Macro-haplogroup L (mtDNA)

In human mitochondrial genetics, L is the mitochondrial DNA macro-haplogroup that is at the root of the anatomically modern human (Homo sapiens) mtDNA phylogenetic tree. As such, it represents the most ancestral mitochondrial lineage of all currently living modern humans, also dubbed "Mitochondrial Eve".

This article is about the human mtDNA haplogroup. For the human Y-DNA haplogroup, see Haplogroup L-M20.
Haplogroup L
Time of origin230 to 150 kya[1][2]
Place of originEastern Africa[3]
DescendantsL0, L1-6
Overview of the main divisions of haplogroup L.

Its two sub-clades are L1-6 and L0. The split occurred during the Penultimate Glacial Period; L1-6 is estimated to have formed ca. 170 kya, and L0 ca. 150 kya. The formation of L0 is associated with the peopling of Southern Africa by populations ancestral to the Khoisan, ca. 140 kya, at the onset of the Eemian interglacial. L1-6 is further subdivided into L2-6 and L1, dated ca. 150 kya and 130 kya, respectively. Haplogroups L5 (120 kya), L2 and L6 (90 kya), L4 (80 kya) and L3 (70 kya) derive from L2-6.

Origin
Main article: Mitochondrial Eve
Further information: Interbreeding between archaic and modern humans

The outgroup for mtDNA phylogeny of modern humans is the mtDNA of archaic humans, specifically Neanderthals and Denisovans. The split of the modern human lineage from the Neanderthal and Denisovan lineage is dated to between ca. 760–550 kya based on full genome analysis. This is consistent with the estimate based on Y-chromosomal DNA, which places the split between ca. 806–447 kya.[4] In terms of mtDNA, however, it appears that modern humans and Neanderthals form a sister clade, with Denisovans as basal outgroup. The split of Neanderthal and modern human mtDNA is dated to about 498–295 kya, i.e. significantly younger than the date estimated based on nuclear DNA. This has been explained as reflecting early gene flow from Africa into the Neanderthal genome, around 270 kya or earlier, i.e. around the time of the first emergence of anatomically modern humans (Jebel Irhoud). Posth et al. (2017) suggest the possibility that early Homo sapiens mtDNA from Africa may have replaced the original Neanderthal mtDNA entirely even when assuming minimal admixture. The Neanderthal and Denisovan lineages diverged before about 430 kya, and Denisovan mtDNA was not affected by the introgression. [4]

The most recent common ancestor of modern human mtDNA (dubbed "Mitochondrial Eve") is dated to ca. 230–150 kya. The emergence of haplogroup L1-6 by definition dates a later time, at an estimated 200–130 kya,[1] possibly in a population in eastern Africa.[3] Haplogroup L0 emerges from the basal haplogroup L1-6* somewhat later, at an estimated 190–110 kya.

The deep time depth of these lineages entails that substructure of this haplogroup within Africa is complex and poorly understood.[5] Date estimates are necessarily imprecise. The intervals cited above represent high and low estimates of the 95% confidence interval following Soares et al. (2009), the most likely ages are to be taken near the center of these intervals.[1]

Phylogeny

L1-6
Haplogroup L1-6
Possible time of origin200 to 130 kya[6]
AncestorL (Mitochondrial Eve)
DescendantsL1, L2-6
Defining mutations146, 182, 4312, 10664, 10915, 11914, 13276, 16230[7]
Haplogroup L phylogeny
L
 L1─6 
L1
 

L1c

 
 

L1b

 
 
 
 

L5

 
 
 

L2

 
 
 

L6

 
 
 

L3

 
 

L4

 
 
 
 
 
 
 L0 
 

L0d

 
 
 

L0k

 
 
 

L0f

 
 
 

L0a

 
 

L0b

 
 
 
 
 
 
Further information: Haplogroup L1 (mtDNA), Haplogroup L5 (mtDNA), Haplogroup L2 (mtDNA), Haplogroup L6 (mtDNA), Haplogroup L3 (mtDNA), and Haplogroup L4 (mtDNA)

