Haplogroup

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In molecular evolution, a haplogroup (from the Greek: ἁπλούς, haploûs, "onefold, single, simple") is a group of similar haplotypes that share a common ancestor having the same single nucleotide polymorphism (SNP) mutation in all haplotypes. Because a haplogroup consists of similar haplotypes, it is possible to predict a haplogroup from haplotypes. An SNP test confirms a haplogroup. Haplogroups are assigned letters of the alphabet, and refinements consist of additional number and letter combinations, for example R1b1. Y-chromosome and mitochondrial DNA haplogroups have different haplogroup designations. Haplogroups pertain to deep ancestral origins dating back thousands of years.[1]

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. According to research, 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. It is believed that 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[edit]

  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, occurred 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 purpose 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 his or her cytoplasm and the organelles contained by that cytoplasm exclusively from the maternal ovum (egg cell); sperm carry only the chromosomal DNA- perhaps due to the necessity of maintaining motility. When a mutation arises in a mtDNA molecule, the mutation is therefore passed in a direct female line of descent. Mutations are copying mistakes in the DNA sequence. Single mistakes are called single nucleotide polymorphisms (SNPs).

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 on from father to son in a direct male line of descent. This means the Y chromosome and mtDNA share specific properties.

Other chromosomes, autosomes and X chromosomes in women, share their genetic material (called crossing over leading to recombination) during meiosis (a special type of cell division that occurs for the purposes of sexual reproduction). 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 men) 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 men 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 men carrying mutation A form a single haplogroup, and all men 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 men 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.

Haplogroup population genetics[edit]

It is usually assumed that there is little natural selection for or against a particular haplotype mutation which has survived to the present day[citation needed], 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 low; however, in a very small interbreeding population the proportions can change much more quickly. The marked geographical variations and concentrations of particular haplotypes 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 cost of full Y-DNA and mtDNA sequence tests has limited the availability of data; however, their cost has dropped dramatically in the last decade. Haplotype coalescence times and current geographical prevalences both carry considerable error uncertainties. This is especially troublesome for coalescence times, because most population geneticists still continue (albeit decreasing a little bit) to use the "Zhivotovski method", which is heavily criticised by DNA-genealogists for its falsehood.[citation needed]

Human Y-chromosome DNA haplogroups[edit]

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.[2]


Evolutionary tree of human Y-chromosome DNA (Y-DNA) haplogroups
MRC Y-ancestor
A00A0'1'2'3'4
A0A1'2'3'4
A1A2'3'4
A2'3A4=BCDEF
A2A3BCDEF
DECF
DECF
GHIJKLT
GHIJKLT
HIJKLT
IJKLT
IJLTK
LTMPSX
MSPNO
QRNO
QR
  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. 

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:

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

Groups without mutation M168[edit]

Groups with mutation M168[edit]

(mutation M168 occurred ~50,000 bp)

  • Haplogroup C (M130) (Oceania, North/Central/East Asia, North America and a minor presence in South America, South Asia, West Asia, and Europe)
  • Haplogroup F (M89) Oceania, Europe, Asia, North- and South- America
  • YAP+ haplogroups

Groups with mutation M89[edit]

(mutation M89 occurred ~45,000 bp)

  • 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; extremely rare in Northern Europe)
  • Haplogroup H (M69) (India, Sri Lanka, Nepal, Pakistan, Iran, Central Asia, and Arabia)

Groups with mutations L15 & L16[edit]

Groups with mutation M9[edit]

(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[edit]

Human mitochondrial DNA haplogroups[edit]

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, 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.[4]

Evolutionary tree of human mitochondrial DNA (mtDNA) haplogroups

 Mitochondrial Eve (L)  
L0L1–6
L1L2L3 L4L5L6
 MN 
CZDEGQ AS R IWXY
CZBFR0 pre-JTP U
HVJTK
HVJT

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[edit]

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 3 main groups, which are designated by the 3 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 out of Africa, following an eastward route along southern coastal areas.

Descendent populations belonging to haplogroup M are found throughout East Africa, Asia, the Americas, and Melanesia, though almost none have been found in Europe. The N group may represent another migration out 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 some Amerindians, Japanese, and Koreans

I- 10% frequency in Northern, Eastern Europe

S- Some Australian aborigines

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

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

Y- Most Nivkhs and many Ainus; 1% in Southern Siberia

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.[6]

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 poupulations; 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.

