Wikipedia

Haplogroup

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A haplotype is a group of alleles in an organism that are inherited together from a single parent,[1][2] and a haplogroup (haploid from the Greek: ἁπλοῦς, haploûs, "onefold, simple" and English: group) is a group of similar haplotypes that share a common ancestor with a single-nucleotide polymorphism mutation.[3] More specifically, a haplotype is a combination of alleles at different chromosomal regions that are closely linked and tend to be inherited together. As a haplogroup consists of similar haplotypes, it is usually possible to predict a haplogroup from haplotypes. Haplogroups pertain to a single line of descent. As such, membership of a haplogroup, by any individual, relies on a relatively small proportion of the genetic material possessed by that individual.

Y-DNA haplogroups map of the world

Each haplogroup originates from, and remains part of, a preceding single haplogroup (or paragroup). As such, any related group of haplogroups may be precisely modelled as a nested hierarchy, in which each set (haplogroup) is also a subset of a single broader set (as opposed, that is, to biparental models, such as human family trees). Haplogroups can be further divided into subclades.

Haplogroups are normally identified by an initial letter of the alphabet, and refinements consist of additional number and letter combinations, such as (for example) A → A1 → A1a. The alphabetical nomenclature was published in 2002 by the Y Chromosome Consortium.[4]

In human genetics, the haplogroups most commonly studied are Y-chromosome (Y-DNA) haplogroups and mitochondrial DNA (mtDNA) haplogroups, each of which can be used to define genetic populations. Y-DNA is passed solely along the patrilineal line, from father to son, while mtDNA is passed down the matrilineal line, from mother to offspring of both sexes. Neither recombines, and thus Y-DNA and mtDNA change only by chance mutation at each generation with no intermixture between parents' genetic material.

Haplogroup formation

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  Ancestral haplogroup
  Haplogroup A (Hg A)
  Haplogroup B (Hg B)
All of these molecules are part of the ancestral haplogroup, but at some point in the past a mutation occurred in the ancestral molecule, mutation A, which produced a new lineage; this is haplogroup A and is defined by mutation A. At some more recent point in the past, a new mutation, mutation B, happened in a person carrying haplogroup A; mutation B defined haplogroup B. Haplogroup B is a subgroup, or subclade of haplogroup A; both haplogroups A and B are subclades of the ancestral haplogroup.

Mitochondria are small organelles that lie in the cytoplasm of eukaryotic cells, such as those of humans. Their primary function is to provide energy to the cell. Mitochondria are thought to be reduced descendants of symbiotic bacteria that were once free living. One indication that mitochondria were once free living is that each contains a circular DNA, called mitochondrial DNA (mtDNA), whose structure is more similar to bacteria than eukaryotic organisms (see endosymbiotic theory). The overwhelming majority of a human's DNA is contained in the chromosomes in the nucleus of the cell, but mtDNA is an exception. An individual inherits their cytoplasm and the organelles contained by that cytoplasm exclusively from the maternal ovum (egg cell); sperm only pass on the chromosomal DNA, all paternal mitochondria are digested in the oocyte. When a mutation arises in a mtDNA molecule, the mutation is therefore passed down in a direct female line of descent. Mutations are changes in the nitrogen bases of the DNA sequence. Single changes from the original sequence are called single nucleotide polymorphisms (SNPs).[dubious – discuss]

Human Y chromosomes are male-specific sex chromosomes; nearly all humans that possess a Y chromosome will be morphologically male. Although Y chromosomes are situated in the cell nucleus and paired with X chromosomes, they only recombine with the X chromosome at the ends of the Y chromosome; the remaining 95% of the Y chromosome does not recombine. Therefore, the Y chromosome and any mutations that arise in it are passed down in a direct male line of descent.

Other chromosomes, autosomes and X chromosomes (when another X chromosome is available to pair with it), share their genetic material during meiosis, the process of cell division which produces gametes. Effectively this means that the genetic material from these chromosomes gets mixed up in every generation, and so any new mutations are passed down randomly from parents to offspring.

