Human Y-chromosome DNA haplogroup

In human genetics, a human Y-chromosome DNA haplogroup is a haplogroup defined by mutations in the non-recombining portions of DNA from the male-specific Y chromosome (called Y-DNA). Many people within a haplogroup share similar numbers of short tandem repeats (STRs) and types of mutations called single-nucleotide polymorphisms (SNPs).^[2]

The human Y-chromosome accumulates roughly two mutations per generation.^[3] Y-DNA haplogroups represent major branches of the Y-chromosome phylogenetic tree that share hundreds or even thousands of mutations unique to each haplogroup.

The Y-chromosomal most recent common ancestor (Y-MRCA, informally known as

]

Naming convention

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Y-DNA haplogroups are defined by the presence of a series of Y-DNA SNP markers. Subclades are defined by a terminal SNP, the SNP furthest down in the Y-chromosome phylogenetic tree.^[7][8] The Y Chromosome Consortium (YCC) developed a system of naming major Y-DNA haplogroups with the capital letters A through T, with further subclades named using numbers and lower case letters (YCC longhand nomenclature). YCC shorthand nomenclature names Y-DNA haplogroups and their subclades with the first letter of the major Y-DNA haplogroup followed by a dash and the name of the defining terminal SNP.^[9]

Y-DNA haplogroup nomenclature is changing over time to accommodate the increasing number of SNPs being discovered and tested, and the resulting expansion of the Y-chromosome phylogenetic tree. This change in nomenclature has resulted in inconsistent nomenclature being used in different sources.^[2] This inconsistency, and increasingly cumbersome longhand nomenclature, has prompted a move toward using the simpler shorthand nomenclature.

Phylogenetic structure

Phylogenetic tree of Y-DNA haplogroups ^[10]

• Haplogroup A
  • Haplogroup A00
  • Haplogroup A0
    (formerly also A1b)
  • Haplogroup A1
    (also A1a-T)
    • Haplogroup A1a (M31)
    • Haplogroup A1b (also A2-T; P108, V221)
      • Haplogroup A1b1a1 (also A2; M14)
      • Haplogroup A1b1b (also A3; M32)
      • Haplogroup BT
        (M91, M42, M94, M139, M299)
        • Haplogroup B
          (M60)
        • Haplogroup CT

Haplogroup CT (P143)

The defining mutations separating CT (all haplogroups except for A and B) are M168 and M294. The site of origin is likely in Africa. Its age has been estimated at approximately 88,000 years old,^[11][12] and more recently at around 100,000^[13] or 101,000 years old.^[14]

Haplogroup C (M130)

• Haplogroup C (M130, M216) Found in Asia, Oceania, and North America
  • Haplogroup C1
    (F3393/Z1426)
    • Haplogroup C1a (CTS11043)
      • Haplogroup C1a1 (M8, M105, M131) Found with low frequency in Japan
      • Haplogroup C1a2 (V20) Found with low frequency in Europe, Armenians, Algeria, and Nepal
    • Haplogroup C1b (F1370, Z16480)
      • Haplogroup C1b1 (AM00694/K281)
        • Haplogroup C1b1a (B66/Z16458)
          • China
          • Haplogroup C1b1a2 (B65)
            • Haplogroup C1b1a2a (B67) Found among Lebbo' people in Borneo, Indonesia
            • Haplogroup C1b1a2b (F725) Found among Han Chinese (Guangdong, Hunan, and Shaanxi), Dai people (Yunnan), Murut people (Brunei), Malay people (Singapore), and Aeta people (Philippines)
          • Haplogroup C1b1a3 (Z16582) Found with low frequency in Saudi Arabia and Iraq
        • Haplogroup C1b1b (B68) Found among Dusun people (Brunei)
      • Haplogroup C1b2 (C-Z16582)
      • Haplogroup C1b3 (B477/Z31885)
        • Haplogroup C1b3a (M38) Found in Indonesia, New Guinea, Melanesia, Micronesia, and Polynesia
        • Haplogroup C1b3b (M347, P309) Found among the indigenous peoples in Australia
  • Na-Dené
    -speaking peoples

Haplogroup D (CTS3946)

• Haplogroup D
  (CTS3946)
  • China (especially Tibet), the Andaman Islands

    Main article: Haplogroup D-M174
    • Haplogroup D1a (CTS11577)
      • Haplogroup D1a1 (Z27276, Z27283, Z29263)
        • Haplogroup D1a1a (M15) Found mainly in
          Hmong-Mien
          peoples
        • Haplogroup D1a1b (P99) Found mainly in
          Naxi, and Turkic peoples
      • Haplogroup D1a2 (M55, M57, M64.1, M179, P12, P37.1, P41.1 (M359.1), 12f2.2) Found mainly in Japan
      • Onge, Jarawa
        )
    • Haplogroup D1b (L1366, L1378, M226.2) Found in
      Mactan Island
      , Philippines
  • Haplogroup D2 (A5580.2) Found in Nigeria, Saudi Arabia and Syria

Haplogroup E (M96)