Haplogroup L1-6 (also L1'2'3'4'5'6, or L(3'4'6'2'5)'1) split off undifferentiated haplogroup L roughly 20,000 years after Mitochondrial Eve, or at roughly 170,000 years ago (167±36 kya in the estimate of Soares et al. 2009). It diverged, in its turn, into L1 (150 kya), L5 (120 kya), and L2 (90 kya) before the recent out-of Africa event of ca. 70 kya. L3 emerges around 70 kya and is closely associated with the out-of-Africa event; it may have arisen either in East Africa or in Asia. L6 and L4 are a sister clades of L3, but they are limited to East Africa and did not participate in the out-of-Africa migration.

Undifferentiated L1'2'3'4'5'6 has been found in Neanderthal fossils from the Caucasus (Mezmaiskaya cave) and the Altai (Denisova Cave), dated to before 50 kya. This suggests that an earlier wave of expansion of Homo sapiens left Africa between about 200–130 kya (during the Penultimate Glacial Period, c.f. Skhul and Qafzeh hominins) and left genetic traces by interbreeding with Neanderthals before disappearing.[8]

Haplogroup L1 diverged from L1-6 at about 140,000 years ago. Its emergence is associated with the early peopling of Africa by anatomically modern humans during the Eemian, and it is now mostly found in African pygmies.

Haplogroup L5 was formerly classified as L1e, but is now recognized as having diverged from L2-6 (also L2'3'4'5'6, or L(3'4'6'2)'5) at about 120 kya. It is also mostly associated with pygmies, with highest frequency in Mbuti pygmies from Eastern Central Africa at 15%.[9]

Haplogroup L2 diverged from L(3'4'6)'2 at about 90 kya, associated with the peopling of West Africa. As a result of the Bantu migration it is now widespread throughout Sub-Saharan Africa, at the expense of the previously more widespread L0, L1 and L5.[10]

Haplogroup L6 diverged from L3'4'6 at about the same time, ca. 90 kya. It is now a minor haplogroup with distribution mostly limited to the Horn of Africa and southern Arabia.

Haplogroup L3 diverged from L3'4 at about 70 kya, likely shortly before the Southern Dispersal event (Out-of-Africa migration), possibly in East Africa. The mtDNA of all non-Africans is derived from L3, divided into two main lineages, M and N.

Haplogroup L4 is a minor haplogroup of East Africa that arose around 70 kya but did not participate in the out-of-Africa migration. The haplogroup formerly named L7 has been re-classified as a subclade of L4, named L4a.

L0
Main article: Haplogroup L0 (mtDNA)

Haplogroup L0 arose between about 200 and 130 kya,[11] that is, at about the same time as L1, before the beginning of the Eemian. It is associated with the peopling of Southern Africa after about 140,000 years ago.

Its subclades are L0d and L0k. Both are almost exclusively restricted to the Khoisan of southern Africa, but L0d has also been detected among the Sandawe people of Tanzania, which suggests an ancient connection between the Khoisan and East African speakers of click languages.[12]

Haplogroup L0f is present in relatively small frequencies in Tanzania among the Sandawe people who are known to be older then the Khoisan. L0a is most prevalent in South-East African populations (25% in Mozambique), and L0b is found in Ethiopia.

Distribution

Putting aside its sub-branches, haplogroups M and N, the L haplogroups are predominant all over sub-Saharan Africa; L is at 96–100%, apart. It is found in North Africa, Arabian Peninsula, Middle East, Americas, Europe, ranging from low to high frequencies depending on the country.

