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Haplogroup L3 (mtDNA)

Haplogroup L3 (mtDNA)

Haplogroup L3 is a human mitochondrial DNA (mtDNA) haplogroup. The clade has played a pivotal role in the early dispersal of anatomically modern humans.

It is strongly associated with the out-of-Africa migration of modern humans at about 50-70,000 years ago. It is inherited by all modern non-African populations, as well as by some populations in Africa.[5][6]

Haplogroup L3
Possible time of origin80,000–60,000 YBP[1]
Possible place of originEast Africa[1][2] or Asia[3]
DescendantsL3a, L3b'f, L3c'd, L3e'i'k'x, L3h, M, N
Defining mutations769, 1018, 16311[4]


Haplogroup L3 arose close to 70,000 years ago, near the time of the recent out-of-Africa event. This dispersal originated in East Africa and expanded to West Asia, and further to South and Southeast Asia in the course of a few millennia, and some research suggests that L3 participated in this migration out of Africa. A 2007 estimate for the age of L3 suggested a range of 104-84,000 years ago.[7] More recent analyses, including Soares et al. (2012) arrive at a more recent date, of roughly 70-60,000 years ago. Soares et al. also suggest that L3 most likely expanded from East Africa into Eurasia sometime around 65-55,000 years ago years ago as part of the recent out-of-Africa event, as well as from East Africa into Central Africa from 60-35,000 years ago.[1]

Haplogroups L6 and L4 form sister clades of L3 which arose in East Africa at roughly the same time but which did not participate in the out-of-Africa migration. The ancestral clade L3'4'6 has been estimated at roughly 110 kya, and the L3'4 clade at 95 kya.[5]

The possibility of an origin of L3 already in Asia has been proposed by Cabrera et al. (2018) based on the similar coalescence dates of L3 and its Eurasian-distributed M and N derivative clades (ca. 70 kya), the distant location in Southeast Asia of the oldest subclades of M and N, and the comparable age of the paternal haplogroup DE. According to this hypothesis, after an initial out-of-Africa migration of bearers of pre-L3 (L3'4*) around 125 kya, there would have been a back-migration of females carrying L3 from Eurasia to East Africa sometime after 70 kya. It is suggested that this back-migration is aligned with bearers of paternal haplogroup E, which is also proposed to have originated in Eurasia. These new Eurasian lineages are then suggested to have largely replaced the old autochthonous male and female North-East African lineages.[3]

According to other research, though earlier migrations out of Africa of anatomically modern humans occurred, current Eurasian populations descend from a later migration from Africa dated between about 65,000 and 50,000 years ago.[8][2][9] Vai et al. (2019) suggest, from a newly discovered old and deeply-rooted branch of maternal haplogroup N found in early Neolithic North African remains, that haplogroup L3 originated in East Africa between 70,000-60,000 years ago, with haplogroup N diverging from it soon after (between 65,000-50,000 years ago) either in Arabia or possibly North Africa, and haplogroup M originating in the Middle East around the same time as N.[2]


L3 is common in Northeast Africa and some other parts of East Africa,[10] in contrast to others parts of Africa where the haplogroups L1 and L2 represent around two thirds of mtDNA lineages.[11] L3 sublineages are also frequent in the Arabian peninsula.

L3 is subdivided into several clades, two of which spawned the macrohaplogroups M and N that are today carried by most people outside Africa.[11] There is at least one relatively deep non-M, non-N clade of L3 outside Africa, L3f1b6, which is found at a frequency of 1% in Asturias, Spain. It diverged from African L3 lineages at least 10,000 years ago.[12]

According to Maca-Meyer et al. (2001), "L3 is more related to Eurasian haplogroups than to the most divergent African clusters L1 and L2".[13] L3 is the haplogroup from which all modern humans outside Africa derive.[14] However, there is a greater diversity of major L3 branches within Africa than outside of it, the two major non-African branches being the L3 offshoots M and N.

Subclade distribution

L3 has seven equidistant descendants: L3a, L3b'f, L3c'd, L3e'i'k'x, L3h, M, N. Five are African, while two are associated with the Out of Africa event.

