The Mitochondrial DNA Evidence In Africa Biology Essay


The Out of Africa model, also referred to as the African origins, total replacement, Noah's ark or Eve model is one model suggesting the origins of humankind. This model hypothesizes that the evolution of the modern humankind from their archaic ancestors occurred in one place at the one time. It suggests that modern humans arose as a new species about 150,000 years ago and that this took place in Africa. It was after this speciation event that the modern humans moved out of Africa, replacing all non-African archaic populations. Africa was identified as the origin of Homo sapiens because of the high genetic diversity among Africans. It is much higher than the genetic diversity of other populations around the world. The last regions to be settled, for instance South America and the Pacific Islands, have the lowest genetic diversity.

This review will focus on the evidence obtained from mitochondrial DNA and Y-chromosomal DNA. Both mtDNA and Y-chromosomal DNA are non-recombinant and their inheritance is easier to analysis than for other parts of the genome. MtDNA is only inherited through the maternal line and can show the female line. Analysis of mtDNA revealed a series of population bottlenecks and a progressive loss of diversity moving away from East Africa. The Y-chromosome is passed from father to show and can show the male lineage. Mutations of both mtDNA and Y-chromosomal DNA accumulate at a fairly constant rate over time, making them useful for estimating the time of human population splits.

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The first lineage to branch off from mitochondrial eve is the L0 haplogroup. The L1, L2 andL3 haplogroups are all descendant of this L0 lineage and are largely confined to Africa. L3 subdivided into the macro haplogroups M and N. These are the lineages found outside of Africa with a low frequency in Africa. The Y-chromosomal haplogroup DE is limited to Africa. Haplogroup F originated in either North Africa or in South Asia. If it originated in North Africa it would indicate a second out of Africa migration.

There are two possible scenarios for modern human's dispersal out of Africa. The first suggests is a single migration in which only about 150 people left Africa by crossing the Red Sea. The second possibility is that there were two migrations out of Africa. Haplogroup M left by crossing the Red Sea, travelling along the coast to India. Haplogroup N is thought to have followed the Nile from East Africa, headed north and crossed into Asia via the Sinai Peninsula.

Historical Background:

Charles Darwin was one of the first to propose the idea that the ancestor of the modern human originated in Africa. In his book "The Descent of Man" he proposed that all living organism originated from a common ancestor and he outlined his views that man descended from apes. He stated that "in each great region of the world the living mammals are closely related to the extinct species of the same region. It is, therefore, probable that Africa was formerly inhabited by extinct apes closely allied to the gorilla and chimpanzee; and as these two species are now man's nearest allies, it is somewhat more probable that our early progenitors lived on the African continent than elsewhere. But it is useless to speculate on this subject, for an ape nearly as large as a man, namely the Dryopithecus of Lartet, which was closely allied to the anthropomorphous Hylobates, existed in Europe during the Upper Miocene period; and since so remote a period the earth has certainly undergone many great revolutions, and there has been ample time for migration on the largest scale". Here he is saying that if his theory of common descent was correct and that man really did descend from apes then it would be likely that man originated in Africa as it was Africa that apes inhabited at that time.

The original paper supporting the Out of Africa theory was written by Cann et al in 1987. They studied mitochondrial DNA from one hundred and forty seven people between five different populations, African, Asian, Australian, Caucasian and New Guinean. They found that out of the one hundred and forty seven mtDNA mapped, one and thirty three were distinct from each other. Using the parsimony method they constructed a tree relating the 133 types of human mtDNA and the reference sequence:

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Figure 1: Genealogical tree for 134 types of human mtDNA. The tree accounts for the site differences observed between restriction maps of these mtDNAs with 398 mutations. No other order of branching tested is more parsimonious than this one. This order of branching was obtained by ignoring every site present in only one type of mtDNA or absent in only one type and confining attention to the remaining 93 polymorphic sites. The computer programme produces an unrooted network which was converted into a tree by placing the root (arrow) at the midpoint of the longest path connecting the two lineages. The numbers refer to mtDNA types found in more than one individual.

