Haplogroup L3 (mtDNA)

Haplogroup L3
Possible time of origin 80,000-104,000 YBP[1] or 60,000-70,000 YBP[2]
Possible place of origin East Africa[3]
Ancestor L3'4
Descendants L3a, L3b'f, L3c'd'j, L3e'i'k'x, L3h, M, N
Defining mutations 769, 1018, 16311[4]

Haplogroup L3 is a human mitochondrial DNA (mtDNA) haplogroup. The clade has played a pivotal role in the prehistory of the human species. It represents the most common parent maternal lineage of all people outside of Africa, and for many individuals within the continent as well.[5]

Origin

Ancient dispersal of haplogroup L3, its descendant M and N lineages, and other mtDNA clades. Numbers represent thousand years before present.

The exact place of origin of haplogroup L3 is uncertain. According to the Recent African origin of modern humans (Out-of-Africa) theory, the clade is believed to have arisen in Africa and dispersed from East Africa between 84,000 and 104,000 years ago.[1] An analysis of 369 complete African L3 sequences placed the maximal date of the clade's expansion at ∼70 ka. This virtually rules out a successful exit out of Africa before 74 ka, the date of the Toba volcanic super-eruption in Sumatra.[2] The Time to Most Recent Common Ancestor for the L3 lineage has also recently been estimated to be between 58,900 and 70,200 years ago.[2]

Distribution

Projected spatial distribution of haplogroup L3 in Africa and the Arabian peninsula.

L3 is common in Northeast Africa, in contrast to others parts of Africa where the haplogroups L1 and L2 represent two thirds of mtDNAs.[6][7] L3 sublineages are also frequent in the Arabian peninsula.

L3 is sub-divided into several clades, two of which spawned the macro-haplogroups M and N that are today carried by most people outside of Africa.[8] There is at least one relatively deep non-M, non-N clade of L3 outside Africa, L3f1b6, found at 1% in Asturias Spain, which diverged from African L3 lineages at least 10,000 years ago.[9]

According to Maca-Meyer et al. (2001), "L3 is more related to Eurasian haplogroups than to the most divergent African clusters L1 and L2".[10] L3 is the haplogroup from which all modern humans outside of Africa derive.[11]

Basal haplogroup L3* is found among Nubians (13.8%),[12] as well as Socotri (4.3%).[13]

Subclade distribution

L3 subclade distribution: L3b, L3d, L3e, L3f, L3h, L3i, L3x and L3w.

Undifferentiated L3 is widely distributed, particularly in the Chad Basin.[14] It is also found among Egyptians inhabiting El-Hayez oasis (11.4%).[7]

Tree

This phylogenetic tree of haplogroup L3 subclades is based on the paper by Mannis van Oven and Manfred Kayser Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation[4] and subsequent published research.

Most Recent Common Ancestor (MRCA)

