Haplogroup L1 (mtDNA)

Haplogroup L1
Possible time of origin	107,600–174,300 YBP[1]
Possible place of origin	Central Africa
Ancestor	L1-6
Descendants	L1b, L1c
Defining mutations	3666, 7055, 7389, 13789, 14178, 14560[2]

Haplogroup L1 is a human mitochondrial DNA (mtDNA) haplogroup. It is most common in Central Africa and West Africa. It diverged from L1-6 at about 140,000 years ago (140.6+33.7
−33.0 kya 95% CI).[3] Its emergence is associated with the early peopling of Africa by anatomically modern humans during the Eemian, and it is now mostly found in African pygmies.

Projected spatial distribution of haplogroup L1 in Africa.

Distribution

Haplogroup L1 is found most commonly in Central Africa and West Africa. It reaches its highest frequency among the Mbenga Pygmies. It is likely that it was formerly more widespread, and was constrained to its current area as a result of the Bantu migration (which is largely associated with haplogroup L2).[4] Haplogroup L1 has been observed in specimens from the island cemetery in Kulubnarti, Sudan, which date from the Early Christian period (AD 550–800).[5] An ancient Beaker culture individual at the Camino de las Yeseras in Spain (San Fernando de Henares, Madrid; [I4245 / RISE695] F) has also been found to carry the L1b1a mitochondrial haplogroup.[6]

Phylogeny

Interpolation maps for haplogroup L1b and L1c.

L1 has two branches, L1c and L1b (the formerly named haplogroups L1d, L1k, L1a, L1f have been re-classified into haplogroup L0, as L0d, L0k, L0a, L0f; L1e as L5).

L1c

Haplogroup L1c emerged at about 85 kya. It reaches its highest frequencies in West and Central Africa, notably among the Mbenga Pygmy peoples. (see map).[7] Among the Mbenga, it is carried by 100% of Ba-Kola, 97% of Ba-Benzélé, and 77% of Biaka.[8] Other populations in which L1c is particularly prevalent include the Tikar (100%), Baka people from Gabon (97%) and Cameroon (90%),[9] the Bakoya (97%), and the Ba-Bongo (82%).[7] Common also in São Tomé (20%) and Angola (16–24%).[10]

Phylogeny:[2]

L1c
- L1c1'2'4'6
  - L1c1
    - L1c1a
      - L1c1a1
        L1c1a1a
        L1c1a1a1
        L1c1a1a1a
        
        L1c1a1a1b
        L1c1a1a1b1
        
        L1c1a1a2
        
        L1c1a1b
      - L1c1a2
        L1c1a2a
        L1c1a2a1
        
        L1c1a2a2
        
        L1c1a2b
        
        L1c1a2c
    - L1c1b'c'd
      - L1c1b
      - L1c1c'd
        L1c1c
        
        L1c1d
  - L1c2'4
    - L1c2
      - L1c2a
        L1c2a1
        L1c2a1a
        
        L1c2a1b
        
        L1c2a2
      - L1c2b
        L1c2b1
        
        L1c2b2
    - L1c4
      - L1c4a
      - L1c4b
  - L1c6
- L1c3
  - L1c3a
    - L1c3a1
    - L1c3a1a
  - L1c3b'c
    - L1c3b
      - L1c3b1
        L1c3b1a
        
        L1c3b1b
      - L1c3b2
    - L1c3c

L1b

Haplogroup L1b is much more recent, dated at about 10 kya. It is frequent in West Africa. It has also been found in Mozambique (1%), Ethiopia (2%), Egypt (1%), the Nile Valley (4%), Kung (1%), Cape Verde (8%), Senegal (17–20%), Niger/Nigeria (15%), Guinea Bissau (11%), Morocco (4–5%), and Algeria (1–2%).[11]

Phylogeny:[2]

L1b
- L1b1
  - L1b1a
    - L1b1a1'4
      - L1b1a1
      - L1b1a4
    - L1b1a2
      - L1b1a2a
    - 189
      - L1b1a3
        L1b1a3a
        L1b1a3a1
    - L1b1a5
    - L1b1a6
    - L1b1b7

gollark: https://media.discordapp.net/attachments/733347369847881838/935562481701650462/unknown.png

gollark: Fear.

gollark: I guess none are safe.

gollark: Rust compilation appears to be consuming my entire CPU.

gollark: Of course, if I didn't have infinite computing power, I think I would do it accursedly by approximating everything as cubes, ??? octrees, and using a regular knapsack solver to decide what to attempt to 3D-pack.

