Human Y-chromosome DNA haplogroup

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Dominant Y-chromosome haplogroups in pre-colonial world populations, with possible migrations routes according to the Coastal Migration Model.

In human genetics, a human Y-chromosome DNA haplogroup is a haplogroup defined by differences in the non-recombining portions of DNA from the Y chromosome (called Y-DNA). It represents human genetic diversity based on single-nucleotide polymorphisms (SNPs) on the Y chromosome.[1]

Y-DNA haplogroups represent major branches of the Y-chromosome phylogenetic tree. Y-chromosomal Adam is the name given by researchers to the patrilineal most recent common ancestor of all living humans at the root of this tree. Estimates of the date when Y-chromosomal Adam lived have varied significantly in different studies.

Naming convention[edit]

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.[2][3] 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.[4]

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.[1] This inconsistency, and increasingly cumbersome longhand nomenclature, has prompted a move towards using the simpler shorthand nomenclature. In September 2012, Family Tree DNA provided the following explanation of its changing Y-DNA haplogroup nomenclature to individual customers on their Y-DNA results pages (note that the haplogroup mentioned below relates to a specific individual):[5]

Long time customers of Family Tree DNA have seen the YCC-tree of Homo Sapiens evolve over the past several years as new SNPs have been discovered. Sometimes these new SNPs cause a substantial change in the "longhand" explanation of your terminal Haplogroup. Because of this confusion, we introduced a shorthand version a few years ago that lists the branch of the tree and your terminal SNP, i.e. J-L147, in lieu of J1c3d. Therefore, in the very near term, Family Tree DNA will discontinue showing the current "longhand" on the tree and we will focus all of our discussions around your terminal defining SNP.
This changes no science – it just provides an easier and less confusing way for us all to communicate.

Major Y-DNA haplogroups[edit]

Major Y-chromosome haplogroups include:[6]

Tree view[edit]

Y─ DNA Adam

Haplogroup A00




Haplogroup A0




Haplogroup A1a




Haplogroup A1b1


BT

Haplogroup B


CT
DE

Haplogroup D



Haplogroup E



CF

Haplogroup C


F

Haplogroups F*, F1-F3




Haplogroup G




Haplogroup H


IJK
IJ

Haplogroup I



Haplogroup J



K

K*


LT

Haplogroup L



Haplogroup T



K(xLT)

Haplogroups K1-K3



Haplogroup M


NO

Haplogroup N



Haplogroup O



P

Haplogroup Q



Haplogroup R




Haplogroup S















Groups A and B[edit]

Haplogroup A is the African macrohaplogroup from which all modern haplogroups descend. BT is a subclade of Haplogroup A. It has two major lineages, Haplogroups B and CT.

Groups with mutation M168 (CT)[edit]

Main article: Haplogroup CT (Y-DNA)

The defining mutations separating CT (all haplogroups excepting A and B) are M168 and M294. These mutations predate the "Out of Africa" migration. The defining mutations of DE probably occurred in Northeastern Africa some 65,000 years ago.[7] The P143 mutation that defines Haplogroup CF may have occurred at that time, bringing modern humans to the southern coast of Asia.

Groups descended from Haplogroup F (G, H & IJK)[edit]

Main article: Haplogroup F (Y-DNA)
The diversion of Haplogroup F and its descendants.

The groups descending from haplogroup F are found in some 90% of the world's population, but almost exclusively outside of sub-Saharan Africa. The mutation of IJ corresponds to a wave of migration out of the Middle East or South Asia some 45 ka that subsequently spread into Europe (Cro-Magnon). Haplogroup G originated in the Middle East or perhaps further east as far as Pakistan some 30 ka, and spread to Europe with the Neolithic Revolution. Haplogroup H probably occurred in India some 30-40 ka, and remains prevalent there, spreading westwards in historical times with the Romani migration. Haplogroup K spread widely to Eurasia, Australia and the South Pacific.

Groups descended from Haplogroup K (M9)[edit]

Haplogroup L is mainly found in South Asia. Haplogroup M is most prevalent in Melanesia. The NO haplogroup appeared ca. 35-40 ka in Asia. Haplogroup N probably originated in Southeast Asia and spread north into Siberia and west, being the most common group found in Uralic peoples. Haplogroup O is found at its highest frequency in East Asia and Southeast Asia, with lower frequencies in the South Pacific, Central Asia, and South Asia. Haplogroup P gave rise to groups Q and R, and is rarely found in its undifferentiated stage. It probably originated in Central Asia or the Altai region. Haplogroup Q also originated in Central Asia, migrating east to North America.

