Haplogroup L3 (mtDNA)


Haplogroup L3 is a human mitochondrial DNA 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 of about 70–50,000 years ago.
It is inherited by all modern non-African populations, as well as by some populations in Africa.

Origin

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.
More recent analyses, including Soares et al. 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.
In 2016, Soares et al. again suggested that haplogroup L3 emerged in East Africa, leading to the Out-of-Africa migration, around 70-60,000 years ago.
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.

The possibility of an origin of L3 already in Asia was also proposed by Cabrera et al. based on the similar coalescence dates of L3 and its Eurasian-distributed M and N derivative clades, 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 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.
According to other research, though earlier migrations out of Africa of anatomically modern humans occurred, current Eurasian populations descend instead from a later migration from Africa dated between about 65,000 and 50,000 years ago. Vai et al. 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, and both spread within Africa and left Africa as part of the Out-of-Africa migration, with haplogroup N diverging from it soon after either in Arabia or possibly North Africa, and haplogroup M originating in the Middle East around the same time as N.
A study by Lipson et al analyzing remains from the Cameroonian site of Shum Laka found them to be more similar to modern-day Pygmy peoples than to West Africans, and suggests that several other groups commonly derived from a human population originating in East Africa between about 80,000-60,000 years ago, which they suggest was also the source and origin zone of haplogroup L3 around 70,000 years ago.

Distribution

L3 is common in Northeast Africa and some other parts of East Africa, in contrast to others parts of Africa where the haplogroups L1 and L2 represent around two thirds of mtDNA lineages. 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. 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.
According to Maca-Meyer et al., "L3 is more related to Eurasian haplogroups than to the most divergent African clusters L1 and L2". L3 is the haplogroup from which all modern humans outside Africa derive. 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.
Haplogroup L3 has been observed in an ancient fossil belonging to the Pre-Pottery Neolithic B culture. 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. Haplogroup L3 has also been found among ancient Egyptian mummies excavated at the Abusir el-Meleq archaeological site in Middle Egypt, with the rest deriving from Eurasian subclades, which date from the Pre-Ptolemaic/late New Kingdom and Ptolemaic periods. The Ancient Egyptian mummies bore Near eastern genomic component most closely related to modern near easterners. 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 with the rest from both islands deriving from Eurasian subclades. 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
A variety of L3 have been uncovered in ancient remains associated with the Pastoral Neolithic and Pastoral Iron Age of East Africa.
CultureGenetic cluster or affinityCountrySiteDateMaternal HaplogroupPaternal HaplogroupSource
Early pastoralPNKenyaPrettejohn's Gully 4060–3860L3f1b–Prendergast 2019
Pastoral NeolithicPNKenyaCole’s Burial 3350–3180L3i2E-V32Prendergast 2019
Pastoral Neolithic or ElmenteitanPNKenyaRigo Cave 2710–2380L3fE-M293Prendergast 2019
Pastoral NeolithicPNKenyaNaishi Rockshelter2750–2500L3x1aE-V1515 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 Prendergast 2019
Pastoral Iron AgePIAKenyaEmurua Ole Polos 420–160L3h1a1E-M293Prendergast 2019
Pastoral Iron AgePN outlierKenyaKokurmatakoreN/AL3a2aE-M35 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 and subsequent published research.
Most Recent Common Ancestor