Africa

With the exception of a number of lineages that returned to Africa from Eurasia after the out of Africa migration, all African lineages belong to haplogroup L. The "back-to-Africa" haplogroups including U6, X1 and possibly M1 have returned to Africa possibly as far back as 45,000 years ago.[13] Haplogroup H, which is common among Berbers, is also believed to have entered Africa from Europe during the post-glacial expansion.[14] The mutations that are used to identify the basal lineages of haplogroup L, are ancient and may be 150,000 years old. The deep time depth of these lineages entails that substructure of this haplogroup within Africa is complex and, at present, poorly understood.[5] The first split within haplogroup L occurred 140–200kya, with the mutations that define macrohaplogroups L0 and L1-6. These two haplogroups are found throughout Africa at varying frequencies and thus exhibit an entangled pattern of mtDNA variation. However the distribution of some subclades of haplogroup L is structured around geographic or ethnic units. For example, the deepest clades of haplogroup L0, L0d and L0k are almost exclusively restricted to the Khoisan of southern Africa. L0d has also been detected among the Sandawe of Tanzania, which suggests an ancient connection between the Khoisan and East African populations.[12]

Macro-haplogroup L (mtDNA) composition within Africa. Approximate frequencies in:
  1. North Africa.[15][16]
  2. Sudan.[16]
  3. Ethiopia.[16][17]
  4. West Africa.[15]
  5. East Africa (Kenya, Uganda, Tanzania).[16][18][19]
  6. Southeast Africa (Mozambique).[20]
  7. Native Southern Africans (!Xung, !Kung and Khwe khoisans).[18][21]
  8. Mbenga Pygmies (Baka, Bi-Aka and Ba-Kola).[18][22]
  9. Ba-Mbuti Pygmies.[18]
  10. Hadza/Sandawe.[18]

North Africa

Haplogroup L is also found at moderate frequencies in North Africa. For example, the various Berber populations have frequencies of haplogroup L lineages that range from 3% to 45%.[23][24] Haplogroup L has also been found at a small frequency of 2.2% in North African Jews from Morocco, Tunisia and Libya. Frequency was the highest in Libyan Jews 3.6%.[25] Moroccan Arabs have more elevated SSA maternal admixture at around 21% to 36% Via L-mtDNA sequences, Highest frequencies of L-mtDNA is reported to Moroccan Arabs of The Surrounding area of El jadida at 33%[26]

West Asia
See also: Archaeogenetics of the Near East

Haplogroup L is also found in West Asia at low to moderate frequencies, most notably in Yemen where frequencies as high as 60% have been reported.[27] It is also found at 15.50% in Bedouins from Israel, 13.68% in Palestinians, 12.55% in Jordanians, 9.48% in Iraqis, 9.15% in Syrians, 7.5% in the Hazara of Afghanistan, 6.66% in Saudi Arabians, 2.84% in Lebanese, 2.60% in Druzes from Israel, 2.44% in Kurds and 1.76% in Turks.[28][29] Overall the Arab slave trade and expansion of foreign empires that encapsulated Saudi Arabia were linked to the negligible presence of haplogroup L in the Saudi Arabian gene pool.[30]

Europe

In Europe, haplogroup L is found at low frequencies, typically less than 1% with the exception of Iberia (Spain and Portugal) where regional frequencies as high as 18.2% have been reported and some regions of Italy where frequencies between 2 and 3% have been found. Overall frequency in Iberia is higher in Portugal than in Spain where frequencies are only high in the south and west of the country. Increasing frequencies are observed for Galicia (3.26%) and northern Portugal (3.21%), through the center (5.02%) and to the south of Portugal (11.38%).[31] Relatively high frequencies of 7.40% and 8.30% were also reported respectively in South Spain, in the present population of Huelva and Priego de Cordoba by Casas et al. 2006.[32] Significant frequencies were also found in the Autonomous regions of Portugal, with L haplogroups constituting about 13% of the lineages in Madeira and 3.4% in the Azores. In the Spanish archipelago of Canary Islands, frequencies have been reported at 6.6%.[33] According to some researchers L lineages in Iberia are associated to Islamic invasions, while for others it may be due to more ancient processes as well as more recent ones through the introduction of these lineages by means of the modern slave trade. The highest frequency (18.2%) of Sub-Saharan lineages found so far in Europe were observed by Alvarez et al. 2010 in the comarca of Sayago in Spain and in Alcacer do Sal in Portugal.[34][35] In Italy, Haplogroup L lineages are present in some regions at frequencies between 2 and 3% in Latium (2.90%), parts of Tuscany,[29] Basilicata and Sicily.[36] In 2015 study found that a prehistoric episode would be the main contributor to the sub-Saharan presence in Mediterranean Europe and Iberia [37] A 2018 study ascribed high levels of African admixture in Spain and Portugal to two separate episodes, one during the North African Islamic expansions into Iberia and one later one, possibly related to the slave trade.[38]

