Haplogroup L2 (mtDNA)

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Haplogroup L2
Possible time of origin80,000–111,100 YBP[1]
Possible place of originCentral Africa[2] or South East Africa
DescendantsL2a─d, L2e
Defining mutations146, 150, 152, 2416, 8206, 9221, 10115, 13590, 16311!, 16390[3]

Haplogroup L2 is a human mitochondrial DNA (mtDNA) haplogroup with a widespread modern distribution, particularly in Sub equatorial Africa. Its L2a subclade is a somewhat frequent and widely distributed mtDNA cluster on the continent, as well as among African Americans, The highest frequency occurs among the Mbuti Pygmies (64%).[9].


L2 is a common lineage in Africa. It is believed to have evolved between 87,000 and 107,000 years ago[4] or approx. 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.[5] L2 Haplotypes is commonly observed in Central & South Eastern African populations, finding shared genetic matches with South East Africa and Central Africa.[6] An origin for L2b, L2c, L2d and L2e is South Eastern Africa seems likely.[5] 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 South East Africa. Most of subclades are largely confined to western-Central Africa.[7]

According to a 2015 study, "results show that lineages in Southern Africa cluster with Central African lineages at a recent time scale, whereas, eastern lineages seem to be substantially more ancient. Three moments of expansion from a Central African source are associated to L2: one migration at 70–50 ka into Eastern or Southern Africa, postglacial movements 15–10 ka into Eastern Africa; and the southward Bantu Expansion in the last 5 ka. The complementary population and L0a phylogeography analyses indicate no strong evidence of mtDNA gene flow between eastern and southern populations during the later movement, suggesting low admixture between Eastern African populations and the Bantu migrants. This implies that, at least in the early stages, the Bantu expansion was mainly a demic diffusion with little incorporation of local populations".[8]


Projected spatial distribution of haplogroup L2 in Africa.

L2 is the most common haplogroup in Africa, and it has been observed throughout the continent. It is found in approximately one third of Africans and their recent descendants.

The highest frequency occurs among the Mbuti Pygmies (64%).[9] Less presence in Western Africa populations in Senegal (43-54%).[6] Also important in Non-Bantu populations of East Africa (44%),[10] in Sudan and Mozambique.

It is particularly abundant in Central Africa and the Kanembou (38% of the sample), Also relatively frequent in South Eastern Africa (33%) [Cerny et al. 2007] [5] and Fang people (~33%)[11]


Haplogroup L2 family tree
Haplogroup L2 







L2 has five main subhaplogroups: L2a, L2b, L2c, L2d and L2e. Of these lineages, the most common subclade is L2a, which is found in both Africa and the Levant.

Haplogroup L2 has been observed among specimens at the island cemetery in Kulubnarti, Sudan, which date from the Early Christian period (AD 550–800).[12]

Haplogroup L2a[edit]

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 Central Africa (38% of the sample; 33% undifferentiated L2,[13]), and in Non-Bantu populations of East Africa (Kenya, Uganda and Tanzania) at 38%.[10] About 33% in Mozambique[14] and 32% in Ghana.[11]

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.[15]

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 South East Africa Corridor in 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.[5][15]

In East Africa L2a was found 15% in Nile ValleyNubia, 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.[14]

Haplogroup L2a also appears in low frequency among in North Africa, with the highest frequency 5% Tuareg, Fulani (1%). Found also among some Algeria Arabs, it is found at 1% among Moroccan Arabs, some Moroccan Berbers and Tunisian Berbers. (watson 1997) et al., (vigilant 1991) et al. 1991.

In patients who are given the drug stavudine to treat HIV, Haplogroup L2a is associated with a lower likelihood of peripheral neuropathy as a side effect.[16]

Haplogroup L2a1[edit]

L2a can be further divided into L2a1, harboring the transition at 16309 (Salas et al. 2002).

This subclade is observed at low varying frequencies in West Africa among the Malinke, Wolof, and others; among the North Africans;in the Sahel among the Hausa, Fulbe, and others; in Central Africa among the Bamileke, Fang, and others; in South Africa among the Khoisan family including the Khwe and Bantu speakers; and in East Africa among the Kikuyu from Kenya.

All L2 clades present in Ethiopia are mainly 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.

Haplogroup L2a1 has also been observed among the Mahra (4.6%).[17]

Haplogroup L2a1 has been found in ancient fossils associated with the Pre-Pottery Neolithic culture at Tell Halula, Syria.[18] A specimen excavated at the Savanna Pastoral Neolithic site of Luxmanda in Tanzania also carried the L2a1 clade. Admixture clustering analysis further indicated that the individual bore significant ancestry from the ancient Levant, confirming ancestral ties between the makers of the Savanna Pastoral Neolithic and the Pre-Pottery Neolithic.[19]

Haplogroup L2a1a[edit]

Subclade L2a1a is defined by substitutions at 3918, 5285, 15244, and 15629. There are two L2a clusters that are 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 South East 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 proposed 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, 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.[20] (Rando et al. 1998; Maca-Meyer et al. 2003)

Haplogroup L2a1a1[edit]

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

Haplogroup L2a1b[edit]

L2a1b is defined by substitutions at 16189 and 10143. 16192 is also common in L2a1b and L2a1c; it appears in North Africa in Egypt, It also appears in Southeastern Africa and so it may also be a marker for the Bantu expansion.[5]

Haplogroup L2a1c[edit]

L2a1c often shares mutation 16189 with L2a1b, but 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.[21] 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), among the Turkana and West Africa (e.g. 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.[21] (citation on page.9 or 443)[22][23]

Haplogroup L2a1c1[edit]

L2a1c1 has a north African origin.[24] It is defined by markers 198, 930, 3308, 8604, 16086. It is observed in Tunisia Sephardic, Ashkenazi, Jews, Hebrews, Moroccans, Egyptians, Nubians, and Yemenis.

Haplogroup L2a1f

Khosian, Zambia, Madagascar

Haplogroup L2a1k[edit]

L2a1k is defined by markers G6722A and T12903C. It was previously described as a European-specific subclade L2a1a and detected in Czechs and Slovaks.[25]

Haplogroup L2a1l2a[edit]

L2a1l2a is recognized as an "Ashkenazi-specific" haplogroup, seen amongst Ashkenazi Jews with ancestry in Central and Eastern Europe. It has also been detected in small numbers in ostensibly non-Jewish Polish populations, where it is presumed to have come from Ashkenazi admixture.[26] However, this haplotype constitutes only a very small proportion of Ashkenazi mitochondrial lineages; various studies (including Behar's) have put its incidence at between 1.4–1.6%.

Haplogroup L2a2[edit]

L2a2 is characteristic of the Mbuti Pygmies.[9]

Haplogroup L2b'c[edit]

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

Haplogroup L2b[edit]

This subclade is predominantly found in West Africa, but it is spread all over Africa.[27]

Haplogroup L2c[edit]

L2c is most frequent in West Africa, and may have arisen there.[15] Specially present in Senegal at 39%, Cape Verde 16% and Guinea-Bissau 16%.[6]

Haplogroup L2d[edit]

L2d is most frequent in West Africa, where it may have arisen.[15] It is also found in Yemen, Mozambique and Sudan.[14]

Haplogroup L2e[edit]

L2e (former L2d2) is typical in West Africa.[5] It is also found in Tunisia,[28] and among Mandinka people from Guinea-Bissau and African Americans.[27]


Phylogenetic tree of haplogroup L2 subclades. Numbers in the left side bar represents estimated time in thousand years ago. Colour scheme corresponding to the probable origin of each clade.

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[3] 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

See also[edit]

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


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External links[edit]