Groups descended from Haplogroup NO (M214)[edit]

The NO haplogroup appeared ca. 35-40 ka in eastern Asia. Haplogroup N possibly originated in eastern Asia and spread both west into Siberia and north, being the most common group found in some Uralic speaking peoples. Haplogroup O is found at its highest frequency in East Asia and Southeast Asia, with lower frequencies in the South Pacific, Central Asia, and South Asia.

Groups descended from Haplogroup P (M45)[edit]

Haplogroup P (M45) has two branches. They are Q-M242 and R-M207, which share the common marker M45 in addition to at least 18 other SNPs.

Haplogroup Q

Q is defined by the SNP M242. It is believed to have arisen in Central Asia approximately 17,000 to 22,000 years ago.[10][11] The subclades of Haplogroup Q with their defining mutation(s), according to the 2008 ISOGG tree[12] 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[13]

The 2008 ISOGG tree

Haplogroup R

The diversion of Haplogroup R and its descendants.

Haplogroup R is defined by the SNP M207. The bulk of Haplogroup R is represented in lineages R1a and R1b. R1a likely originated in the Eurasian Steppes, and is associated with the Scythian culture and Proto-Indo-European expansion. It is primarily found in Central Asia, South Asia, and Eastern Europe. R1b probably originated in Central Asia. It is the dominant haplogroup of Western Europe and also found sparsely distributed among various peoples of Asia and Africa. Its subclade R1b1a2 (M269) is the haplogroup that is most commonly found among modern European populations, especially those of Western Europe.

Chronological development of haplogroups in Europe[edit]

Haplogroup Possible time of origin
(years ago)
Possible place of origin Highest frequencies
K 40,000 South Asia or West Asia
T 30,000 West Asia
J 30,000 Middle East
R 28,000 Central Asia
E1b1b-M35 26,000 East Africa
I 25,000 Balkans
R1a1 21,000 Southern Russia
R1b 20,000 Around the Caspian Sea or Central Asia
E1b1b-M78 18,000 Egypt/Libya
G 17,000 Between India and the Caucasus
I2 17,000 Balkans
J2 15,000 Northern Mesopotamia
I2b 13,000 Central Europe
N1c1 12,000 Siberia
I2a 11,000 Balkans
R1b1b2 10,000 North or south of the Caucasus
J1 10,000 Arabian peninsula
E1b1b-V13 10,000 Balkans Albania
I2b1 9,000 Central Europe Germany
I2a1 8,000 Pyrenees[17]
I2a2 7,500 Dinaric Alps
E1b1b-M81 5,500 Maghreb Berbers
I1 5,000 Scandinavia
R1b-L21 4,000 Central or Eastern Europe
R1b-S28 3,500 around the Alps
R1b-S21 3,000 Frisia or Central Europe
I2b1a < 3,000 Britain

See also[edit]


Evolutionary tree of human Y-chromosome DNA (Y-DNA) haplogroups
MRC Y-ancestor
A00 A0'1'2'3'4
A0 A1'2'3'4
A1 A2'3'4
A2'3 A4=BCDEF
A2 A3 B CDEF
DE CF
D E C F
GHIJKLT
G HIJKLT
H IJKLT
IJ KLT
I J LT K
L T MPS X
MS P NO
Q R N O
  1. ^ van Oven M, Van Geystelen A, Kayser M, Decorte R, Larmuseau HD (2013). "Seeing the wood for the trees: a minimal reference phylogeny for the human Y chromosome". Human Mutation. doi:10.1002/humu.22468. PMID 24166809. 

References[edit]

