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Haplogroup L3

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Haplogroup L3
Possible time of origin60,000–70,000 YBP[1]
Possible place of originEast Africa[1][2] or Asia[3]
AncestorL3'4
DescendantsL3a, L3b'f, L3c'd, L3e'i'k'x, L3h, M, N
Defining mutations769, 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 Africa, and for many people within the Africa continent as well.[5][6]

Origin

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

Haplogroup L3's exact place of origin is uncertain. According to the Recent African origin of modern humans (Out-of-Africa) theory, the clade is believed to have arisen and dispersed from East Africa, initially thought to have occurred between 84,000 and 104,000 years ago.[7] An analysis of 369 complete African L3 sequences placed the maximal date of the clade's expansion at around 70,000 years ago. This virtually rules out a successful exit out of Africa before 74,000, the date of the Toba volcanic super-eruption in Sumatra, thus making an origin and expansion around 70,000 years ago most likely.[1] The Time to Most Recent Common Ancestor for the L3 lineage has also recently been estimated to date to between 58,900 and 70,200 years ago, around the time of and associated with the Out-of-Africa expansion of the ancestors of non-African modern humans from Eastern Africa into Eurasia around 70,000 years ago, and also with a similar expansion within Africa around that time also from the East of the continent.[1]

Phylogenetically, haplogroup L6 and L4 are the closest to L3 out of the L lineages. Both L6 and L4 are primarily distributed and have their greatest diversity in Eastern Africa. L4'6 (L3'4'6) has a TMRCA of 114,288 years before present while L3'4 link at 95,240 ybp in the middle paleolithic.[5]

Migration route according to the Asian origin hypothesis.[3]
a: Exit of the L3 precursor to Eurasia. b: Return to Africa and expansion to Asia of basal L3 lineages with subsequent differentiation in both continents.

An Asian center of origin and dispersal for haplogroup L3 has also been hypothesized based on the similar coalescence dates of L3 and its Eurasian-distributed M and N derivative clades (~71 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 early anatomically modern humans around 125 kya, fully modern human L3-carrying females are thus proposed to have back-migrated from the maternal haplogroup's place of origin in Eurasia around 70 kya along with males bearing the 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 50,000 and 70,000 years ago.[8][2][9] A study (by Vai et al. 2019) on a newly discovered basal branch of maternal haplogroup N found in early Neolithic North African remains, suggests that haplogroup L3 may have originated in East Africa between 60-70,000 years ago, with haplogroup N diverging from it soon after (between about 50,000-65,000 years ago) either in Arabia or possibly North Africa, and haplogroup M originating in the Middle East.[2]

Distribution

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

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

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.

  • N – Eurasia 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][Note 1]
  • 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
  • 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]
    • 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[Note 2][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]

Culture Genetic cluster or affinity Country Site Date Maternal Haplogroup Paternal Haplogroup Source
Early pastoral PN Kenya Prettejohn's Gully (GsJi11) 4060-3860 L3f1b - Prendergast 2019
Pastoral Neolithic PN Kenya Cole’s Burial (GrJj5a) 3350-3180 L3i2 E-V32 Prendergast 2019
Pastoral Neolithic or Elmenteitan PN Kenya Rigo Cave (GrJh3) 2710-2380 L3f E-M293 Prendergast 2019
Pastoral Neolithic PN Kenya Naishi Rockshelter 2750-2500 L3x1a E-V1515 (prob. E-M293) Prendergast 2019
Pastoral Neolithic PN Tanzania Gishimangeda Cave 2490-2350 L3x1 - Prendergast 2019
Pastoral Neolithic PN Kenya Naivasha Burial Site 2350-2210 L3h1a1 E-M293 Prendergast 2019
Pastoral Neolithic PN Kenya Naivasha Burial Site 2320-2150 L3x1a E-M293 Prendergast 2019
Pastoral Neolithic PN Tanzania Gishimangeda Cave 2150-2020 L3i2 E-M293 Prendergast 2019
Pastoral Neolithic or Elmenteitan PN Kenya Njoro River Cave II 2110-1930 L3h1a2a1 - Prendergast 2019
Pastoral Neolithic N/A Tanzania Gishimangeda Cave 2000-1900 L3h1a2a1 - Prendergast 2019
Pastoral Neolithic PN Kenya Ol Kalou 1810-1620 L3d1d E-M293 Prendergast 2019
Pastoral Iron Age PIA Kenya Kisima Farm, C4 1060-940 L3h1a1 E-M75 (excl. M98) Prendergast 2019
Pastoral Iron Age PIA Kenya Emurua Ole Polos (GvJh122) 420-160 L3h1a1 E-M293 Prendergast 2019
Pastoral Iron Age PN outlier Kenya Kokurmatakore N/A L3a2a E-M35 (not E-M293) Prendergast 2019

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.[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

Wikimedia Commons has media related to Haplogroup L3 (mtDNA).

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

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Notes

  1. ^ See Supplemental_TreeUpdatedOctober.xls found under the Supplementary data of Soares et al. 2011 harvnb error: multiple targets (3×): CITEREFSoaresAlshamaliPereiraFernandes2011 (help)
  2. ^ GUR46 on table 1. is a mtDNA haplogroup L3x2a.
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