This is a tree of minimum length. On this tree there are two primary branches, one composed of Africans only and the other composed of all five populations studied. From this tree it was suggested that Africa was the source of the human mitochondrial gene pool. This is because two of the primary branches lead solely to African mtDNAs and the second branch also leads to African mtDNAs. The common ancestor a must be of African origin in order to minimise the number of migrations that occurred. This tree also indicates that every population except for Africa must have multiple origins. For example, mtDNA type 49 is New Guinean but its nearest relative is not New Guinean and is in fact Asian. New Guinea seems to have been colonised by at least seven maternal lineages. This seems to be the same for all other populations apart from Africa. By assuming that human mitochondrial DNA sequence divergence accumulates at a constant rate they were able to work out that the common ancestor of all surviving mtDNA types existed 140,000 to 290,000 years ago. The mtDNA results do not show when the migrations out of Africa took place. Nuclear DNA studies carried out based on polymorphic blood groups, red cell enzymes and serum proteins showed that differences between racial groups are smaller than within and that the largest gene frequency differences are between Africans and other populations. This supports the Out of Africa theory because it suggests that the human nuclear gene pool also originated in Africa.

Mitochondrial DNA evidence:

The mitochondrial DNA evidence generally fits the Out of Africa theory. When observed reality is compared with results expected under a given hypothesis then it can be taken as strong evidence for that model. Therefore mitochondrial DNA can be taken as strong support for the Out of Africa model. Mitochondrial DNA is a powerful tool in understanding human evolution because mutations accumulate in this DNA several times faster than in nuclear DNA, mtDNA is inherited maternally and doesn't recombine, and has a high substitution rate.

A studied was carried out by Ingman et al describing the global human diversity in humans based on analyses of the complete mtDNA sequence of 53humans of varied origins. They created a neighbour-joining phylogram on complete mtDNA sequences:

Figure 2: Neighbour joining phylogram based on complete mtDNA genome sequences (excluding the D-loop). The population origin of the individual is given at the twigs. Individuals of African descent are found below the dashed line and non-Africans above. The node marked with an asterisk refers to the MRCA of the youngest clade containing both African and non-African indivdulals.

In this tree, the three deepest branches lead to exlusively African mtDNAs and the fourth deepest branch contains both African and non-African mtDNA. The deepest branch provides excellent support for the origin of human mtDNA in Africa. The amount of mtDNA sequence diversity among Africans is more than double that of non-Africans. This suggests that ther is a longer genetic history for African mtDNA than for non-African mtDNA. The "star" shaped phylogeny of the non -African sequences suggest a population bottleneck. This is more than likely associatd with the colonisation of Euroasia from Africa, in which the previous populations are replaced with the modern human's dispersal into Euroasia.

The figures below show the mtDNA mismatch distributions for Africans and non-Africans The mtDNA from the non-Africans show a bell-shaped distribution , indicating a recent population expansion. The mtDNA from individuals of African origin show a ragged distribution, indicating a constant population size.

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Figure 3: Mismatch distributions of pairwise nucleotide differences between mtDNA genomes (excluding the D-loop) a) African; b) Non-African.

Single nucleotide polymorphism studies have shown that human mitochondrial DNA can be classified into groups of related haplotypes.

An early paper by Chen et al analysed mitochondrial DNA variation in Africa, revealing continent specific groups of mtDNA haplotypes (haplogroups). There is a HpaI site gain at nucleotide pair (np) 3592 which is found in sub-Saharan populations with a low frequency in populations, such as Arabs and Southern Italy, that have been known to have mixed with Africans. The mtDNA that contain the HpaI site at np 3592 form the most divergent mtDNA haplogroups in the world. Continent specific polymorphisms characterize mtDNAs from European, Asian and Native American populations.