• Haplogroup E (M40, M96) Found in Africa and parts of the Middle East
  and Europe
  • Haplogroup E1
    (P147)
    • Haplogroup E1a
      (M33, M132) formerly E1
    • Haplogroup E1b
      (P177)
      • Haplogroup E1b1
        (P2, DYS391p); formerly E3
        • Haplogroup E1b1a
          (V38)
          • Haplogroup E1b1a1 (M2) Found in Africa, especially among Niger–Congo
            -speaking populations.; formerly E3a
          • Haplogroup E1b1a2 (M329) Found in Africa, especially in Ethiopia among Omotic
            -speaking populations.; formerly E3*
        • Haplogroup E1b1b
          (M215)
          • Haplogroup E1b1b1 (M35) Found in Horn of Africa, North Africa, the Middle East, and Europe (especially in areas near the Mediterranean and the Balkans
            ); formerly E3b
  • Haplogroup E2
    (M75)

G-M201 is also found in small numbers in northwestern China and India, Bangladesh, Pakistan, Sri Lanka, Malaysia, and North Africa.

• Haplogroup G1
• Haplogroup G2
  • Haplogroup G2a
    • Haplogroup G2a1
    • Haplogroup G2a2
    • Haplogroup G2a3
      • Haplogroup G2a3a
      • Haplogroup G2a3b
        • Haplogroup G2a3b1
    • Haplogroup G2b
    • Haplogroup G2c
      (formerly Haplogroup G5)
      • Haplogroup G2c1

Haplogroup H (M69)

Haplogroup H (M69) probably emerged in Southern Central Asia, South Asia or West Asia, about 48,000 years BP, and remains largely prevalent there in the forms of H1 (M69) and H3 (Z5857). Its sub-clades are also found in lower frequencies in Iran, Central Asia, across the middle-east, and the Arabian peninsula.

However, H2 (P96) is present in Europe since the Neolithic and H1a1 (M82) spread westward in the

This section needs expansion. You can help by adding to it. (September 2016)

Haplogroup I (M170)

Haplogroup I (M170, M258) is found mainly in Europe and the Caucasus.

• Haplogroup I1
  Nordid/Nordic Europids (M253) Found mainly in northern Europe
• Haplogroup I2
  Dinarid/Dinaric Europids (P215) Found mainly in Balkans, southeast Europe and Sardinia save for I2B1 (m223) which is found at a moderate frequency in Western, Central, and Northern Europe.

Haplogroup J (M304)

• Haplogroup J* (J-M304*) is rare outside the island of Socotra.
  • Haplogroup J1 Semitid/Bedouinid Arabids (M267) are associated with Northeast Caucasian peoples in Dagestan and Semitic languages speaking people in the Middle East, Ethiopia, and North Africa
    and also found in Mediterranean Europe in smaller frequencies much like haplogroup T.
  • Haplogroup J2 Syrid/Nahrainid Arabids (M172) is found mainly in the Semitic-speaking peoples, Anatolia, Greece, the Balkans, Italy, Iran, the Caucasus, South Asia, and Central Asia
    .

Haplogroup K (M9) is spread all over Eurasia, Oceania and among Native Americans.

K(xLT,K2a,K2b) – that is, K*, K2c, K2d or K2e – is found mainly in

Haplogroups L and T (K1)

Haplogroup L (M20) is found in South Asia, Central Asia, South-West Asia, and the Mediterranean.

The only living males reported to carry the basal

This section needs expansion. You can help by adding to it. (September 2016)

Haplogroups K2a, K2a1, NO & NO1

This section needs expansion. You can help by adding to it. (September 2016)

Haplogroup N

Haplogroup N possibly originated in eastern Asia and spread both northward and westward into Siberia, being the most common group found in some Uralic-speaking peoples.

Haplogroup O

Haplogroup O (M175) is found with its highest frequency in East Asia and Southeast Asia, with lower frequencies in the South Pacific, Central Asia, South Asia, and islands in the Indian Ocean (e.g. Madagascar, the Comoros).

• Haplogroup O1 (F265/M1354, CTS2866, F75/M1297, F429/M1415, F465/M1422)
  • Tai–Kadai
    peoples
  • Haplogroup O1b
    (P31, M268)
    • Tai–Kadai-speaking peoples, Malays, and Indonesians
    • Haplogroup O1b2 (SRY465, M176) Found in Japan, Korea, Manchuria, and Southeast Asia
• Austronesia including Polynesia

No examples of the basal

• Haplogroup S (B254) also known as K2b1a: found in the highlands of Papua New Guinea
  and;
• Haplogroup M (P256) also known as K2b1b: found in New Guinea
  and Melanesia.

This section needs expansion. You can help by adding to it. (September 2016)

Haplogroup P (K2b2)

Haplogroup P (P295) has two primary branches: P1 (P-M45) and the extremely rare P2 (P-B253).^[21]

P*, P1* and P2 are found together only on the island of

• Haplogroup Q
  (Q-M242) and;
• Haplogroup R (R-M207). These share the common marker M45 in addition to at least 18 other SNPs.

