Haplogroup

In the study of molecular evolution, a haplogroup (from the απλούς, haploûs, "onefold, single, simple") is a group of similar haplotypes that share a common ancestor with a single nucleotide polymorphism (SNP) mutation. Because a haplogroup consists of similar haplotypes, this is what makes it possible to predict a haplogroup from haplotypes. A 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.

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 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. 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
Mitochondria are small organelles that lie in the cytoplasm of eucaryotic 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 their cytoplasm and the organelles it contains exclusively from their mother, as these are derived from the ovum (egg cell), sperm only carry chromosomal DNA due to the necessity of maintaining motility. When a mutation arises in mtDNA molecule, the mutation is therefore passed in a direct female line of descent. These mutations are derived from copying mistakes, when the DNA is copied it is possible that a single mistake occurs in the DNA sequence, these 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. Y chromosomes are therefore passed from father to son; although Y chromosomes are situated in the cell nucleus, they only recombine with the X chromosome at the ends of the Y chromosome; the vast majority of the Y chromosome (95%) does not recombine. When mutations (SNPs) arise in the Y chromosome, they are passed on directly from father to son in a direct male line of descent. The Y chromosome and mtDNA therefore 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, 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, 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 which men carrying only mutation A do not belong to. Both mtDNA and Y chromosomes are grouped into lineages and haplogroups; these are often presented as tree like diagrams.

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 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.

Human Y-chromosome DNA haplogroups
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.

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) (Oceania, North/Central/East Asia, North America and significant presence in India)
 * Haplogroup F (M89) Oceania, Europe, Asia, North- and South- America
 * YAP+ haplogroups
 * Haplogroup DE (M1, M145, M203)
 * Haplogroup D (M174) (Tibet, Japan, the Andaman Islands)
 * Haplogroup E (M96)
 * Haplogroup E1b1a (V38) West Africa and surrounding regions; formerly known as E3a
 * Haplogroup E1b1b (M215) East Africa, North Africa, the Middle East, the Mediterranean, the Balkans; formerly known as E3b

Groups with mutation M89
(mutation M89 occurred ~45,000 bp)


 * Haplogroup F (P14, M213) (southern India, Sri Lanka, China, 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 Greece, Italy, Iberia, the Tyrol, Bohemia; extremely rare in Northern Europe)


 * Haplogroup H (M69) (India, Sri Lanka, Nepal, and at low frequency in Pakistan, Iran, Central Asia, and Arabia)


 * Haplogroup IJK (L15, L16)

Groups with mutations L15 & L16

 * Haplogroup IJK (L15, L16)
 * Haplogroup IJ (S2, S22)
 * Haplogroup I (M170, P19, M258) (widespread in Europe, found infrequently in parts of the Middle East, and virtually absent elsewhere )
 * Haplogroup I1 (M253, M307, P30, P40) (Northern Europe)
 * Haplogroup I2 (S31) (Central and Southeast Europe, Sardinia)
 * Haplogroup J (M304) (the Middle East, Turkey, Caucasus, Italy, Greece, the Balkans, North and Northeast Africa)
 * Haplogroup J* (Mainly found in Socotra, with a few observations in Pakistan, Oman, Greece, Czechia, and among Turkic peoples)
 * Haplogroup J1 (M267) (Mostly associated with Semitic peoples in the Middle East, Ethiopia, and North Africa, and with Northeast Caucasian peoples in Dagestan; J1 with DYS388=13 is associated with eastern Anatolia)
 * Haplogroup J2 (M172) (Mainly found in West Asia, Central Asia, South Asia, Southern Europe, and North Africa)
 * Haplogroup K (M9, P128, P131, P132)

Groups with mutation M9
(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

 * Haplogroup M (P256) (New Guinea, Melanesia, eastern Indonesia)
 * Haplogroup NO (M214)
 * Haplogroup N (M231) (northernmost Eurasia, especially among the Uralic peoples)
 * Haplogroup O (M175) (East Asia, Southeast Asia, the South Pacific, South Asia, Central Asia)
 * Haplogroup O1 (MSY2.2)
 * Haplogroup O2 (P31, M268)
 * Haplogroup O3 (M122)
 * Haplogroup P (M45, 92R7, M74/N12) (M45 occurred ~35,000 bp)
 * Haplogroup Q (MEH2, M242, P36) (Occurred ~15,000-20,000 years ago. Found in Asia and the Americas)
 * Haplogroup Q1a3a1 (M3) (North America, Central America, and South America)
 * Haplogroup R (M207)
 * Haplogroup R1 (M173)
 * Haplogroup R1a (M17) (Central Asia, South Asia, and Central, Northern, and Eastern Europe)
 * Haplogroup R1b (M343) (Europe, Caucasus, Central Asia, South Asia, North Africa, Central Africa)
 * Haplogroup R2 (M124) (South Asia, Caucasus, Central Asia)
 * Haplogroup S (M230, P202, P204) (New Guinea, Melanesia, eastern Indonesia)

Human mitochondrial DNA haplogroups
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.

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:


 * African: L0, L1, L2, L3, L4, L5, L6
 * 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, Y (note: C, D, E, and G belong to macro-haplogroup M)
 * Native American: A, B, C, D, X
 * Australo-Melanesian: 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 L1-6. 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, 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- 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.

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 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:

General

 * World Families Network
 * Haplogroups.com
 * The Genographic Project

News

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

all DNA haplogroups
Y-Chromosome - *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

 * PhyloTree - The phylogenetic tree of global human mitochondrial DNA variation
 * HaploGrep - automatic classification of mitochondrial DNA haplogroups based on PhyloTree
 * 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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