogroup classification and analysis platform". Nucleic Acids Research.
17. García-Olivares, Victor. (2021-10-15). "A benchmarking of human mitochondrial DNA haplogroup classifiers from whole-genome and whole-exome sequence data". Scientific Reports.
18. (2020-04-23). "Haplotracker: a web application for simple and accurate mitochondrial haplogrouping using short DNA fragments".
19. (2008-10-13). "Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation". Human Mutation.
20. Various. (2017-05-30). "Rosenblatt's ancient DNA map".
21. (2018-09-24). "AmtDB: a database of ancient human mitochondrial genomes". Nucleic Acids Research.
22. (1996-01-01). "MITOMAP: A Human Mitochondrial Genome Database". Nucleic Acids Research.