  • NEurasia and parts of Africa due to back-migration.[6][15]

  • M – Asia, the Mediterranean Basin, and parts of Africa due to back-migration.[6][15]

  • L3a – East Africa.[5][6] Moderate to high frequencies found among the Sanye, Samburu, Iraqw, Yaaku, El-Molo and other minor indigenous populations from the East African Rift Valley. It is infrequent to nonexistent in Sudan and the Sahel zone.[16] L3a1 – Found across Eastern Africa. Estimated age of 35.8-39.3 ka.[6] L3a2 – Found across Eastern Africa. Estimated age of 48.3-57.7 ka.[17][37]

  • L3b'f L3b – Spread from East Africa in the upper paleolithic to West-Central Africa. Some subclades spread from Central Africa to East Africa with the Bantu migration.[6] L3b1a – Common subclade. Estimated age of 11.7-14.8 ka.[6] L3b1a2 – Subclade found in Northeast Africa, the Maghreb, and Middle East. Emerged 12-14 ka.[18][17] L3f – Northeast Africa, Sahel, Arabian peninsula, Iberia. Gaalien,[19] Beja[19] L3f1 L3f1a – Carried by migrants from Eastern Africa into the Sahel and Central Africa.[6] L3f1b – Carried by migrants from Eastern Africa into the Sahel and Central Africa.[6] L3f1b1 - Carried from Central Africa into Southern and Eastern Africa with the Bantu migration.[6] L3f1b4 - Carried from Central Africa into Southern and Eastern Africa with the Bantu migration.[6] L3f1b6 – Rare, found in Iberia.[12] L3f2 – Primarily distributed in East Africa.[6] Also found in North Africa and Central Africa.[18] L3f3 – Spread from Eastern Africa to Chad and the Sahel around 8-9 ka.[6] Found in the Chad Basin.[18][20]

  • L3c'd L3c – Extremely rare lineage with only two samples found so far in Eastern Africa and the Near East.[6] L3d – Spread from East Africa in the upper paleolithic to Central Africa. Some subclades spread to East Africa with the Bantu migration.[6] Found among the Fulani,[5] Chadians,[5] Ethiopians,[21] Akan people,[22] Mozambique,[21] Yemenites,[21] Egyptians, Berbers[23] L3d3a1 - Primarily found in Southern Africa.[17][18]

  • L3e'i'k'x L3e – Spread from East Africa in the upper paleolithic to West-Central Africa. It is the most common L3 sub-clade in Bantu-speaking populations.[24] L3e is suggested to be associated with a Central African origin and is also the most common L3 subclade amongst African Americans, Afro-Brazilians and Caribbeans[25] L3e1 – Spread from West-Central Africa to Southwest Africa with the Bantu migration. Found in Angola (6.8%).[26] Mozambique, Sudanese and Kikuyu from Kenya as well as in Yemen and among the Akan people[22] L3e5 – Originated in the Chad Basin. Found in Algeria,[27] as well as Burkina Faso, Nigeria, South Tunisia, South Morocco and Egypt[28] L3i Almost exclusively found in East Africa.[6] L3i1 L3i1b – Subclade is found in Yemen, Ethiopia, and among Gujarati Indians.[18] L3i2 (former L3w) – Found in the Horn of Africa and Oman.[18] L3k – Rare haplogroup primarily found in North Africa and the Sahel.[6][18] L3x – Almost exclusively found in East Africa.[6] Found among Ethiopian Oromos,[21] Egyptians[38][29]

  • L3h – Almost exclusively found in East Africa.[6] L3h1 – Primarily found in East Africa with branches of L3h1b1 sporadically found in the Sahel and North Africa.[17][18] L3h2 – Found in Northeast Africa and Socotra. Split from other L3h branches as early as 65-69 ka during the middle paleolithic.[17][18]

Ancient and historic samples

Haplogroup L3 has been observed in an ancient fossil belonging to the Pre-Pottery Neolithic B culture.[30] L3x2a was observed in a 4,500 year old hunter-gather excavated in Mota, Ethiopia, with the ancient fossil found to be most closely related to modern Southwest Ethiopian populations.[31][32] Haplogroup L3 has also been found among ancient Egyptian mummies excavated at the Abusir el-Meleq archaeological site in Middle Egypt, which date from the Pre-Ptolemaic/late New Kingdom and Ptolemaic periods.[33] Additionally, haplogroup L3 has been observed in ancient Guanche fossils excavated in Gran Canaria and Tenerife on the Canary Islands, which have been radiocarbon-dated to between the 7th and 11th centuries CE. All of the clade-bearing individuals were inhumed at the Gran Canaria site, with most of these specimens found to belong to the L3b1a subclade (3/4; 75%). The Guanche skeletons also bore an autochthonous Maghrebi genomic component that peaks among modern Berbers, which suggests that they originated from ancestral Berber populations inhabiting northwestern Affoundnat a high ncy[34]

