Haplogroup L2 (mtDNA)

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Haplogroup L2
Possible time of origin 68,100-111,100 YBP[1]
Possible place of origin East Africa
Ancestor L2─6
Descendants L2a─d, L2e
Defining mutations 146, 150, 152, 2416, 8206, 9221, 10115, 13590, 16311!, 16390[2]

In human mitochondrial genetics, Haplogroup L2 is a human mitochondrial DNA (mtDNA) haplogroup typical of Africa. Its subclade L2a is a somewhat frequent and widespread mtDNA cluster in Africa, as well as in the African diaspora Americans (19%).(Salas 2002) et al.

Contents

[edit] Origin

L2 is a common African lineage. It is believed to have evolved between 87,000 to 107,000 years ago[3] or aprox. 90,000 YBP.[1] Its age and widespread distribution and diversity across the continent makes its exact origin point within Africa difficult to trace with any confidence.[4] Several L2 haplotypes observed in Guineans and other West Africa populations shared genetic matches with East Africa and North Africa.[5] An origin for L2b, L2c, L2d and L2e in West or Central Africa seems likely.[4] The early diversity of L2 can be observed all over the African Continent, but as we can see in Subclades section below, the highest diversity is found in West Africa. Most of subclades are largely confined to West and western-Central Africa.[6]

[edit] Distribution

L2 is the most common African haplogroup and it can be observed all over the African Continent. L2 is found in approximately one third of Africans and their recent descendants.

The highest frequency is in Mbuti Pygmies (64%).[7] Important presence in Western Africa, specially in Senegal (43-54%).[5] Also important in Non-Bantu populations of East Africa (44%),[8] in Sudan and Mozambique.

It is particularly abundant in Chad and the Kanembou (38% of the sample), but is also relatively frequent in Nomadic Arabs (33%) [Cerny et al. 2007] [4] and Akan people (~33%)[9]

[edit] Subclades

Haplogroup L2 family tree
Haplogroup L2 
 
 

 L2a


 

 L2b


 L2c



 L2d



 L2e


L2 has five main subgroups: L2a, L2b, L2c, L2d and L2e. The most common L2 sub group is Haplogroup L2a, both in Africa and the Levant.

[edit] Haplogroup L2a

L2a is widespread in Africa and the most common and widely distributed sub-Saharan African Haplogroup and is also somewhat frequent at 19% in the Americas among descendants of Africans (Salas et al., 2002). L2a has a possible date of origin approx. 48,000 YBP.[1]

It is particularly abundant in Chad (38% of the sample), and in Non-Bantu populations of East Africa (Kenya, Uganda and Tanzania) at 38%.[8] About 33% in Mozambique[10] and 32% in Ghana.[9]

This subclade is characterised by mutations at 2789, 7175, 7274, 7771, 11914, 13803, 14566 and 16294. It represents 52% of the total L2 and is the only subclade of L2 to be widespread all over Africa.[11]

The wide distribution of L2a and diversity makes identifying a geographical origin difficult. The main puzzle is the almost ubiquitous Haplogroup L2a, which may have spread East and West along the Sahel Corridor in North Africa after the Last Glacial Maximum, or the origins of these expansions may lie earlier, at the beginnings of the Later Stone Age, ∼40,000 years ago.[4][11]

In East Africa L2a was found 15% in Nile Valley- Nubia, 5% of Egyptians, 14% of Cushite speakers, 15% of Semitic Amhara people, 10% of Gurage, 6% of Tigray-Tigrinya people, 13% of Ethiopians and 5% of Yemenis.[10]

Haplogroup L2a also appears in North Africa, with the highest frequency 20% Tuareg, Fulani (14%). Found also among some Algeria Arabs, it is found at 10% among Moroccan Arabs, some Moroccan Berbers and Tunisian Berbers. (watson 1997) et al., (vigilant 1991) et al. 1991.

[edit] Haplogroup L2a1

L2a can be further divided into L2a1, harboring the transition at 16309 (Salas et al. 2002). The most extensive pan-African haplotype (16189 16192 16223 16278 16294 16309 16390) is in the L2a1 haplogroup.

This sequence is observed in West Africa among the Malinke, Wolof, and others; in North Africa among the Maure/Moor, Hausa, Fulbe, and others; in Central Africa among the Bamileke, Fali, and others; in South Africa among the Khoisan family including the Khwe and Bantu speakers; and in East Africa among the Kikuyu from Kenya. Closely related variants are observed among the Tuareg in North Africa and West Africa and among the East African Dinka and Somali People. (Ely et al. 2006; Watson et al. 1997)

All Ethiopian L2 lineages can be seen as derived from the two subclades L2a1 and L2b. L2a1 is defined by mutations at 12693, 15784 and 16309. Most Ethiopian L2a1 sequences share mutations at nps 16189 and 16309. However, whereas the majority (26 out of 33) "African Americans" share Haplogroup L2a complete sequences could be partitioned into four subclades by substitutions at nps L2a1e-3495, L2a1a-3918, L2a1f-5581, and L2a1i-15229. None of those sequences, were observed in Ethiopian 16309 L2a1 samples. (salas 2002) et al.

