Haplogroup

Haplogroup formation

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 only pass on the chromosomal DNA, all mitochondria are digested in the oocyte. 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

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. The eusocial wasp Angiopolybia pallens presents with 8 haplogroups depending on its location. This displays the idea of genetic drift.

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:

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:

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.

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.

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-chromosome and MtDNA geographic haplogroup assignation

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

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.