Haplotype

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A haplotype (

Many organisms contain genetic material (

or a small set of alleles.

Specific contiguous parts of the chromosome are likely to be inherited together and not be split by

Other parts of the genome are almost always haploid and do not undergo crossover: for example, humans mitochondrial DNA is pass down through the maternal line and the Y chromosome is passed down the paternal line. In these cases, the entire sequence can be grouped into a simple evolutionary tree, with each branch founded by a unique-event polymorphism mutation (often, but not always, a single-nucleotide polymorphism (SNP)). Each clade under a branch, containing haplotypes with a single shared ancestor, is called a haplogroup.^[8][9][10]

Haplotype resolution

An organism's

- in these cases, an observer does not know which haplotype the individual has, e.g., TA vs AT.

Locus 1 Locus 2	AA	AT	TT
GG	AG AG	AG TG	TG TG
GC	AG AC	AG TC or AC TG	TG TC
CC	AC AC	AC TC	TC TC

The only unequivocal method of resolving phase ambiguity is by sequencing. However, it is possible to estimate the probability of a particular haplotype when phase is ambiguous using a sample of individuals.

Given the genotypes for a number of individuals, the haplotypes can be inferred by haplotype resolution or

(HMM).

Microfluidic whole genome haplotyping is a technique for the physical separation of individual chromosomes from a metaphase cell followed by direct resolution of the haplotype for each allele.

Gametic phase

In

Y-DNA haplotypes from genealogical DNA tests

Unlike other chromosomes, Y chromosomes generally do not come in pairs. Every human male (excepting those with

haplotypes, there is effectively not any randomisation of the Y-chromosome haplotype between generations. A human male should largely share the same Y chromosome as his father, give or take a few mutations; thus Y chromosomes tend to pass largely intact from father to son, with a small but accumulating number of mutations that can serve to differentiate male lineages. In particular, the Y-DNA represented as the numbered results of a Y-DNA genealogical DNA test should match, except for mutations.

UEP results (SNP results)

).

The UEP results represent the inheritance of events it is believed can be assumed to have happened only once in all human history. These can be used to identify the individual's

patrilineal

ancestors of current individuals.

Y-STR haplotypes

Genetic results also include the Y-STR haplotype, the set of results from the Y-STR markers tested.

Unlike the UEPs, the Y-STRs mutate much more easily, which allows them to be used to distinguish recent genealogy. But it also means that, rather than the population of descendants of a genetic event all sharing the same result, the Y-STR haplotypes are likely to have spread apart, to form a cluster of more or less similar results. Typically, this cluster will have a definite most probable center, the modal haplotype (presumably similar to the haplotype of the original founding event), and also a haplotype diversity — the degree to which it has become spread out. The further in the past the defining event occurred, and the more that subsequent population growth occurred early, the greater the haplotype diversity will be for a particular number of descendants. However, if the haplotype diversity is smaller for a particular number of descendants, this may indicate a more recent common ancestor, or a recent population expansion.

It is important to note that, unlike for UEPs, two individuals with a similar Y-STR haplotype may not necessarily share a similar ancestry. Y-STR events are not unique. Instead, the clusters of Y-STR haplotype results inherited from different events and different histories tend to overlap.

In most cases, it is a long time since the haplogroups' defining events, so typically the cluster of Y-STR haplotype results associated with descendants of that event has become rather broad. These results will tend to significantly overlap the (similarly broad) clusters of Y-STR haplotypes associated with other haplogroups. This makes it impossible for researchers to predict with absolute certainty to which Y-DNA haplogroup a Y-STR haplotype would point. If the UEPs are not tested, the Y-STRs may be used only to predict probabilities for haplogroup ancestry, but not certainties.

A similar scenario exists in trying to evaluate whether shared surnames indicate shared genetic ancestry. A cluster of similar Y-STR haplotypes may indicate a shared common ancestor, with an identifiable modal haplotype, but only if the cluster is sufficiently distinct from what may have happened by chance from different individuals who historically adopted the same name independently. Many names were adopted from common occupations, for instance, or were associated with habitation of particular sites. More extensive haplotype typing is needed to establish genetic genealogy. Commercial DNA-testing companies now offer their customers testing of more numerous sets of markers to improve definition of their genetic ancestry. The number of sets of markers tested has increased from 12 during the early years to 111 more recently.

Establishing plausible relatedness between different surnames data-mined from a database is significantly more difficult. The researcher must establish that the very nearest member of the population in question, chosen purposely from the population for that reason, would be unlikely to match by accident. This is more than establishing that a randomly selected member of the population is unlikely to have such a close match by accident. Because of the difficulty, establishing relatedness between different surnames as in such a scenario is likely to be impossible, except in special cases where there is specific information to drastically limit the size of the population of candidates under consideration.

Diversity

Haplotype diversity is a measure of the uniqueness of a particular haplotype in a given population. The haplotype diversity (H) is computed as:^[13]

where ${\displaystyle x_{i}}$ is the (relative) haplotype frequency of each haplotype in the sample and ${\displaystyle N}$ is the sample size. Haplotype diversity is given for each sample.

See also

• Haplotype 35
• Haplotype estimation
• International HapMap Project
• Genealogical DNA test
• Haplogroup
• Y-STR
• PLINK (genetic tool-set)
• Haplogroup E-M215 (Y-DNA)

References

External links

• HapMap Archived 2014-04-16 at the Wayback Machine — homepage for the International HapMap Project.
• Haplotype versus Haplogroup — the difference between haplogroup & haplotype explained.