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Haplogroup



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, specifically by means of UEPs, have been rapidly evolving over the past several years as new markers are found.

Contents

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 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 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[1].

Human Y-chromosome DNA (Y-DNA) haplogroups

Y-most recent common ancestor
|
A BR
B CR
DE CF
D E C F
G H IJ K
I J L M NO P
N O Q R

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, Ethiopians, and Nilotes)
  • Haplogroup B (M60) (Africa, especially the Pygmies and Hadzabe)

Groups with mutation M168

(mutation M168 occurred ~50,000 bp)

  • Haplogroup C (M130) (Australia and surrounding areas, Siberia, Japan, North America)
  • YAP+ haplogroups
    • Haplogroup DE (M1, M145, M203)
      • Haplogroup D (M174) (Tibet, Japan, the Andaman Islands)
      • Haplogroup E (M96) (Africa, the Middle East, the Mediterranean)
        • Haplogroup E3a (M2) (Africa)
        • Haplogroup E3b (M35) (East Africa (Ethiopians and Somalians), North Africa (especially Berbers and Egyptians), the Middle East, the Mediterranean)

Groups with mutation M89

(mutation M89 occurred ~45,000 bp)

  • Haplogroup F (P14, M213) (southern India, Sri Lanka, Korea)
  • 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 Sardinia, northern Italy, northern Spain, the Tyrol, as well as Bohemia, Moravia; Britain and Norway at only 2%)
  • Haplogroup IJ (S2, S22)
    • Haplogroup I (M170, P19, M258) (widespread in Europe, virtually absent elsewhere [2])
    • Haplogroup J (M304) (the Middle East, Turkey, Georgia (Caucasus), Italy, Greece, the Balkans, North and East Africa)
      • Haplogroup J* (minimal distribution)
      • Haplogroup J1 (M267) (associated with Semitic peoples: mainly in the Middle East, Ethiopia, and North Africa; J1 with DYS388=13 is associated with eastern Anatolia)
      • Haplogroup J2 (M172) (mainly in Southern Europe, Turkey, Georgia, Kurds, the Middle East, Central Asia, South Asia)

Groups with mutation M9

(mutation M9 occurred ~40,000 bp)

Groups with mutation M45

(M45 occurred ~35,000 bp)

  • Haplogroup Q (MEH2, M242, P36) (Occurred ~15,000-20,000 years ago. Found in Asia and the Americas)
    • Haplogroup Q3 (M3) (North America, Central America, and South America)

Human mitochondrial DNA haplogroups

Main article: Human mitochondrial DNA haplogroup

Human mtDNA haplogroups are lettered: A, B, C, CZ, D, E, F, G, H, pre-HV, HV, I, J, pre-JT, JT, K, L0, L1, L2, L3, L4, L5, L6, L7, M, N, O, P, Q, R, S, T, U, UK, V, W, X, Y, and Z.

Human mitochondrial DNA (mtDNA) haplogroups

  most recent common mt-ancestor    
L0   L1  
L2 L3   L4 L5 L6 L7
  M N  
CZ D E G Q   A I O   R   S W X Y
C Z B F pre-HV   pre-JT P  UK
HV JT U 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

  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: L0, L1, L2, L3, L4, L5, L6, L7
  • West Eurasian: H, T, U, V, X, K, I, J, W (all listed West Eurasian haplogroups are derived from macro-haplogroup N)[3]
  • 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
  • Australo-Melanesian: O, P, Q, S

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. L1 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 and eastern route along side southern coastal areas. Descendent populations are found throughout East Asia, South Asia, South America, and Australia, though none have been found in Europe. The N group comprises the second migration out of Africa, heading northward instead of east. Shortly after the migration, the large R group split off of from the N. This comprises 2 haplogroups, one found in East Asia and the other containing almost all of the modern European populations.

The L type consists of Africans, and especially Sub-Saharan Africans.

The M type consists of:

M1- Ethiopian 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, Taiwan 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- Ainus and Nivkhs; 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 Central Chinese, Tibetans, Mongolians, Central Asians, Koreans, Amerindians, South Siberians, Japanese, Austronesians

F- 10% of Chinese population, 5.1% in Korean population, 5.1% in Japanese population, 8.7% in Mongolian population, 8.3% in Hvar Island in Croatia (Tolk et al 2001)

Pre-HV- High frequency in Arabia; branch HV(branch H; branch V)- Western Europe, Middle-East;

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

UK- High frequency in Finland, Scandinavia, Baltic countries, Mediterranean

Overlap between y-haplogroups and mt-haplogroups

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
A L0 South Africa, Khoisan
B L1, L2 Pygmies and related people
E1, E2, E3a L3 Sub-Saharan Africa, especially the Bantus
C3/N/O CZ/C/Z, D, G (M types) East Asia, Siberia
K, M (M9-positive, M45-negative) R, P (N types), Q (M type) as well as various Oceanian-specific M subclades Oceania
R, I, J HV/H/V, JT/J/T, U/K (N types) Europe, West Asia
Q A, X, Y (N types), C, D (M types) Easternmost Siberia, the Americas

References

  1. ^ Y Chromosome Consortium
  2. ^ http://www.familytreedna.com/pdf/DNA.RootsiHaplogroupISpread.pdf
  3. ^ Loogvali et al, 2004

3. http://evolutsioon.ut.ee/publications/Tolk2001.pdf

See also

News

  • Indian maternal gene pool, Journal of Human Genetics
  • Dienekes' Anthropology Blog frequent highlights of new results.

all DNA haplogroups

  • http://www.scs.uiuc.edu/~mcdonald/WorldHaplogroupsMaps.pdf

Y chromosome DNA haplogroups

  • Y Chromosome Consortium
  • ISOGG Y-DNA Haplogroup Tree 2006
  • DNA Heritage's Y-haplogroup map
  • Haplogroup Predictor
  • The Y Chromosome Consortium (2002), A Nomenclature System for the Tree of Human Y-Chromosomal Binary Haplogroups, Genome Research, Vol. 12(2), 339-348, February 2002. (Detailed hierarchical chart has conversions from previous naming schemes)
  • DNA Consulting's Conversion Chart for Male Haplogroups (PDF)
  • Semino et al (2000), The Genetic Legacy of Paleolithic Homo sapiens sapiens in Extant Europeans, Science, Vol 290 (paper which introduced the "Eu" haplogroups).

Mitochondrial DNA haplogroups

  • graphical mtDNA haplogroup skeleton
  • The Making of the African mtDNA Landscape
  • Do the Four Clades of the mtDNA Haplogroup L2 Evolve at Different Rates?
 
This article is licensed under the GNU Free Documentation License. It uses material from the Wikipedia article "Haplogroup". A list of authors is available in Wikipedia.
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