Overlap between y-haplogroups and mt-haplogroups[edit]

The ranges of specific y-haplogroups and specific mt-haplogroups overlap, indicating populations that have a specific combination of a y-haplogroup and an mt-haplogroup. Y mutations and mt mutations do not necessarily occur at a similar time, and differential rates of sexual selection between the two genders combined with founder effect and genetic drift can alter the haplogroup composition of a population, so the overlaps are only rough.

The very rough overlaps between Y-DNA haplogroups and mtDNA haplogroups are as follows:

Y-DNA haplogroup(s)mtDNA haplogroup(s)Geographical area and/or peoples
AL0Eastern and Southern Africa
BL1, L4Eastern and Middle Africa
EL2, L3Africa wide
D, O, N, C3CZ/C/Z, D, G (M types); A, N9/Y (N types); B, F (R types)East Asia, Siberia
K, M (M9-positive, M45-negative)B, P (R types); N; Q (M type) as well as various Oceanian-specific M subcladesOceania
R, I, T, J, E (V13, M81, and M123 types)R0, HV/H/V, JT/J/T, U/K (R types)South Asia, Europe, West Asia, North Africa, Horn of Africa
Q, C3A, X (N types); C, D (M types)Easternmost Siberia, the Americas

Y-chromosome and MtDNA geographic haplogroup assignation[edit]

Here is a list of Y-chromosome and MtDNA geographic haplogroup assignation proposed by Bekada et al. 2013.[7]

Y-chromosome[edit]

OriginHaplogroupMarker
EuropeE1b1b1a2V13
EuropeIM170,M253,P259,M227,M507
EuropeI1bP215,M438,P37.2,M359,P41.2
EuropeI1b2M26
EuropeI1cM223,M284,P78,P95
EuropeJ2a1M47
EuropeJ2a2M67,M166
EuropeJ2a2aM92
EuropeJ2bM12,M102,M280, M241
EuropeR1b1b1aM412,P310
EuropeR1b1b1a1L11
EuropeR1b1b1a1aU106
EuropeR1b1b1a1bU198,P312,S116
EuropeR1b1b1a1b1U152
EuropeR1b1b1a1b2M529
EuropeR1b1b1a1b3,4M65,M153
EuropeR1b1b1a1b5SRY2627
Middle EastCRPS4Y,M130,M217,M48,M356,M168
Middle EastFM89,M282
Middle EastGM201,M285,P15,P16,M406
Middle EastHM69,M52,M82,M197,M370
Middle EastJ1M304,M267,P58,M365,M368,M369
Middle EastJ2M172,M410,M158,M319,DYS445=6,M339,M340
Middle EastKM9,M184
Middle EastLM11, M20, M27,M76,M317,M274,M349,M357
Middle EastNM231,M214,LLY22g,Tat,M178
Middle EastOM175,M119
Middle EastP,R92R7,M207,M173, M45
Middle EastQMEH2,M242,P36.2,M25,M346
Middle EastR1a1M420,M17, M198, M204, M458
Middle EastR1bM173, M343,P25,M73
Middle EastR1b1bM269
Middle EastR1b1b1L23
Middle EastR2M479,M124
Middle EastTM70
North AfricaE1b1b1aM78
North AfricaE1b1b1a1V12
North AfricaE1b1b1a1bV32
North AfricaE1b1b1a3V22
North AfricaE1b1b1a4V65
North AfricaE1b1b1bM81
East AfricaAM91,M13
East AfricaBM60, M181, SRY10831.1,M150,M109,M112
East AfricaDEM1,YAP,M174,M40,M96,M75,M98
East AfricaE1b1b1M35
East AfricaE1b1b1cM123,M34
West AfricaE1aM33
West AfricaE1b1P2,M2,U175,M191
West AfricaR1b1aV88,M18

mtDNA[edit]