The special feature that both Y chromosomes and mtDNA display is that mutations can accrue along a certain segment of both molecules and these mutations remain fixed in place on the DNA. Furthermore, the historical sequence of these mutations can also be inferred. For example, if a set of ten Y chromosomes (derived from ten different individuals) contains a mutation, A, but only five of these chromosomes contain a second mutation, B, then it must be the case that mutation B occurred after mutation A.

Furthermore, all ten individuals who carry the chromosome with mutation A are the direct male line descendants of the same man who was the first person to carry this mutation. The first man to carry mutation B was also a direct male line descendant of this man, but is also the direct male line ancestor of all men carrying mutation B. Series of mutations such as this form molecular lineages. Furthermore, each mutation defines a set of specific Y chromosomes called a haplogroup.

All humans carrying mutation A form a single haplogroup, and all humans carrying mutation B are part of this haplogroup, but mutation B also defines a more recent haplogroup (which is a subgroup or subclade) of its own to which humans carrying only mutation A do not belong. Both mtDNA and Y chromosomes are grouped into lineages and haplogroups; these are often presented as tree-like diagrams.

Human Y-chromosome DNA haplogroups

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Main article: Human Y-chromosome DNA haplogroup

Human Y chromosome DNA (Y-DNA) haplogroups are named from A to T, and are further subdivided using numbers and lower case letters. Y chromosome haplogroup designations are established by the Y Chromosome Consortium.[5]

Y-chromosomal Adam is the name given by researchers to the male who is the most recent common patrilineal (male-lineage) ancestor of all living humans.

Major Y-chromosome haplogroups, and their geographical regions of occurrence (prior to the recent European colonization), include:

Groups without mutation M168

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Groups with mutation M168

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(mutation M168 occurred ~50,000 bp)

  • Haplogroup C (M130) (Oceania, North/Central/East Asia, North America and a minor presence in South America, Southeast Asia, South Asia, West Asia, and Europe)
  • YAP+ haplogroups
    • Haplogroup DE (M1, M145, M203)
      • Haplogroup D (CTS3946) (Tibet, Nepal, Japan, the Andaman Islands, Central Asia, and a sporadic presence in Nigeria, Syria, and Saudi Arabia)
      • Haplogroup E (M96)
        • Haplogroup E1b1a (V38) West Africa and surrounding regions; formerly known as E3a
        • Haplogroup E1b1b (M215) Associated with the spread of Afroasiatic languages; now concentrated in North Africa and the Horn of Africa, as well as parts of the Middle East, the Mediterranean, and the Balkans; formerly known as E3b

Groups with mutation M89

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(mutation M89 occurred ~45,000 bp)

  • Haplogroup F (M89) Oceania, Europe, Asia, North and South America
  • Haplogroup G (M201) (present among many ethnic groups in Eurasia, usually at low frequency; most common in the Caucasus, the Iranian plateau, and Anatolia; in Europe mainly in Greece, Italy, Iberia, the Tyrol, Bohemia; rare in Northern Europe)
  • Haplogroup H (L901/M2939)
    • H1'3 (Z4221/M2826, Z13960)
      • H1 (L902/M3061)
        • H1a (M69/Page45) India, Sri Lanka, Nepal, Pakistan, Iran, Central Asia
        • H1b (B108) Found in a Burmese individual in Myanmar.[7]
      • H3 (Z5857) India, Sri Lanka, Pakistan, Bahrain, Qatar
    • H2 (P96) Formerly known as haplogroup F3. Found with low frequency in Europe and western Asia.
  • Haplogroup IJK (L15, L16)

Groups with mutations L15 & L16

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Groups with mutation M9

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(mutation M9 occurred ~40,000 bp)

  • Haplogroup K
    • Haplogroup LT (L298/P326)
      • Haplogroup L (M11, M20, M22, M61, M185, M295) (South Asia, Central Asia, Southwestern Asia, the Mediterranean)
      • Haplogroup T (M70, M184/USP9Y+3178, M193, M272) (North Africa, Horn of Africa, Southwest Asia, the Mediterranean, South Asia); formerly known as Haplogroup K2
    • Haplogroup K(xLT) (rs2033003/M526)
Groups with mutation M526
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Human mitochondrial DNA haplogroups