A variety of L3 have been uncovered in ancient remains associated with the Pastoral Neolithic and Pastoral Iron Age of East Africa.[35]

CultureGenetic cluster or affinityCountrySiteDateMaternal HaplogroupPaternal HaplogroupSource
Early pastoralPNKenyaPrettejohn's Gully (GsJi11)4060-3860L3f1b
Prendergast 2019
Pastoral NeolithicPNKenyaCole’s Burial (GrJj5a)3350-3180L3i2E-V32Prendergast 2019
Pastoral Neolithic or ElmenteitanPNKenyaRigo Cave (GrJh3)2710-2380L3fE-M293Prendergast 2019
Pastoral NeolithicPNKenyaNaishi Rockshelter2750-2500L3x1aE-V1515 (prob. E-M293)Prendergast 2019
Pastoral NeolithicPNTanzaniaGishimangeda Cave2490-2350L3x1
Prendergast 2019
Pastoral NeolithicPNKenyaNaivasha Burial Site2350-2210L3h1a1E-M293Prendergast 2019
Pastoral NeolithicPNKenyaNaivasha Burial Site2320-2150L3x1aE-M293Prendergast 2019
Pastoral NeolithicPNTanzaniaGishimangeda Cave2150-2020L3i2E-M293Prendergast 2019
Pastoral Neolithic or ElmenteitanPNKenyaNjoro River Cave II2110-1930L3h1a2a1
Prendergast 2019
Pastoral NeolithicN/ATanzaniaGishimangeda Cave2000-1900L3h1a2a1
Prendergast 2019
Pastoral NeolithicPNKenyaOl Kalou1810-1620L3d1dE-M293Prendergast 2019
Pastoral Iron AgePIAKenyaKisima Farm, C41060-940L3h1a1E-M75 (excl. M98)Prendergast 2019
Pastoral Iron AgePIAKenyaEmurua Ole Polos (GvJh122)420-160L3h1a1E-M293Prendergast 2019
Pastoral Iron AgePN outlierKenyaKokurmatakoreN/AL3a2aE-M35 (not E-M293)Prendergast 2019


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.[36]

Most Recent Common Ancestor (MRCA)

  • L1-6 L2-6 L2'3'4'6 L3'4'6 L3'4 L3 L3a L3a1 L3a1a L3a1b L3a2 L3a2a L3b'f L3b L3b1 L3b1a L3b1a1 L3b1a2 L3b1a3 L3b1a4 L3b1a5 L3b1a5a L3b1a6 L3b1a7 L3b1a7 L3b1a8 L3b1a9 L3b1a9a L3b1a10 L3b1a11 L3b1b L3b1b1 L3b2 L3b2a L3b2a L3b3 L3f L3f1 L3f1a L3f1a1 L3f1b L3f1b1 L3f1b2 L3f1b2a L3f1b3 L3f1b4 L3f1b4a L3f1b4a1 L3f1b4b L3f1b4c L3f1b5 L3f2 L3f2a L3f2b L3f3 L3f3a L3f3b L3c'd L3c L3d L3d1-5 L3d1 L3d1a L3d1a1 L3d1a1a L3d1b L3d1b1 L3d1c L3d1d 199 L3d2 L3d5 L3d3 L3d3a L3d4 L3d5 L3e'i'k'x L3e L3e1 L3e1a L3e1a1 L3e1a1a 152 L3e1a2 L3e1a3 L3e1b L3e1c L3e1d L3e1e L3e2 L3e2a L3e2a1 L3e2a1a L3e2a1b L3e2a1b1 L3e2b L3e2b1 L3e2b1a L3e2b2 L3e2b3 L3e3'4'5 L3e3'4 L3e3 L3e3a L3e3b L3e3b1 L3e4 L3e5 L3i L3i1 L3i1a L3i1b L3i2 L3k L3k1 L3x L3x1 L3x1a L3x1a1 L3x1a2 L3x1b L3x2 L3x2a L3x2a1 L3x2a1a L3x2b L3h L3h1 L3h1a L3h1a1 L3h1a2 L3h1a2a L3h1a2b L3h1b L3h1b1 L3h1b1a L3h1b1a1 L3h1b2 L3h2 M N

See also

  • Genealogical DNA test

  • Genetic Genealogy

  • Haplogroup

  • Population genetics

Phylogenetic tree of human mitochondrial DNA (mtDNA) haplogroups
Mitochondrial Eve (L)


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