OriginHaplogroup
EuropeH1
EuropeH11a
EuropeH1a
EuropeH1b
EuropeH2a
EuropeH3
EuropeH5a
EuropeH6a
EuropeH7
EuropeHV0/HV0a/V
EuropeI4
EuropeJ1c7
EuropeJ2b1
EuropeT2b*
EuropeT2b4
EuropeT2e
EuropeU4c1
EuropeU5*
EuropeU5a
EuropeU5a1b1
EuropeU5b*
EuropeU5b1b*
EuropeU5b1c
EuropeU5b3
EuropeX2c'e
Middle EastI
Middle EastA
Middle EastB
Middle EastC/Z
Middle EastD/G/M9/E
Middle EastF
Middle EastH*
Middle EastH13a1
Middle EastH14a
Middle EastH20
Middle EastH2a1
Middle EastH4
Middle EastH6b
Middle EastH8
Middle EastHV1
Middle EastI1
Middle EastJ / J1c / J2
Middle EastJ1a'b'e
Middle EastJ1b1a1
Middle EastJ1b2a
Middle EastJ1d / J2b
Middle EastJ1d1
Middle EastJ2a
Middle EastJ2a2a1
Middle EastK*
Middle EastK1a*
Middle EastK1b1*
Middle EastN1a*
Middle EastN1b
Middle EastN1c
Middle EastN2
Middle EastN9
Middle EastR*
Middle EastR0a
Middle EastT
Middle EastT1*
Middle EastT1a
Middle EastT2
Middle EastT2c
Middle EastT2i
Middle EastU1*
Middle EastU2*
Middle EastU2e
Middle EastU3*
Middle EastU4
Middle EastU4a*
Middle EastU7
Middle EastU8*
Middle EastU9a
Middle EastX
Middle EastX1a
Middle EastX2b1
North AfricaL3e5
North AfricaM1
North AfricaM1a1
North AfricaU6a
North AfricaU6a1'2'3
North AfricaU6b'c'd
East AfricaL0*
East AfricaL0a1
East AfricaL0a1b
East AfricaL0a2*
East AfricaL3c/L4/M
East AfricaL3d1a1
East AfricaL3d1d
East AfricaL3e1*
East AfricaL3f*
East AfricaL3h1b*
East AfricaL3i*
East AfricaL3x*
East AfricaL4a'b*
East AfricaL5*
East AfricaL6
East AfricaN* / M* / L3*
West AfricaL1b*
West AfricaL1b3
West AfricaL1c*
West AfricaL1c2
West AfricaL2*
West AfricaL2a
West AfricaL2a1*
West AfricaL2a1a2'3'4
West AfricaL2a1b
West AfricaL2a1b'f
West AfricaL2a1c1'2
West AfricaL2a1(16189)
West AfricaL2a2
West AfricaL2b*
West AfricaL2c1'2
West AfricaL2d
West AfricaL2e
West AfricaL3b
West AfricaL3b1a3
West AfricaL3b(16124!)
West AfricaL3b2a
West AfricaL3d*
West AfricaL3e2'3'4
West AfricaL3f1b*

See also[edit]

References[edit]

  1. ^ The International Society of Genetic Genealogy see Haplogroup definition in DNA--NEWBIE GLOSSARY [1]
  2. ^ Y Chromosome Consortium
  3. ^ http://www.familytreedna.com/pdf/DNA.RootsiHaplogroupISpread.pdf
  4. ^ PhyloTree.org
  5. ^ Loogvali et al., 2004
  6. ^ Tolk, Helle-Viivi; Lovorka Barac, Marijana Pericic, Irena Martinovic Klaric, Branka Janicijevic, Harry Campbell, Igor Rudan, Toomas Kivisild, Richard Villems and Pavao Rudan (2001). "The evidence of mtDNA haplogroup F in a European population and its ethnohistoric implications". European Journal of Human Genetics 9 (9): 717–723. doi:10.1038/sj.ejhg.5200709. PMID 11571562. 
  7. ^ Bekada A, Fregel R, Cabrera VM, Larruga JM, Pestano J, et al. (2013) Introducing the Algerian Mitochondrial DNA and Y-Chromosome Profiles into the North African Landscape" PLoS ONE 8(2) e56775. doi:10.1371/journal.pone.0056775, Table 9. Table S9.-MtDNA and Y-chromosome geographic haplogroup assignation

External links[edit]

General[edit]

News[edit]

all DNA haplogroups[edit]

Y-Chromosome - *http://www.scs.uiuc.edu/~mcdonald/WorldHaplogroupsMaps.pdf

Y chromosome DNA haplogroups[edit]

Mitochondrial DNA haplogroups[edit]

Software[edit]