The Americas

Haplogroup L lineages are found in the African diaspora of the Americas as well as indigenous Americans. Haplogroup L lineages are predominant among African Americans, Afro-Caribbeans and Afro-Latin-Americans. In Brazil, Pena et al. report that 85% of self-identified Afro-Brazilians have Haplogroup L mtDNA sequences.[39] Haplogroup L lineages are also found at moderate frequencies in self-identified White Brazilians. Alves Silva reports that 28% of a sample of White Brazilians belong to haplogroup L.[40] In Argentina, a minor contribution of African lineages was observed throughout the country.[41] Haplogroup L lineages were also reported at 8% in Colombia,[42] and at 4.50% in North-Central Mexico.[43] In North America, haplogroup L lineages were reported at a frequency of 0.90% in White Americans of European ancestry.[44]

Haplogroup L Frequencies (> 1%)
Region Population or Country Number tested Reference %
North AfricaLibya (Jews)83Behar et al. (2008)3.60%
North AfricaTunisia (Jews)37Behar et al. (2008)2.20%
North AfricaMorocco (Jews)149Behar et al. (2008)1.34%
North AfricaTunisia64Turchi et al. (2009)48.40%
North AfricaTunisia (Takrouna)33Frigi et al. (2006)3.03%
North AfricaTunisia (Zriba)50Turchi et al. (2009)8.00%
North AfricaMorocco56Turchi et al. (2009)26.80%
North AfricaMorocco (Berbers)64Turchi et al. (2009)3.20%
North AfricaAlgeria (Mozabites)85Turchi et al. (2009)12.90%
North AfricaAlgeria47Turchi et al. (2009)20.70%
EuropeItaly (Latium)138Achilli et al. (2007)2.90%
EuropeItaly (Volterra)114Achilli et al. (2007)2.60%
EuropeItaly (Basilicata)92Ottoni et al. (2009)2.20%
EuropeItaly (Sicily)154Ottoni et al. (2009)2.00%
EuropeMalta132Caruana et al. (2016)15.90%[45]
EuropeSpain312Alvarez et al. (2007)2.90%
EuropeSpain (Galicia)92Pereira et al. (2005)3.30%
EuropeSpain (North East)118Pereira et al. (2005)2.54%
EuropeSpain (Priego de Cordoba)108Casas et al. (2006)8.30%
EuropeSpain (Zamora)214Alvarez et al. (2010)4.70%
EuropeSpain (Sayago)33Alvarez et al. (2010)18.18%
EuropeSpain (Catalonia)101Alvarez-Iglesias et al. (2009)2.97%
EuropeSouth Iberia310Casas et al. (2006)7.40%
EuropeSpain (Canaries)300Brehm et al. (2003)6.60%
EuropeSpain (Balearic Islands)231Picornell et al. (2005)2.20%
EuropeSpain (Andalusia)1004Barral-Arca et al. (2016)2.6%
EuropeSpain (Castilla y Leon)428Barral-Arca et al. (2016)2.1%
EuropeSpain (Aragón)70Barral-Arca et al. (2016)4.3%
EuropeSpain (Asturias)99Barral-Arca et al. (2016)4.0%
EuropeSpain (Galicia)98Barral-Arca et al. (2016)2.0%
EuropeSpain (Madrid)178Barral-Arca et al. (2016)1.70%
EuropeSpain (Castilla-La Mancha)207Barral-Arca et al. (2016)1.40%
EuropeSpain (Extremadura)87Barral-Arca et al. (2016)1.10%
EuropeSpain (Huelva)280Hernández et al. (2015)3.93%
EuropeSpain (Granada)470Hernández et al. (2015)1.49%
EuropePortugal594Achilli et al. (2007)6.90%
EuropePortugal (North)188Achilli et al. (2007)3.19%
EuropePortugal (Central)203Achilli et al. (2007)6.40%
EuropePortugal (South)203Achilli et al. (2007)10.84%
EuropePortugal549Pereira et al. (2005)5.83%
EuropePortugal (North)187Pereira et al. (2005)3.21%
EuropePortugal (Central)239Pereira et al. (2005)5.02%
EuropePortugal (South)123Pereira et al. (2005)11.38%
EuropePortugal (Madeira)155Brehm et al. (2003)12.90%
EuropePortugal (Açores)179Brehm et al. (2003)3.40%
EuropePortugal (Alcacer do Sal)50Pereira et al. (2010)22.00%
EuropePortugal (Coruche)160Pereira et al. (2010)8.70%
EuropePortugal (Pias)75Pereira et al. (2010)3.90%
EuropePortugal1429Barral-Arca et al. (2016)6.16%
West AsiaYemen115Kivisild et al. (2004)45.70%
West AsiaYemen (Jews)119Behar et al. (2008)16.81%
West AsiaBedouins (Israel)58Behar et al. (2008)15.50%
West AsiaPalestinians (Israel)117Achilli et al. (2007)13.68%
West AsiaJordania494Achilli et al. (2007)12.50%
West AsiaIraq116Achilli et al. (2007)9.48%
West AsiaSyria328Achilli et al. (2007)9.15%
West AsiaSaudi Arabia120Abu-Amero et al. (2007)6.66%
West AsiaLebanon176Achilli et al. (2007)2.84%
West AsiaDruzes (Israel)77Behar et al. (2008)2.60%
West AsiaKurds82Achilli et al. (2007)2.44%
West AsiaTurkey340Achilli et al. (2007)1.76%
South AmericaColombia (Antioquia)113Bedoya et al. (2006)8.00%
North AmericaMexico (North-Central)223Green et al. (2000)4.50%
South AmericaArgentina246Corach et al. (2009)2.03%
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See also

