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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".

Haplogroup L
Time of origin230 to 150 ka[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. 140,000 years ago, 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.

OriginEdit

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 the admixed African mtDNA 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]

PhylogenyEdit

L1-6Edit

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

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 (150kya), 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 is 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, 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.

L0Edit

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 oldest 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. L0a is most prevalent in South-East African populations (25% in Mozambique), and L0b is found in Ethiopia.

See alsoEdit

ReferencesEdit

  1. ^ a b c 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.
  3. ^ a b Gonder MK, Mortensen HM, Reed FA, de Sousa A, Tishkoff SA (March 2007). "Whole-mtDNA genome sequence analysis of ancient African lineages". Mol. Biol. Evol. 24 (3): 757–68. doi:10.1093/molbev/msl209. PMID 17194802.
  4. ^ a b Cosimo Posth et al., "Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals" Nature Communications 8 (23 March 2017), doi:10.1038/ncomms16046.
  5. ^ Behar DM, Villems R, Soodyall H, et al. (May 2008). "The dawn of human matrilineal diversity". American Journal of Human Genetics. 82 (5): 1130–40. doi:10.1016/j.ajhg.2008.04.002. PMC 2427203. PMID 18439549.
  6. ^ 166.8+36.7
    −36.1
     kya
    (Soares et al. 2009).
  7. ^ van Oven, Mannis; Manfred Kayser (13 Oct 2008). "Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation". Human Mutation. 30 (2): E386–E394. doi:10.1002/humu.20921. PMID 18853457. Archived from the original on 4 December 2012. Retrieved 2009-05-20.
  8. ^ Briggs, A. W., Good, J. M., Green, R. E., Krause, J., Maricic, T., Stenzel, U., et al. "Targeted Retrieval and Analysis of Five Neandertal mtDNA Genomes", Science 325 (2009), 318–321, doi:10.1126/science.1174462. Renata C. Ferreira, Camila R. Rodrigues, James R. Broach, "Neandertal signatures in modern human mitochondrial genome haplogroups?" (2018), doi:10.1101/190363.
  9. ^ Sarah A. Tishkoff et al. 2007, History of Click-Speaking Populations of Africa Inferred from mtDNA and Y Chromosome Genetic Variation. Molecular Biology and Evolution 2007 24(10):2180-2195
  10. ^ Marina Silva, Farida Alshamali, Paula Silva, Carla Carrilho, Flávio Mandlate, Maria Jesus Trovoada, Viktor Černý, Luísa Pereira, Pedro Soares, "60,000 years of interactions between Central and Eastern Africa documented by major African mitochondrial haplogroup L2", Sci Rep. 2015; 5: 12526, doi:10.1038/srep12526
  11. ^ point estimate 168.5 ka (136.3–201.1 ka 95% CI) according to Heinz, Tanja; et al. (2017). "Updating the African human mitochondrial DNA tree: Relevance to forensic and population genetics". Forensic Science International: Genetics. 27: 156–159. doi:10.1016/j.fsigen.2016.12.016. PMID 28086175. (table 2). 150 ka suggested in:Soares, Pedro; Ermini, Luca; Thomson, Noel; Mormina, Maru; Rito, Teresa; Röhl, Arne; Salas, Antonio; Oppenheimer, Stephen; MacAulay, Vincent (2009). "Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock". The American Journal of Human Genetics. 84 (6): 740–59. doi:10.1016/j.ajhg.2009.05.001. PMC 2694979. PMID 19500773..
  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

External linksEdit

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