Haplogroup Q (MEH2, M242, P36) found in Siberia and the Americas Haplogroup R (M207, M306): found in Europe, West Asia, Central Asia, and South Asia

Haplogroup Q M242

Q is defined by the SNP M242. It is believed to have arisen in Central Asia approximately 32,000 years ago.^[24][25] The subclades of Haplogroup Q with their defining mutation(s), according to the 2008 ISOGG tree^[26] are provided below. ss4 bp, rs41352448, is not represented in the ISOGG 2008 tree because it is a value for an STR. This low frequency value has been found as a novel Q lineage (Q5) in Indian populations^[27]

The 2008 ISOGG tree

• Q (M242)
  • Q*
  • Q1 (P36.2)
    • Q1*
    • Q1a (MEH2)
      • Q1a*
      • Q1a1 (M120, M265/N14) Found with low frequency among
        Tibetans^[30][31]
      • Q1a2 (M25, M143) Found at low to moderate frequency among some populations of
        Southwest Asia, Central Asia, and Siberia
      • Q1a3 (M346)
        • Q1a3* Found at low frequency in Pakistan, India, and Tibet
        • Q1a3a (M3) Typical of indigenous peoples of the Americas
          • Q1a3a*
          • Q1a3a1 (M19) Found among some indigenous peoples of
            Ticuna and the Wayuu^[32]
          • Q1a3a2 (M194)
          • Q1a3a3 (M199, P106, P292)
      • Q1a4 (P48)
      • Q1a5 (P89)
      • Q1a6 (M323) Found in a significant minority of Yemeni Jews
    • Q1b (M378) Found at low frequency among samples of
      Sindhis

Haplogroup R (M207)

Haplogroup R is defined by the SNP M207. The bulk of Haplogroup R is represented in the descendant subclade R1 (M173), which originated on the Siberia. R1 has two descendant subclades: R1a and R1b.

R1a is associated with the proto-Indo-Iranian and Balto-Slavic peoples, and is now found primarily in Central Asia, South Asia, and Eastern Europe.

• Haplogroup R1
  (M173) Found throughout western Eurasia
  • Haplogroup R1a
    (M420) Found in Central Asia, South Asia, and Central, Northern and Eastern Europe, Balkans
  • Haplogroup R1b (M343) Found in Western Europe, West Asia, Central Asia, North Africa, and northern Cameroon
• Haplogroup R2
  (M124) Found in South Asia, Caucasus, Central Asia, and Eastern Europe

• List of Y-chromosome haplogroups in populations of the world
• Y-DNA haplogroups in populations of Europe
• Genetic history of Europe
• List of Y-DNA single-nucleotide polymorphisms
• List of Y-STR markers
• Human mitochondrial DNA haplogroup
• * (haplogroup)
• Molecular phylogeny
• Genetic genealogy
• Genealogical DNA test
• Conversion table for Y chromosome haplogroups

References

• ^ 2005 Y-chromosome Phylogenetic Tree, from FamilyTreeDNA.com
• ^ A Nomenclature system for the Tree of Human Y-Chromosomal Haplogroups, Genome.org

Further reading

• Mendez, Fernando; Krahn, Thomas; Schrack, Bonnie; Krahn, Astrid-Maria; Veeramah, Krishna; Woerner, August; Fomine, Forka Leypey Mathew; Bradman, Neil; Thomas, Mark; Karafet, Tatiana M.; Hammer, Michael F. (7 March 2013). "An African American paternal lineage adds an extremely ancient root to the human Y chromosome phylogenetic tree" (PDF).
  PMID 23453668. Archived from the original
  (PDF) on 24 September 2019. Retrieved 31 March 2013.
• "Y-Haplogroup A Phylogenetic Tree". March 2013. Archived from the original on 18 August 2018. Retrieved 30 March 2013. (chart highlighting new branches added to the A phylotree in March 2013)

External links

Wikimedia Commons has media related to Human Y-DNA haplogroups.

• ISOGG Y-DNA Haplogroup Tree
• Family Tree DNA Public Haplotree
• Chart of the speed of different Y chromosomal STR mutation rates
• Map of Y Haplogroups
• Atlas of the Human Journey, from the Genographic Project, National Geographic
• DNA Heritage's Y-haplogroup map Archived 2006-02-18 at the Wayback Machine
• Video tutorial on Discovering Paternal Ancestry with Y-Chromosomes
• Haplogroup Predictor
• Semino O, Passarino G, Oefner PJ, et al. (November 2000). "The genetic legacy of Paleolithic Homo sapiens sapiens in extant Europeans: a Y chromosome perspective". Science. 290 (5494): 1155–59.
  PMID 11073453. As PDF
  Paper that defined "Eu" haplogroups
• Y-DNA Haplogroup and Sub-clade Projects
• Kerchner's YDNA Haplogroup Descriptions, Projects & Links
• Y-DNA Testing Company STR Marker Comparison Chart
• Y-DNA Ethnographic and Genographic Atlas and Open-Source Data Compilation
• Y Chromosome Consortium