  1. ^ a b "Understanding Haplogroups: How are the haplogroups named?". Family Tree DNA. Retrieved 31 March 2013. 
  2. ^ "Understanding Results: Y-DNA Single Nucleotide Polymorphism (SNP): What is a Y-chromosome DNA (Y-DNA) haplogroup?". Family Tree DNA. Retrieved 31 March 2013. "Y-chromosome DNA (Y-DNA) haplogroups are the major branches on the human paternal family tree. Each haplogroup has many subbranches. These are subclades." 
  3. ^ "myFTDNA 2.0 User Guide: Y-DNA: What is the Y-DNA - Matches page?". Family Tree DNA. Retrieved 31 March 2013. "A terminal SNP determines the terminal (final) subbranch on the Y-DNA Tree to which someone belongs." 
  4. ^ "Understanding Results: Y-DNA Single Nucleotide Polymorphism (SNP): How are haplogroups and their subclades named?". Family Tree DNA. Retrieved 31 March 2013. 
  5. ^ Family Tree DNA
  6. ^ Y-DNA Haplogroup Tree 2014
  7. ^ Karafet TM, Mendez FL, Meilerman MB, Underhill PA, Zegura SL, Hammer MF (2008). "New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree". Genome Research 18 (5): 830–8. doi:10.1101/gr.7172008. PMC 2336805. PMID 18385274. 
  8. ^ Passarino, Giuseppe, Cavalleri, Gianpiero L, Lin, Alice A, Cavalli-Sforza, LL, Børresen-Dale, AL, Underhill, PA (2002). "Different genetic components in the Norwegian population revealed by the analysis of mtDNA and Y chromosome polymorphisms". European Journal of Human Genetics 10 (9): 521–529. doi:10.1038/sj.ejhg.5200834. PMID 12173029. 
  9. ^ Karlsson, Andreas O, Wallerström, Thomas, Götherström, Anders, Holmlund, Gunilla (2006). "Y-chromosome diversity in Sweden – A long-time perspective". European Journal of Human Genetics 14 (8): 963–970. doi:10.1038/sj.ejhg.5201651. PMID 16724001. 
  10. ^ Fagundes, Nelson J.R.; Ricardo Kanitz, Roberta Eckert, Ana C.S. Valls, Mauricio R. Bogo, Francisco M. Salzano, David Glenn Smith, Wilson A. Silva, Marco A. Zago, Andrea K. Ribeiro-dos-Santos, Sidney E.B. Santos, Maria Luiza Petzl-Erler, and Sandro L.Bonatto (2008). "Mitochondrial Population Genomics Supports a Single Pre-Clovis Origin with a Coastal Route for the Peopling of the Americas" (pdf). American Journal of Human Genetics 82 (3): 583–592. doi:10.1016/j.ajhg.2007.11.013. PMC 2427228. PMID 18313026. "Since the first studies, it has been found that extant Native American populations exhibit almost exclusively five "mtDNA haplogroups" (A–D and X)6 classified in the autochthonous haplogroups A2, B2, C1, D1, and X2a.7 Haplogroups A–D are found all over the New World and are frequent in Asia, supporting a northeastern Asian origin of these lineages" 
  11. ^ Zegura, S. L.; Karafet, TM; Zhivotovsky, LA; Hammer, MF (2003). "High-Resolution SNPs and Microsatellite Haplotypes Point to a Single, Recent Entry of Native American Y Chromosomes into the Americas". Molecular Biology and Evolution 21 (1): 164–75. doi:10.1093/molbev/msh009. PMID 14595095. 
  12. ^ "Y-DNA Haplogroup Tree 2010". International Society of Genetic Genealogy. Retrieved July 2010. 
  13. ^ Sharma, Swarkar; Rai, Ekta; Bhat, Audesh K; Bhanwer, Amarjit S; Bamezaicorresponding, Rameshwar NK (2007). "A novel subgroup Q5 of human Y-chromosomal haplogroup Q in India". BMC Evol Biol 7: 232. doi:10.1186/1471-2148-7-232. PMC 2258157. PMID 18021436. 
  14. ^ Wen B, Li H, Lu D, et al. (September 2004). Supplementary Table 2: NRY haplogroup distribution in Han populations. "Genetic evidence supports demic diffusion of Han culture". Nature 431 (7006): 302–5. doi:10.1038/nature02878. PMID 15372031. 
  15. ^ Wells RS, Yuldasheva N, Ruzibakiev R, et al. (August 2001). Table 1: Y-chromosome haplotype frequencies in 49 Eurasian populations, listed according to geographic region. "The Eurasian heartland: a continental perspective on Y-chromosome diversity". Proc. Natl. Acad. Sci. U.S.A. 98 (18): 10244–9. doi:10.1073/pnas.171305098. PMC 56946. PMID 11526236. 
  16. ^ Bortolini MC, Salzano FM, Thomas MG, et al. (September 2003). "Y-chromosome evidence for differing ancient demographic histories in the Americas". Am. J. Hum. Genet. 73 (3): 524–39. doi:10.1086/377588. PMC 1180678. PMID 12900798. 
  17. ^ Rootsi S, Magri C, Kivisild T, et al. (July 2004). "Phylogeography of Y-chromosome haplogroup I reveals distinct domains of prehistoric gene flow in europe". Am. J. Hum. Genet. 75 (1): 128–37. doi:10.1086/422196. PMC 1181996. PMID 15162323. 

External links[edit]

Further reading[edit]