A haplotype is a group of alleles in an organism that are inherited together from a single parent,[1][2] and a haplogroup (haploid from the Greek: ἁπλοῦς, haploûs, "onefold, simple" and English: group) is a group of similar haplotypes that share a common ancestor with a single-nucleotide polymorphismmutation.[3] More specifically, a haplotype is a combination of alleles at different chromosomal regions that are closely linked and tend to be inherited together. As a haplogroup consists of similar haplotypes, it is usually possible to predict a haplogroup from haplotypes. Haplogroups pertain to a single line of descent. As such, membership of a haplogroup, by any individual, relies on a relatively small proportion of the genetic material possessed by that individual.
Y-DNA haplogroups map of the world
Each haplogroup originates from, and remains part of, a preceding single haplogroup (or paragroup). As such, any related group of haplogroups may be precisely modelled as a nested hierarchy, in which each set (haplogroup) is also a subset of a single broader set (as opposed, that is, to biparental models, such as human family trees). Haplogroups can be further divided into subclades.
Haplogroups are normally identified by an initial letter of the alphabet, and refinements consist of additional number and letter combinations, such as (for example) A → A1 → A1a. The alphabetical nomenclature was published in 2002 by the Y Chromosome Consortium.[4]
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, happened 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 function is to provide energy to the cell. Mitochondria are thought to be reduced descendants of symbioticbacteria 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 contained by that cytoplasm exclusively from the maternal ovum (egg cell); sperm only pass on the chromosomal DNA, all paternal mitochondria are digested in the oocyte. When a mutation arises in a mtDNA molecule, the mutation is therefore passed down in a direct female line of descent. Mutations are changes in the nitrogen bases of the DNA sequence. Single changes from the original sequence are called single nucleotide polymorphisms (SNPs).[dubious – discuss]
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 down in a direct male line of descent.
Other chromosomes, autosomes and X chromosomes (when another X chromosome is available to pair with it), share their genetic material during meiosis, the process of cell division which produces gametes. 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 individuals) 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 individuals 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 humans carrying mutation A form a single haplogroup, and all humans 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 humans 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.
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.[5]
^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. PMID24166809. S2CID23291764.
^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)
^ Haplogroup S, as of 2017, is also known as K2b1a. (Previously the name Haplogroup S was assigned to K2b1a4.)
^ Haplogroup M, as of 2017, is also known as K2b1b. (Previously the name Haplogroup M was assigned to K2b1d.)
Haplogroup C (M130) (Oceania, North/Central/East Asia, North America and a minor presence in South America, Southeast Asia, South Asia, West Asia, and Europe)
Haplogroup E1b1a (V38) West Africa and surrounding regions; formerly known as E3a
Haplogroup E1b1b (M215) Associated with the spread of Afroasiatic languages; now concentrated in North Africa and the Horn of Africa, as well as parts of the Middle East, the Mediterranean, and the Balkans; formerly known as E3b
Groups with mutation M89
(mutation M89 occurred ~45,000 bp)
Haplogroup F (M89) Oceania, Europe, Asia, North and South America
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; rare in Northern Europe)
Haplogroup J1 (M267) (Mostly associated with Semitic peoples in the Middle East but also found in; Mediterranean Europe, Ethiopia, North Africa, Pakistan, India 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, Iran, Italy, Greece, the Balkans and North Africa)
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
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,
O,
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.[9]
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 three main groups, which are designated by the 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 which is thought to have evolved outside of Africa, following an eastward route along southern coastal areas. Descendant lineages of haplogroup M are now found throughout Asia, the Americas, and Melanesia, as well as in parts of the Horn of Africa and North Africa; almost none have been found in Europe. The N haplogroup may represent another macrolineage that evolved outside 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
G – Many Northeast Siberians, northern East Asians, and Central Asians
Q – Melanesian, Polynesian, New Guinean populations
The N type consists of:
A – Found in many Amerindians and some East Asians and Siberians
I – 10% frequency in Northern, Eastern Europe
S – Some Indigenous Australian (First Nations People of Australia)
W – Some Eastern Europeans, South Asians, and southern East Asians
X – Some Amerindians, Southern Siberians, Southwest Asians, and Southern Europeans
Y – Most Nivkhs and people of Nias; many Ainus, Tungusic people, and Austronesians; also found with low frequency in some other populations of Siberia, East Asia, and Central Asia
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.[11]
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 populations; 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.