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Human migrations and mitochondrial haplogroups
Main article: Human mitochondrial DNA haplogroup

Human mtDNA haplogroups are lettered: A, B, C, CZ, D, E, F, G, H, HV, I, J, pre-JT, JT, K, L0, L1, L2, L3, L4, L5, L6, M, N, O, P, Q, R, R0, S, T, U, V, W, X, Y, and Z. The most up-to-date version of the mtDNA tree is maintained by Mannis van Oven on the PhyloTree website.[9]

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

Mitochondrial Eve is the name given by researchers to the woman who is the most recent common matrilineal (female-lineage) ancestor of all living humans.

Defining populations

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Map of human haplotype migration, according to mitochondrial DNA, with key (coloured) indicating periods in numbered thousands of years before the present.

Haplogroups can be used to define genetic populations and are often geographically oriented. For example, the following are common divisions for mtDNA haplogroups:

The mitochondrial haplogroups are divided into three main groups, which are designated by the sequential letters L, M, N. Humanity first split within the L group between L0 and L1-6. L1-6 gave rise to other L groups, one of which, L3, split into the M and N group.

The M group comprises the first wave of human migration which is thought to have evolved outside of Africa, following an eastward route along southern coastal areas. Descendant lineages of haplogroup M are now found throughout Asia, the Americas, and Melanesia, as well as in parts of the Horn of Africa and North Africa; almost none have been found in Europe. The N haplogroup may represent another macrolineage that evolved outside of Africa, heading northward instead of eastward. Shortly after the migration, the large R group split off from the N.

Haplogroup R consists of two subgroups defined on the basis of their geographical distributions, one found in southeastern Asia and Oceania and the other containing almost all of the modern European populations. Haplogroup N(xR), i.e. mtDNA that belongs to the N group but not to its R subgroup, is typical of Australian aboriginal populations, while also being present at low frequencies among many populations of Eurasia and the Americas.

The L type consists of nearly all Africans.

The M type consists of:

M1 – Ethiopian, Somali and Indian populations. Likely due to much gene flow between the Horn of Africa and the Arabian Peninsula (Saudi Arabia, Yemen, Oman), separated only by a narrow strait between the Red Sea and the Gulf of Aden.

CZ – Many Siberians; branch C – Some Amerindian; branch Z – Many Saami, some Korean, some North Chinese, some Central Asian populations.

D – Some Amerindians, many Siberians and northern East Asians

E – Malay, Borneo, Philippines, Taiwanese aborigines, Papua New Guinea

G – Many Northeast Siberians, northern East Asians, and Central Asians

Q – Melanesian, Polynesian, New Guinean populations

The N type consists of:

A – Found in many Amerindians and some East Asians and Siberians

I – 10% frequency in Northern, Eastern Europe

S – Some Indigenous Australian (First Nations People of Australia)

W – Some Eastern Europeans, South Asians, and southern East Asians

X – Some Amerindians, Southern Siberians, Southwest Asians, and Southern Europeans

Y – Most Nivkhs and people of Nias; many Ainus, Tungusic people, and Austronesians; also found with low frequency in some other populations of Siberia, East Asia, and Central Asia

R – Large group found within the N type. Populations contained therein can be divided geographically into West Eurasia and East Eurasia. Almost all European populations and a large number of Middle-Eastern population today are contained within this branch. A smaller percentage is contained in other N type groups (See above). Below are subclades of R:

B – Some Chinese, Tibetans, Mongolians, Central Asians, Koreans, Amerindians, South Siberians, Japanese, Austronesians

F – Mainly found in southeastern Asia, especially Vietnam; 8.3% in Hvar Island in Croatia.[11]

R0 – Found in Arabia and among Ethiopians and Somalis; branch HV (branch H; branch V) – Europe, Western Asia, North Africa;

Pre-JT – Arose in the Levant (modern Lebanon area), found in 25% frequency in Bedouin populations; branch JT (branch J; branch T) – North, Eastern Europe, Indus, Mediterranean

U – High frequency in West Eurasia, Indian sub-continent, and Algeria, found from India to the Mediterranean and to the rest of Europe; U5 in particular shows high frequency in Scandinavia and Baltic countries with the highest frequency in the Sami people.

