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Both mt DNA and Y chromosomes are grouped into lineages and haplogroups; these are often presented as tree like diagrams.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.Mutations are copying mistakes in the DNA sequence.

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One indication that mitochondria were once free living is that each contains a circular DNA, called mitochondrial DNA (mt DNA), 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 mt DNA is an exception.Y-DNA is passed solely along the patrilineal line, from father to son, while mt DNA is passed down the matrilineal line, from mother to offspring of both sexes.Neither recombines, and thus Y-DNA and mt DNA change only by chance mutation at each generation with no intermixture between parents' genetic material.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.

The special feature that both Y chromosomes and mt DNA 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.

Human Y chromosomes are male-specific sex chromosomes; nearly all humans that possess a Y chromosome will be morphologically male.