Y-chromosome and MtDNA geographic haplogroup assignment
Here is a list of Y-chromosome and MtDNA geographic haplogroup assignment proposed by Bekada et al. 2013.[12]
Y-chromosome
According to SNPS haplogroups which are the age of the first extinction event tend to be around 45–50 kya. Haplogroups of the second extinction event seemed to diverge 32–35 kya according to Mal'ta. The ground zero extinction event appears to be Toba during which haplogroup CDEF* appeared to diverge into C, DE and F. C and F have almost nothing in common while D and E have plenty in common. Extinction event #1 according to current estimates occurred after Toba, although older ancient DNA could push the ground zero extinction event to long before Toba, and push the first extinction event here back to Toba. Haplogroups with extinction event notes by them have a dubious origin and this is because extinction events lead to severe bottlenecks, so all notes by these groups are just guesses. Note that the SNP counting of ancient DNA can be highly variable meaning that even though all these groups diverged around the same time no one knows when.[13][14]
Origin
Haplogroup
Marker
Europe (Second Extinction Event?)
I
M170, M253, P259, M227, M507
Europe
I1b
P215, M438, P37.2, M359, P41.2
Europe
I1b2
M26
Europe
I1c
M223, M284, P78, P95
Europe
J2a1
M47
Europe
J2a2
M67, M166
Europe
J2a2a
M92
Europe
J2b
M12, M102, M280, M241
Europe
R1b1b1a
M412, P310
Europe
R1b1b1a1
L11
Europe
R1b1b1a1a
U106
Europe
R1b1b1a1b
U198, P312, S116
Europe
R1b1b1a1b1
U152
Europe
R1b1b1a1b2
M529
Europe
R1b1b1a1b3,4
M65, M153
Europe
R1b1b1a1b5
SRY2627
South Asia or Melanesia
C1(formerly known as CxC3)
Z1426
North Asia
C2 (formerly known as C3)
M217+
Indonesia or South Asia
F
M89, M282
Europe (Caucasus)
G
M201, M285, P15, P16, M406
South Asia
H
M69, M52, M82, M197, M370
Europe or Middle East
J1
M304, M267, P58, M365, M368, M369
Europe or Middle East
J2
M172, M410, M158, M319, DYS445=6, M339, M340
West of Burma in Eurasia (First Extinction Event?)[15]
^Rootsi S, Magri C, Kivisild T, Benuzzi G, Help H, Bermisheva M, Kutuev I, Barać L, Pericić M, Balanovsky O, Pshenichnov A, Dion D, Grobei M, Zhivotovsky LA, Battaglia V, Achilli A, Al-Zahery N, Parik J, King R, Cinnioğlu C, Khusnutdinova E, Rudan P, Balanovska E, Scheffrahn W, Simonescu M, Brehm A, Goncalves R, Rosa A, Moisan JP, Chaventre A, Ferak V, Füredi S, Oefner PJ, Shen P, Beckman L, Mikerezi I, Terzić R, Primorac D, Cambon-Thomsen A, Krumina A, Torroni A, Underhill PA, Santachiara-Benerecetti AS, Villems R, Semino O (Jul 2004). "Phylogeography of Y-chromosome haplogroup I reveals distinct domains of prehistoric gene flow in europe"(PDF). American Journal of Human Genetics. 75 (1): 128–37. doi:10.1086/422196. PMC1181996. PMID15162323. Archived from the original(PDF) on 2009-06-24. Retrieved 2007-03-08.