Y-chromosome and MtDNA geographic haplogroup assignment

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Here is a list of Y-chromosome and MtDNA geographic haplogroup assignment proposed by Bekada et al. 2013.[12]

Y-chromosome

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According to SNPS haplogroups which are the age of the first extinction event tend to be around 45–50 kya. Haplogroups of the second extinction event seemed to diverge 32–35 kya according to Mal'ta. The ground zero extinction event appears to be Toba during which haplogroup CDEF* appeared to diverge into C, DE and F. C and F have almost nothing in common while D and E have plenty in common. Extinction event #1 according to current estimates occurred after Toba, although older ancient DNA could push the ground zero extinction event to long before Toba, and push the first extinction event here back to Toba. Haplogroups with extinction event notes by them have a dubious origin and this is because extinction events lead to severe bottlenecks, so all notes by these groups are just guesses. Note that the SNP counting of ancient DNA can be highly variable meaning that even though all these groups diverged around the same time no one knows when.[13][14]

Origin Haplogroup Marker
Europe (Second Extinction Event?) I M170, M253, P259, M227, M507
Europe I1b P215, M438, P37.2, M359, P41.2
Europe I1b2 M26
Europe I1c M223, M284, P78, P95
Europe J2a1 M47
Europe J2a2 M67, M166
Europe J2a2a M92
Europe J2b M12, M102, M280, M241
Europe R1b1b1a M412, P310
Europe R1b1b1a1 L11
Europe R1b1b1a1a U106
Europe R1b1b1a1b U198, P312, S116
Europe R1b1b1a1b1 U152
Europe R1b1b1a1b2 M529
Europe R1b1b1a1b3,4 M65, M153
Europe R1b1b1a1b5 SRY2627
South Asia or Melanesia C1(formerly known as CxC3) Z1426
North Asia C2 (formerly known as C3) M217+
Indonesia or South Asia F M89, M282
Europe (Caucasus) G M201, M285, P15, P16, M406
South Asia H M69, M52, M82, M197, M370
Europe or Middle East J1 M304, M267, P58, M365, M368, M369
Europe or Middle East J2 M172, M410, M158, M319, DYS445=6, M339, M340
West of Burma in Eurasia (First Extinction Event?)[15]
Indonesia (First Extinction Event?) [15] K2 (NOPS) M526
South Asia L M11, M20, M27, M76, M317, M274, M349, M357
East Asia, South East Asia N M231, M214, LLY22g, Tat, M178
East Asia, South East Asia, South Asia O M175, M119
Indonesia, Philippines P (xQR) 92R7, M207, M173, M45
South Asia, Siberia R and Q (QR) split [15] MEH2, M242, P36.2, M25, M346
Middle East, Europe, Siberia, South Asia R1a1 M420, M17, M198, M204, M458
Anatolia, South East Europe ? R1b M173, M343, P25, M73
Europe R1b1b M269
Europe R1b1b1 L23
Pakistan, India R2 M479, M124
Middle East T M70
North Africa E1b1b1 M35
North Africa E1b1b1a M78
West Asia E1b1b1a2 V13
North Africa E1b1b1a1 V12
North Africa E1b1b1a1b V32
North Africa E1b1b1a3 V22
North Africa E1b1b1a4 V65
North Africa E1b1b1b M81
North Africa E1b1b1c M123, M34
West Africa, North Africa A M91, M13
East Africa B M60, M181, SRY10831.1, M150, M109, M112
Asia, Africa DE M1, YAP, M174, M40, M96, M75, M98
East Asia, Nepal D M174
West Africa (First Extinction Event?) E1a M33
East Africa (First Extinction Event is the split between E1b1 and E1a, second extinction event is the split between E1b1b and E1b1a) E1b1 P2, M2, U175, M191
Middle East J1 P58

