Human mitochondrial DNA haplogroup

File:MtDNA haplogroup tree and distribution map.gif|thumb|350px|mtDNA haplogroup tree and distribution map. The numbers are haplogroup labels, reported according to the http://www.phylotree.org/ nomenclature, 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==

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)http://www.els.net • 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 • 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. • 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 • 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. • 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). • 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. ==See also==