Matrilineal Ancestry of Ashkenazi Jewry: Haplogroup L2a1: A Portrait of a Recent Founder Event, displays the small frequency of L2a1/L2a1f {Doron M. Behar, Ene Metspalu, Toomas Kivisild,} 2006.

[edit] Haplogroup L2a1a

Subclade L2a1a is defined by substitutions at 3918, 5285, 15244, and 15629. There are two L2a clusters well represented in southeastern Africans, L2a1a and L2a1b, both defined by transitions at quite stable HVS-I positions. Both of these appear to have an origin in West Africa or North West Africa (as indicated by the distribution of matching or neighboring types), and to have undergone dramatic expansion either in South East Africa or in a population ancestral to present-day Southeastern Africans.

The very recent starbursts in subclades L2a1a and L2a2 suggest a signature for the Bantu expansions, as also suggested by Pereira et al. (2001).

L2a1a is defined by a mutation at 16286. The L2a1a founder candidate dates to 2,700 (SE 1,200) years ago. (Pereira et al. 2001). However, a prehistoric introgression of African mtDNA lineages into Eastern Europe (approximately 10 000 years ago) seems to be probable only for European- specific subclade L2a1a, defined by coding region mutations at positions 6722 and 12903 and detected in Czechs and Slovaks. It was previously known as L2a1a and found at its highest frequency in southeastern Africa. However, L2a1a, as defined by a substitution at (np 16286) (Salas et al. 2002), is now supported by a coding-region marker (np 3918) (fig. 2A) and was found in four of six Yemeni L2a1 lineages. L2a1a occurs at its highest frequency in Southeastern Africa (Pereira et al. 2001; Salas et al. 2002). Both the frequent founder haplotype and derived lineages (with 16092 mutation) found among Yemenis have exact matches within Mozambique sequences (Pereira et al. 2001; Salas et al. 2002). L2a1a also occurs at a smaller frequency in North West Africa, among the Maure and Bambara of Mali and Mauritania.[12] (Rando et al. 1998; Maca-Meyer et al. 2003)

Haplogroup L2a1a1

L2a1a1 is defined by markers 6152C, 15391T, 16368C

[edit] Haplogroup L2a1b

L2a1b is defined by substitutions at 16189 and 10143. 16192 is also common in L2a1b and L2a1c; it appears in Southeastern Africa and so appears to be a marker for the Bantu expansion.[4]

[edit] Haplogroup L2a1c

L2a1c shares mutation 16189 with L2a1b, and has its own markers at 3010 and 6663. 16192 is also common in L2a1b and L2a1c; it appears in Southeastern Africa as well as East Africa.[13] This suggests some diversification of this clade in situ.

Positions T16209C C16301T C16354T on top of L2a1 define a small sub-clade, dubbed L2a1c by Kivisild et al. (2004, Figure 3) (see also Figure 6 in Salas et al. 2002), which mainly appears in East Africa (e.g. Sudan, Nubia, Ethiopia) and West Africa (e.g. Turkana, Kanuri).

In the Chad Basin four different L2a1c types, one or two mutational steps from the East and West African types, were identified. (Kivisild et al.) 2004.[13] (citation on page.9 or 443)[14]

Haplogroup L2a1c1

L2a1c1 has a North African origin. It is defined by markers 198, 930, 3308, 8604, 16086.

L2a1c1 haplogroup is observed among Tunisia Sephardic, Ashkenazi, Hebrews, Moroccans, Egyptians, Nubians, Yemenis etc.

[edit] Haplogroup L2a2

It is characteristic of Mbuti Pygmies.[7]

[edit] Haplogroup L2b'c

L2b'c probably evolved c. 62,000 years ago.[1]

[edit] Haplogroup L2b

This subclade is predominantly found in West Africa, but it spreads all over Africa.[15]

[edit] Haplogroup L2c

L2c is most frequent in Western Africa and may have arisen there.[11] Specially present in Senegal at 39%, Cape Verde 16% and Guinea-Bissau 16%.[5]

[edit] Haplogroup L2d

L2d is most frequent in Western Africa and may have arisen there.[11] It is found in Yemen, Mozambique and Sudan.[10]

[edit] Haplogroup L2e

L2e (former L2d2) is typical in West Africa.[4] It is found in Tunisia,[16] in Mandinka people from Guinea-Bissau and in Afro-Americans.[15]

[edit] Ancient DNA

No ancient DNA has so far been retrieved from African remains, with the exception of Haplogroup L2a1, which was found in two specimens from the Southern Levant Pre-Pottery Neolithic B site at Tell Halula, Syria, dating from the period between ca. 9600 and ca. 8000 BP or 7500 - 6000 BCE.[17]

[edit] Tree

This phylogenetic tree of haplogroup L2 subclades is based on the paper by Mannis van Oven and Manfred Kayser Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation[2] and subsequent published research.