mtDNA

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Origin Haplogroup
Europe H1
Europe H11a
Europe H1a
Europe H1b
Europe H2a
Europe H3
Europe H5a
Europe H6a
Europe H7
Europe HV0/HV0a/V
Europe I4
Europe J1c7
Europe J2b1
Europe T2b*
Europe T2b4
Europe T2e
Europe U4c1
Europe U5*
Europe U5a
Europe U5a1b1
Europe U5b*
Europe U5b1b*
Europe U5b1c
Europe U5b3
Europe X2c'e
Middle East I
Middle East A
Middle East B
Middle East C/Z
Middle East D/G/M9/E
India F
Middle East H*
Middle East H13a1
Middle East H14a
Middle East H20
Middle East H2a1
Middle East H4
Middle East H6b
Middle East H8
Middle East HV1
Middle East I1
Middle East J / J1c / J2
Middle East J1a'b'e
Middle East J1b1a1
Middle East J1b2a
Middle East J1d / J2b
Middle East J1d1
Middle East J2a
Middle East J2a2a1
Middle East K*
Middle East K1a*
Middle East K1b1*
Middle East N1a*
Middle East N1b
Middle East N1c
Middle East N2
Middle East N9
Middle East R*
Middle East R0a
Middle East T
Middle East T1*
West Asia T1a
Middle East T2
Middle East T2c
Middle East T2i
Middle East U1*
Middle East U2*
Middle East U2e
Eurasia U3*
Middle East U4
Middle East U4a*
Middle East U7
Middle East U8*
Middle East U9a
Middle East X
Middle East X1a
Middle East X2b1
North Africa L3e5
North Africa M1
North Africa M1a1
North Africa U6a
North Africa U6a1'2'3
North Africa U6b'c'd
East Africa L0*
East Africa L0a1
East Africa L0a1b
East Africa L0a2*
East Africa L3c/L4/M
East Africa L3d1a1
East Africa L3d1d
East Africa L3e1*
East Africa L3f*
East Africa L3h1b*
East Africa L3i*
East Africa L3x*
East Africa L4a'b*
East Africa L5*
East Africa L6
East Africa N* / M* / L3*
West Africa L1b*
West Africa L1b3
West Africa L1c*
West Africa L1c2
West Africa L2*
West Africa L2a
West Africa L2a1*
West Africa L2a1a2'3'4
West Africa L2a1b
West Africa L2a1b'f
West Africa L2a1c1'2
West Africa L2a1(16189)
West Africa L2a2
West Africa L2b*
West Africa L2c1'2
West Africa L2d
West Africa L2e
West Africa L3b
West Africa L3b1a3
West Africa L3b(16124!)
West Africa L3b2a
West Africa L3d*
West Africa L3e2'3'4
West Africa L3f1b*

