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"Haplotype Blocks"
[A Clue to Our History
as a Species]

E-Newsletter No. 42

The mosaic nature of our Genome is made of DNA sequences which are 99.9 percent identical to all other individuals within our species. It has revealed the remarkable genetic similarity we share with each other as well as with our closest primate relatives.

The variation found along a chromosome is structured in blocks where the nucleotide substitutions are associated in so-called "haplotype blocks"- likely a result of recombination, that is, a result of reshuffling of chromosome segments that occur during formation of sex cells (meiosis). This tends to occur in certain areas of the chromosome more often than in others.

In addition, chance occurrence of recombination events at certain spots and not at others in the genealogy of human chromosomes will influence the structure of these blocks. Thus, any single human chromosome is a mosaic of different haplotype blocks, where each block has its own pattern of variation.

Although the delineation of such blocks depends on the methods used to define them, they are typically 5,000-200,000 base pairs in length. As few as four to five common haplotypes account for most of the variations in each block.

Of the 928 such haplotype blocks recently studied in humans from Africa, Asia and Europe, 51 percent were found on all three continents , 72 percent on two continents, and only 28 percent on one continent. Of those haplotypes that were found on one continent only, 90 percent were found in Africa, and African DNA sequences differ on average more among themselves than they differ from Asian or European DNA sequences. Therefore, within the human gene pool, most variation is found in Africa and what is seen outside Africa is a subset of the variation found within Africa.

Two parts of the human genome can be regarded as haplotype blocks where the history is particularly straightforward to reconstruct, as no recombination occurs at all. The first of these is the genome of the mitochondrion (the cellular organelle that produces energy and has its own genetic material), which is passed on to the next generation from the mother's side. The second is the Y chromosomes, which is passed on from the father's side. 

Variation in DNA sequences from both the mitochondrial genome and the Y chromosome, as well as many sections of the nuclear genome, have their geographical origin in Africa. Because other evidence suggest that humans expanded some 50,000 to 200,000 years ago from a population of about 10,000 individuals, this suggests that we expanded from a rather small African population. Thus, from a genomic perspective, we are all Africans, either living in Africa or in quite recent exile outside Africa.

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