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.

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 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 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
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.

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:

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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) (in many ethnic groups in Eurasia and Oceana; most common in the Caucasus 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 H (M52) (India, Sri Lanka)


 * Haplogroup IJ (S2, S22)
 * Haplogroup I (M170, P19, M258) (widespread in Europe, virtually absent elsewhere )
 * Haplogroup I1a (M253, M307, P30, P40) (northern Europe)
 * Haplogroup I1b (S31) (southeast Europe, Sardinia)
 * 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)


 * Haplogroup K (no additional major mutations) (New Guinea, Australia)
 * Haplogroup K2 (M70) (Africa (Somalians), the Middle East, the Mediterranean)
 * Haplogroup K5 (M230) (New Guinea)
 * Haplogroup L (M20) (South Asia, Central Asia, Southwest Asia, the Mediterranean)
 * Haplogroup M (M4) (New Guinea)
 * Haplogroup NO (M214)
 * Haplogroup NO* (minimal distribution)
 * Haplogroup N (LLY22g) (northernmost Eurasia, especially among the Uralic people)
 * Haplogroup O (M175) (East Asia, the South Pacific)
 * Haplogroup O1 (MSY2.2)
 * Haplogroup O2 (P31, M268)
 * Haplogroup O3 (M122)

Groups with mutation M45
(M45 occurred ~35,000 bp)


 * Haplogroup P (M45)


 * 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)


 * Haplogroup R (M207)
 * Haplogroup R1 (M173) (Europe, West Asia)
 * Haplogroup R1a (M17) (Central Asia, India, Sri Lanka, central and Eastern Europe)
 * Haplogroup R1b (M343) (Western Europe, Asia Minor)
 * Haplogroup R2 (M124) (India, Pakistan, Sri Lanka, Caucasus, Central Asia, Turkey and Eastern Europe)

Human mitochondrial DNA haplogroups
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.

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)
 * 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 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 (excluding M1 which is East African) 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.

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:

General

 * World Families Network

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?

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