  • Most Recent Common Ancestor (MRCA)
    • L1'2'3'4'5'6
      • L2'3'4'6
        • L2
          • L2a'b'c'd
            • L2a
              • L2a1
                • L2a1a
                  • L2a1a1
                  • L2a1a2
                    • L2a1a2a
                      • L2a1a2a1
                    • L2a1a2b
                  • L2a1a3
                • 16189 (16192)
                  • L2a1b
                    • L2a1b1
                  • L2a1f
                    • L2a1f1
                • 143
                  • L2a1c
                    • L2a1c1
                    • L2a1c2
                    • L2a1c3
                    • L2a1c4
                  • L2a1d
                  • L2a1e
                    • L2a1e1
                  • L2a1h
                  • 16189
                    • L2a1i
                    • L2a1j
                    • L2a1k
                    • 16192
                      • L2a1l
                        • L2a1l1
                          • L2a1l1a
                        • L2a1l2
              • L2a2
                • L2a2a
                  • L2a2a1
                • L2a2b
                  • L2a2b1
            • L2b'c
              • L2b
                • L2b1
                  • L2b1a
                    • L2b1a2
                    • L2b1a3
              • L2c
                • L2c2
                  • L2c2a
                • L2c3
            • L2d
              • L2d1
                • L2d1a
          • L2e

[edit] See also

Evolutionary 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   A S   R   I W X Y
C Z B F R0   pre-JT P  U
HV JT K
H V J T

[edit] References

  1. ^ a b c d Soares, Pedro; Luca Ermini, Noel Thomson, Maru Mormina, Teresa Rito, Arne Röhl, Antonio Salas, Stephen Oppenheimer, Vincent Macaulay and Martin B. Richards (04 Jun 2009). "Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock". The American Society of Human Genetics 84 (6): 82–93. doi:10.1016/j.ajhg.2009.05.001. PMC 2694979. PMID 19500773. http://www.cell.com/AJHG/abstract/S0002-9297(09)00163-3. Retrieved 2009-08-13. 
  2. ^ a b 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. http://www3.interscience.wiley.com/journal/121449735/abstract?CRETRY=1&SRETRY=0. Retrieved 2009-05-20. 
  3. ^ Tishkoff et al., Whole-mtDNA Genome Sequence Analysis of Ancient African Lineages, Molecular Biology and Evolution, vol. 24, no. 3 (2007), pp.757-68.
  4. ^ a b c d e f Salas, Antonio et al., The Making of the African mtDNA Landscape, American Journal of Human Genetics, vol. 71, no. 5 (2002), pp. 1082–1111.
  5. ^ a b c Rosa, Alexandra et al.; Brehm, A; Kivisild, T; Metspalu, E; Villems, R (2004). "MtDNA Profile of West Africa Guineans: Towards a Better Understanding of the Senegambia Region". Annals of Human Genetics 68 (Pt 4): 340–352. doi:10.1046/j.1529-8817.2004.00100.x. PMID 15225159. 
  6. ^ Atlas of the Human Journey: Haplogroup L2 The Genographic Proyect, National Geographic.
  7. ^ a b 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): 1599
  8. ^ a b Sadie Anderson-Mann 2006, Phylogenetic and phylogeographic analysis of African mitochondrial DNA variation.
  9. ^ a b Veeramah, Krishna R et al 2010, Little genetic differentiation as assessed by uniparental markers in the presence of substantial language variation in peoples of the Cross River region of Nigeria.
  10. ^ a b c Toomas Kivisild et al., Ethiopian Mitochondria DNA Heritage: Tracking Gene Flow Across and Around the Gate of Tears, American Journal of Human Genetics, vol. 75, no. 5 (November 2004), pp. 752–770.
  11. ^ a b c d Antonio Torroni et al., Do the Four Clades of the mtDNA Haplogroup L2 Evolve at Different Rates?, American Journal of Human Genetics, vol. 69 (2001), pp. 348–1356.
  12. ^ González, A. M. et al 2006, Mitochondrial DNA Variation in Mauritania and Mali and their Genetic Relationship to Other Western Africa Populations
  13. ^ a b http://www3.interscience.wiley.com
  14. ^ Cˇerny, V et al 2006, A Bidirectional Corridor in the Sahel-Sudan Belt and the Distinctive Features of the Chad Basin Populations: A History Revealed by the Mitochondrial DNA Genome.
  15. ^ a b Behar et al 2008b, The Dawn of Human Matrilineal Diversity Am J Hum Genet. 2008 May 9; 82(5): 1130–1140
  16. ^ Costa MD et al 2009, Data from complete mtDNA sequencing of Tunisian centenarians: testing haplogroup association and the "golden mean" to longevity. ([1])
  17. ^ Fernández, E. et al., MtDNA analysis of ancient samples from Castellón (Spain): Diachronic variation and genetic relationships, International Congress Series, vol. 1288 (April 2006), pp. 127-129.

[edit] External links

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