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Haplogroup

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In the study of molecular evolution, a haplogroup is a large group of haplotypes, which are series of alleles at specific locations on a chromosome.

In human genetics, the haplogroups most commonly studied are Y-chromosome (Y-DNA) haplogroups and mitochondrial DNA (mtDNA) haplogroups, both of which can be used to define genetic populations. Y-DNA has the advantage of being passed solely along the patrilineal line, while mtDNA is passed solely on the matrilineal line.

Classifications of human haplogroups of either sort based on genetic markers have been rapidly evolving over the past several years as new markers are found.

Haplogroup population genetics

It is usually assumed that there is little natural selection for or against a particular haplotype mutation which has survived to the present day, so apart from mutation rates (which may vary from one marker to another) the main driver of population genetics affecting the proportions of haplotypes in a population is genetic drift - random fluctuation caused by the sampling randomness of which members of the population happen to pass their DNA on to members of the next generation of the appropriate sex. This causes the prevalence of a particular marker in a population to continue to fluctuate, until it either hits 100%, or falls out of the population entirely. In a large population with efficient mixing the rate of genetic drift for common alleles is very slow; however, in a very small interbreeding population the proportions can change much more quickly. The marked geographical variations and concentrations of particular haplotyes and groups of haplotypes therefore witness the distinctive effects of repeated population bottlenecks or founder events followed by population separations and increases. The lineages which can be traced back from the present will not reflect the full genetic variation of the older population: genetic drift means that some of the variants will have died out. The price of full mtDNA sequence tests has limited the availability of data. Haplotype coalescence times and current geographical prevalences both carry considerable error uncertainties.

Human Y-chromosome DNA haplogroups

Main article: Human Y-chromosome DNA haplogroup

Human Y chromosome DNA (Y-DNA) haplogroups are lettered A through R, and are further subdivided using numbers and lower case letters. Y chromosome haplogroup designations are established by the Y Chromosome Consortium.

Phylogenetic tree of human Y-chromosome DNA haplogroups
This article needs to be updated. Please help update this article to reflect recent events or newly available information. (February 2021)
"Y-chromosomal Adam"
A00 A0-T 
A0 A1 
A1a A1b
A1b1 BT
B CT
DE CF
D E C F
F1  F-Y27277   F3  GHIJK
G HIJK
IJK H
IJ K
I   J     LT        K2 
I1   I2  J1   J2  L     T  K2e K2d K2c K2b   K2a
K2b1    P  K-M2313 
S   M     P1   NO1
P1c P1b P1a N O
R Q
Footnotes
  1. Van Oven M, Van Geystelen A, Kayser M, Decorte R, Larmuseau HD (2014). "Seeing the wood for the trees: a minimal reference phylogeny for the human Y chromosome". Human Mutation. 35 (2): 187–91. doi:10.1002/humu.22468. PMID 24166809. S2CID 23291764.
  2. International Society of Genetic Genealogy (ISOGG; 2015), Y-DNA Haplogroup Tree 2015. (Access date: 1 February 2015.)
  3. Haplogroup A0-T is also known as A-L1085 (and previously as A0'1'2'3'4).
  4. Haplogroup A1 is also known as A1'2'3'4.
  5. F-Y27277, sometimes known as F2'4, is both the parent clade of F2 and F4 and a child of F-M89.
  6. Haplogroup LT (L298/P326) is also known as Haplogroup K1.
  7. Between 2002 and 2008, Haplogroup T-M184 was known as "Haplogroup K2". That name has since been re-assigned to K-M526, the sibling of Haplogroup LT.
  8. Haplogroup K2b (M1221/P331/PF5911) is also known as Haplogroup MPS.
  9. Haplogroup K2b1 (P397/P399) is also known as Haplogroup MS, but has a broader and more complex internal structure.
  10. Haplogroup P (P295) is also klnown as K2b2.
  11. K-M2313*, which as yet has no phylogenetic name, has been documented in two living individuals, who have ethnic ties to India and South East Asia. In addition, K-Y28299, which appears to be a primary branch of K-M2313, has been found in three living individuals from India. See: Poznik op. cit.; YFull YTree v5.08, 2017, "K-M2335", and; PhyloTree, 2017, "Details of the Y-SNP markers included in the minimal Y tree" (Access date of these pages: 9 December 2017)
  12. Haplogroup S, as of 2017, is also known as K2b1a. (Previously the name Haplogroup S was assigned to K2b1a4.)
  13. Haplogroup M, as of 2017, is also known as K2b1b. (Previously the name Haplogroup M was assigned to K2b1d.)

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

  • Haplogroup A (M91) (Africa, especially the khoisan and nilotes)

Groups with mutation M168

(mutation M168 occurred ~50,000 bp)

  • Haplogroup C (M130) (Australia and surrounding areas, Siberia, Japan, North America)

Groups with mutation M89

(mutation M89 occurred ~45,000 bp)

  • Haplogroup F (no additional major mutations) (southern India, Sri Lanka, Korea)
  • Haplogroup G (M201) (the Caucasus, Anatolia; small distribution in Italy, Sardinia, northern Spain, west Austria)

Groups with mutation M9

(mutation M9 occurred ~40,000 bp)

  • Haplogroup L (M20) (South Asia, Central Asia, Southwest Asia, the Mediterranean)

Groups with mutation M45

(mutation M45 occurred ~35,000 bp)

  • Haplogroup P (no additional major mutations) (minimal distribution)

Human mitochondrial DNA haplogroups

Main article: Human mitochondrial DNA haplogroup

Human mitochondrial DNA (mtDNA) haplogroups are lettered A, B, C, D, E, F, G, H, I, J, K, L, L1, L2, L3, M, N, T, U, V, W X, and Z.

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

Map of human race migration, according to mitochondrial DNA.

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

  • Sub-Saharan African: L, L1, L2, L3, L3*
  • West Eurasian: H, T, U, V, X, K, I, J, W (all listed West Eurasian haplogroups are derived from macro-haplogroup N)
  • East Eurasian: A, B, C, D, E, F, G (note: C, D, E, and G belong to macro-haplogroup M)
  • Native American: A, B, C, D, X

The mitochondrial haplogroups are divided into 3 main groups, which are designated by the 3 sequential letters L, M, N. Humanity first split between the L group and the rest, and then the M and N groups split. The L type consists of Africans, and especially Sub-Saharan Africans. The M type consists of most South Asians, East Asians, North Asians, Amerindians (containing a minority of north and central Amerindians and a majority of south Amerindians), and many Central Asians and Melanesians. The N type consists of everyone else, including nearly all Europeans, West Asians, North Africans, and Australian aborigines as well as many East Asians, South Asians, Amerindians (containing a majority of north and central Amerindians and a minority of south Amerindians), and Polynesians.

Within the N group is the large R group, which contains many haplogroups within it. The R type contains the vast majority of Europeans and Middle Easterners, Polynesians, many Melanesians, some Australian aborigines, some East Asians, and some Amerindians. In contrast, the varieties of the N group that do not belong to the R group contain the majority of Australian aborigines, the majority of north and central Amerindians, and some East Siberians.

The haplogroups within the R group consist of 2 sets of haplogroups, one which occurs in and around Europe, and consists of haplogroups HV / H / V, J / T, and U / K, and another which occurs in and around Southeast Asia, and consists of haplogroups R, B, F, and P.


References

  1. Loogvali et al, 2004

See also

External links

General

News

all DNA haplogroups

Y chromosome DNA haplogroups

Mitochondrial DNA haplogroups

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