See also

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

References

  1. 1 2 Gonder, M. K.; Mortensen, H. M.; Reed, F. A.; De Sousa, A.; Tishkoff, S. A. (2006). "Whole-mtDNA Genome Sequence Analysis of Ancient African Lineages". Molecular Biology and Evolution. 24 (3): 757–68. doi:10.1093/molbev/msl209. PMID 17194802.
  2. 1 2 3 http://mbe.oxfordjournals.org/content/early/2011/11/16/molbev.msr245.short?rss=1
  3. ↑ Salas, A; Richards, Martin; de la Fe, Tomás; Lareu, María-Victoria; Sobrino, Beatriz; Sánchez-Diz, Paula; MacAulay, Vincent; Carracedo, Ángel (2002). "The Making of the African mtDNA Landscape". The American Journal of Human Genetics. 71 (5): 1082–111. doi:10.1086/344348. PMC 385086Freely accessible. PMID 12395296.
  4. 1 2 Van Oven, Mannis; Kayser, Manfred (2009). "Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation". Human Mutation. 30 (2): E386–94. doi:10.1002/humu.20921. PMID 18853457.
  5. 1 2 3 4 5 6 7 8 9 Behar, Doron M.; Villems, Richard; Soodyall, Himla; Blue-Smith, Jason; Pereira, Luisa; Metspalu, Ene; Scozzari, Rosaria; Makkan, Heeran; et al. (2008). "The Dawn of Human Matrilineal Diversity". The American Journal of Human Genetics. 82 (5): 1130–40. doi:10.1016/j.ajhg.2008.04.002. PMC 2427203Freely accessible. PMID 18439549.
  6. ↑ Wallace DC et al. (2000), Origin of haplogroup M in Ethiopia, Am J Hum Genet 67(Suppl):217
  7. 1 2 Martina Kujanova; Luisa Pereira; Veronica Fernandes; Joana B. Pereira; Viktor Cerny (2009). "Near Eastern Neolithic Genetic Input in a Small Oasis of the Egyptian Western Desert". American Journal of Physical Anthropology. 140 (2): 336–346. doi:10.1002/ajpa.21078. PMID 19425100.
  8. ↑ Wallace, D; Brown, MD; Lott, MT (1999). "Mitochondrial DNA variation in human evolution and disease". Gene. 238 (1): 211–30. doi:10.1016/S0378-1119(99)00295-4. PMID 10570998.
  9. 1 2 Pardiñas, AF; Martínez, JL; Roca, A; García-Vazquez, E; López, B (2014). "Over the sands and far away: Interpreting an Iberian mitochondrial lineage with ancient Western African origins". Am J Hum Biol. 26 (6): 777–83. doi:10.1002/ajhb.22601 (inactive 2015-01-13). PMID 25130626.
  10. ↑ Maca-Meyer, Nicole; González, Ana M; Larruga, José M; Flores, Carlos; Cabrera, Vicente M (2001). "Major genomic mitochondrial lineages delineate early human expansions". BMC Genetics. 2: 13. doi:10.1186/1471-2156-2-13. PMC 55343Freely accessible. PMID 11553319.
  11. ↑ https://www.cambridgedna.com/genealogy-dna-ancient-migrations-slideshow.php?view=step3
  12. 1 2 3 Mohamed, Hisham Yousif Hassan. "Genetic Patterns of Y-chromosome and Mitochondrial DNA Variation, with Implications to the Peopling of the Sudan" (PDF). University of Khartoum. Retrieved 14 June 2016.
  13. ↑ Černý, Viktor; et al. (2009). "Out of Arabia—the settlement of island Soqotra as revealed by mitochondrial and Y chromosome genetic diversity" (PDF). American journal of Physical Anthropology. 138 (4): 439–447. Retrieved 14 June 2016.
  14. ↑ Cerezo, María; et al. (2011). "New insights into the Lake Chad Basin population structure revealed by high-throughput genotyping of mitochondrial DNA coding SNPs". PLoS One. 6 (4).
  15. ↑ Černý, Viktor; Fernandes, Verónica; Costa, Marta D; Hájek, Martin; Mulligan, Connie J; Pereira, Luísa (2009). "Migration of Chadic speaking pastoralists within Africa based on population structure of Chad Basin and phylogeography of mitochondrial L3f haplogroup". BMC Evolutionary Biology. 9: 63. doi:10.1186/1471-2148-9-63. PMC 2680838Freely accessible. PMID 19309521.
  16. 1 2 3 4 5 6 7 Kivisild, T; Reidla, M; Metspalu, E; Rosa, A; Brehm, A; Pennarun, E; Parik, J; Geberhiwot, T; et al. (2004). "Ethiopian Mitochondrial DNA Heritage: Tracking Gene Flow Across and Around the Gate of Tears". The American Journal of Human Genetics. 75 (5): 752–70. doi:10.1086/425161. PMC 1182106Freely accessible. PMID 15457403.
  17. 1 2 Liane Fendt et al., MtDNA diversity of Ghana: a forensic and phylogeographic view, 2011
  18. ↑ Sheet1 - PLOS Pathogens
  19. ↑ Anderson, S. 2006, Phylogenetic and phylogeographic analysis of African mitochondrial DNA variation.
  20. ↑ Bandelt, HJ; Alves-Silva, J; Guimarães, PE; Santos, MS; Brehm, A; Pereira, L; Coppa, A; Larruga, JM; et al. (2001). "Phylogeography of the human mitochondrial haplogroup L3e: a snapshot of African prehistory and Atlantic slave trade". Annals of Human Genetics. 65 (Pt 6): 549–63. doi:10.1017/S0003480001008892 (inactive 2015-01-13). PMID 11851985.
  21. ↑ Plaza, Stéphanie; Salas, Antonio; Calafell, Francesc; Corte-Real, Francisco; Bertranpetit, Jaume; Carracedo, Ángel; Comas, David (2004). "Insights into the western Bantu dispersal: mtDNA lineage analysis in Angola". Human Genetics. 115 (5): 439–47. doi:10.1007/s00439-004-1164-0. PMID 15340834.
  22. ↑ Asmahan Bekada; Lara R. Arauna; Tahria Deba; Francesc Calafell; Soraya Benhamamouch; David Comas (September 24, 2015). "Genetic Heterogeneity in Algerian Human Populations". PLoS ONE. 10 (9). doi:10.1371/journal.pone.0138453. Retrieved 13 May 2016.; S5 Table
  23. ↑ Fadhlaoui-Zid, K.; Plaza, S.; Calafell, F.; Ben Amor, M.; Comas, D.; Bennamar, A.; Gaaied, El (2004). "Mitochondrial DNA Heterogeneity in Tunisian Berbers". Annals of Human Genetics. 68 (Pt 3): 222–33. doi:10.1046/j.1529-8817.2004.00096.x. PMID 15180702.
  24. ↑ Stevanovitch, A.; Gilles, A.; Bouzaid, E.; Kefi, R.; Paris, F.; Gayraud, R. P.; Spadoni, J. L.; El-Chenawi, F.; Beraud-Colomb, E. (2004). "Mitochondrial DNA Sequence Diversity in a Sedentary Population from Egypt". Annals of Human Genetics. 68 (Pt 1): 23–39. doi:10.1046/j.1529-8817.2003.00057.x. PMID 14748828.

Notes

  1. ↑ GUR46 on table 1. is a mtDNA haplogroup L3x2a.

External links

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