See also

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References

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  1. ^ By C. Barry Cox, Peter D. Moore, Richard Ladle. Wiley-Blackwell, 2016. ISBN 978-1-118-96858-1 p. 106. Biogeography: An Ecological and Evolutionary Approach
  2. ^ Editorial Board, V&S Publishers, 2012, ISBN 9381588643 p. 137. Concise Dictionary of Science
  3. ^ International Society of Genetic Genealogy 2015 Genetics Glossary
  4. ^ Consortium, The Y Chromosome (2002-02-01). "A Nomenclature System for the Tree of Human Y-Chromosomal Binary Haplogroups". Genome Research. 12 (2). Cold Spring Harbor Laboratory: 339–348. doi:10.1101/gr.217602. ISSN 1088-9051. PMC 155271. PMID 11827954.
  5. ^ "Y Chromosome Consortium". Archived from the original on 2017-01-16. Retrieved 2005-07-27.
  6. ^ Poznik, G. David; Xue, Yali; Mendez, Fernando L.; et al. (2016). "Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences". Nature Genetics. 48 (6): 593–599. doi:10.1038/ng.3559. PMC 4884158. PMID 27111036.
  7. ^ a b Karmin, Monika; Saag, Lauri; Vicente, Mário; et al. (2015). "A recent bottleneck of Y chromosome diversity coincides with a global change in culture". Genome Research. 25 (4): 459–466. doi:10.1101/gr.186684.114. PMC 4381518. PMID 25770088.
  8. ^ Rootsi S, Magri C, Kivisild T, Benuzzi G, Help H, Bermisheva M, Kutuev I, Barać L, Pericić M, Balanovsky O, Pshenichnov A, Dion D, Grobei M, Zhivotovsky LA, Battaglia V, Achilli A, Al-Zahery N, Parik J, King R, Cinnioğlu C, Khusnutdinova E, Rudan P, Balanovska E, Scheffrahn W, Simonescu M, Brehm A, Goncalves R, Rosa A, Moisan JP, Chaventre A, Ferak V, Füredi S, Oefner PJ, Shen P, Beckman L, Mikerezi I, Terzić R, Primorac D, Cambon-Thomsen A, Krumina A, Torroni A, Underhill PA, Santachiara-Benerecetti AS, Villems R, Semino O (Jul 2004). "Phylogeography of Y-chromosome haplogroup I reveals distinct domains of prehistoric gene flow in europe" (PDF). American Journal of Human Genetics. 75 (1): 128–37. doi:10.1086/422196. PMC 1181996. PMID 15162323. Archived from the original (PDF) on 2009-06-24. Retrieved 2007-03-08.
  9. ^ "PhyloTree.org".
  10. ^ Loogväli EL, Roostalu U, Malyarchuk BA, Derenko MV, Kivisild T, Metspalu E, et al. (2004). "Disuniting uniformity: a pied cladistic canvas of mtDNA haplogroup H in Eurasia". Mol. Biol. Evol. 21 (11): 2012–21. doi:10.1093/molbev/msh209. PMID 15254257.
  11. ^ Tolk HV, Barac L, Pericic M, Klaric IM, Janicijevic B, Campbell H, Rudan I, Kivisild T, Villems R, Rudan P (Sep 2001). "The evidence of mtDNA haplogroup F in a European population and its ethnohistoric implications". European Journal of Human Genetics. 9 (9): 717–23. doi:10.1038/sj.ejhg.5200709. PMID 11571562.
  12. ^ Bekada A, Fregel R, Cabrera VM, Larruga JM, Pestano J, Benhamamouch S, González AM (2013). "Introducing the Algerian mitochondrial DNA and Y-chromosome profiles into the North African landscape". PLOS ONE. 8 (2): e56775. Bibcode:2013PLoSO...856775B. doi:10.1371/journal.pone.0056775. PMC 3576335. PMID 23431392.
  13. ^ "Common genetic ancestors lived during roughly same time period". 1 Aug 2013. Retrieved 23 Jan 2015.
  14. ^ Raghavan M, Skoglund P, Graf KE, Metspalu M, Albrechtsen A, Moltke I, Rasmussen S, Stafford TW, Orlando L, Metspalu E, Karmin M, Tambets K, Rootsi S, Mägi R, Campos PF, Balanovska E, Balanovsky O, Khusnutdinova E, Litvinov S, Osipova LP, Fedorova SA, Voevoda MI, DeGiorgio M, Sicheritz-Ponten T, Brunak S, Demeshchenko S, Kivisild T, Villems R, Nielsen R, Jakobsson M, Willerslev E (Jan 2014). "Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans". Nature. 505 (7481): 87–91. Bibcode:2014Natur.505...87R. doi:10.1038/nature12736. PMC 4105016. PMID 24256729.
  15. ^ a b c Karafet TM, Mendez FL, Sudoyo H, Lansing JS, Hammer MF (Mar 2015). "Improved phylogenetic resolution and rapid diversification of Y-chromosome haplogroup K-M526 in Southeast Asia". European Journal of Human Genetics. 23 (3): 369–73. doi:10.1038/ejhg.2014.106. PMC 4326703. PMID 24896152.
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General

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all DNA haplogroups

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Y-Chromosome

Y chromosome DNA haplogroups

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Mitochondrial DNA haplogroups

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Software

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