References

Soares, Pedro; Luca Ermini; Noel Thomson; Maru Mormina; Teresa Rito; Arne Röhl; Antonio Salas; Stephen Oppenheimer; Vincent Macaulay; Martin B. Richards (4 Jun 2009). "Supplemental Data Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock". The American Journal of Human Genetics. 84 (6): 82–93. doi:10.1016/j.ajhg.2009.05.001. PMC 2694979. PMID 19500773.
van Oven, Mannis; Manfred Kayser (13 Oct 2008). "Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation". Human Mutation. 30 (2): E386–E394. doi:10.1002/humu.20921. PMID 18853457. Archived from the original on 4 December 2012. Retrieved 2009-05-20.
"Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock Supplementary material (p. 82)" (PDF). 2009: 89. Archived from the original (PDF) on 2009-12-29. Cite journal requires |journal= (help)
Silva, Marina; Alshamali, Farida; Silva, Paula; Carrilho, Carla; Mandlate, Flávio; Jesus Trovoada, Maria; Černý, Viktor; Pereira, Luísa; Soares, Pedro (2015). "60,000 years of interactions between Central and Eastern Africa documented by major African mitochondrial haplogroup L2". Sci. Rep. 5: 12526. doi:10.1038/srep12526. PMC 4515592. PMID 26211407.
Sirak, Kendra; Frenandes, Daniel; Novak, Mario; Van Gerven, Dennis; Pinhasi, Ron (2016). Abstract Book of the IUAES Inter-Congress 2016 - A community divided? Revealing the community genome(s) of Medieval Kulubnarti using next- generation sequencing. IUAES.
Iñigo Olalde et al. The Beaker Phenomenon And The Genomic Transformation Of Northwest Europe, 2017
Quintana-Murci; et al. (2008). "Maternal traces of deep common ancestry and asymmetric gene flow between Pygmy hunter–gatherers and Bantu-speaking farmers". Proceedings of the National Academy of Sciences of the United States of America. 105 (5): 1596–601. doi:10.1073/pnas.0711467105. PMC 2234190. PMID 18216239.
Sarah A. Tishkoff et al. 2007, History of Click-Speaking Populations of Africa Inferred from mtDNA and Y Chromosome Genetic Variation. Molecular Biology and Evolution 2007 24(10):2180-2195
Lluis Quintana-Murci et al. MtDNA diversity in Central Africa: from hunter-gathering to agriculturalism. CNRS-Institut Pasteur, Paris
Batini, Chiara et al 2006, Phylogeography of the human mitochondrial L1c haplogroup: Genetic signatures of the prehistory of Central Africa
Rosa, Alexandra; et al. (2004). "MtDNA profile of West Africa Guineans: towards a better understanding of the Senegambia region" (PDF). Annals of Human Genetics. 68 (4): 340–52. doi:10.1046/j.1529-8817.2004.00100.x. PMID 15225159. Retrieved 5 June 2017.

Notes

External links

PhyloTree.org - mtDNA subtree L, van Oven & Kayser M. 2009.
Spread of Haplogroup L1, from National Geographic
African Haplogroup L mtDNA Sequences Show Violations of Clock-like Evolution
Ian Logan's Haplogroup L1b.
Ian Logan's Haplogroup L1c.
L1 YFull MTree 1.02.00 (under construction)

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[Soares-1] Soares, Pedro; Luca Ermini; Noel Thomson; Maru Mormina; Teresa Rito; Arne Röhl; Antonio Salas; Stephen Oppenheimer; Vincent Macaulay; Martin B. Richards (4 Jun 2009). "Supplemental Data Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock". The American Journal of Human Genetics. 84 (6): 82–93. doi:10.1016/j.ajhg.2009.05.001. PMC 2694979. PMID 19500773.

[vanOven-2] van Oven, Mannis; Manfred Kayser (13 Oct 2008). "Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation". Human Mutation. 30 (2): E386–E394. doi:10.1002/humu.20921. PMID 18853457. Archived from the original on 4 December 2012. Retrieved 2009-05-20.

[soares_supplementary-3] "Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock Supplementary material (p. 82)" (PDF). 2009: 89. Archived from the original (PDF) on 2009-12-29. Cite journal requires |journal= (help)

[4] Silva, Marina; Alshamali, Farida; Silva, Paula; Carrilho, Carla; Mandlate, Flávio; Jesus Trovoada, Maria; Černý, Viktor; Pereira, Luísa; Soares, Pedro (2015). "60,000 years of interactions between Central and Eastern Africa documented by major African mitochondrial haplogroup L2". Sci. Rep. 5: 12526. doi:10.1038/srep12526. PMC 4515592. PMID 26211407.

[5] Sirak, Kendra; Frenandes, Daniel; Novak, Mario; Van Gerven, Dennis; Pinhasi, Ron (2016). Abstract Book of the IUAES Inter-Congress 2016 - A community divided? Revealing the community genome(s) of Medieval Kulubnarti using next- generation sequencing. IUAES.

[IOlalde-6] Iñigo Olalde et al. The Beaker Phenomenon And The Genomic Transformation Of Northwest Europe, 2017

[Quintana08-7] Quintana-Murci; et al. (2008). "Maternal traces of deep common ancestry and asymmetric gene flow between Pygmy hunter–gatherers and Bantu-speaking farmers". Proceedings of the National Academy of Sciences of the United States of America. 105 (5): 1596–601. doi:10.1073/pnas.0711467105. PMC 2234190. PMID 18216239.

[Tishkoff-8] Sarah A. Tishkoff et al. 2007, History of Click-Speaking Populations of Africa Inferred from mtDNA and Y Chromosome Genetic Variation. Molecular Biology and Evolution 2007 24(10):2180-2195

[9] Lluis Quintana-Murci et al. MtDNA diversity in Central Africa: from hunter-gathering to agriculturalism. CNRS-Institut Pasteur, Paris

[Batini-10] Batini, Chiara et al 2006, Phylogeography of the human mitochondrial L1c haplogroup: Genetic signatures of the prehistory of Central Africa

[Rosa2004-11] Rosa, Alexandra; et al. (2004). "MtDNA profile of West Africa Guineans: towards a better understanding of the Senegambia region" (PDF). Annals of Human Genetics. 68 (4): 340–52. doi:10.1046/j.1529-8817.2004.00100.x. PMID 15225159. Retrieved 5 June 2017.