References
  1. 151.6–233.6 ka 95% CI according to: Soares P, Ermini L, Thomson N, et al. (June 2009). "Correcting for purifying selection: an improved human mitochondrial molecular clock". Am. J. Hum. Genet. 84 (6): 740–59. doi:10.1016/j.ajhg.2009.05.001. PMC 2694979. PMID 19500773.
  2. Age estimates (ka, 95% CI in angular brackets): ML whole-mtDNA age estimate: 178.8 [155.6; 202.2], ρ whole-mtDNA age estimate: 185.2 [153.8; 216.9], ρ synonymous age estimate (ka): 174.8 [153.8; 216.9]: Rito T, Richards MB, Fernandes V, Alshamali F, Cerny V, Pereira L, Soares P., "The first modern human dispersals across Africa", PLoS One 2013 Nov 13; 8(11):e80031. doi: 10.1371/journal.pone.0080031.
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  6. 166.8+36.7
    −36.1     kya     (Soares et al. 2009).
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  12. Gonder MK, Mortensen HM, Reed FA, de Sousa A, Tishkoff SA (March 2007). "Whole-mtDNA genome sequence analysis of ancient African lineages". Molecular Biology and Evolution. 24 (3): 757–68. doi:10.1093/molbev/msl209. PMID 17194802. the presence of haplogroups N1 and J in Tanzania suggest "back" migration from the Middle East or Eurasia into eastern Africa, which has been inferred from previous studies of other populations in eastern Africa
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  18. Tishkoff SA, Gonder MK, Henn BM, et al. (October 2007). "History of click-speaking populations of Africa inferred from mtDNA and Y chromosome genetic variation". Mol. Biol. Evol. 24 (10): 2180–95. doi:10.1093/molbev/msm155. PMID 17656633.
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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
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