Mitochondrial Dna And Genetic Evidence Biology Essay

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Introduction:

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 further away, geographically, from Africa the less genetically diverse the populations are. 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 therefore be used to determine the female lineage. 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 son and can be used to determine the male lineage. The Y chromosome does not undergo recombination because it is so different from the X chromosome that they don't swap information. This means that the Y-chromosome passed on is the same in father and son (unless it undergoes mutation) making it useful for studying 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. Mitochondrial DNA is also a very good indicator of migration routes and range expansion due to its high distribution and variation.

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 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 taking the Southern route. Haplogroup N is thought to have followed the Nile from East Africa, headed north and crossed into Asia via the Sinai Peninsula in Egypt.

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 Africa was the region inhabited at that time by apes.

Mitochondrial Eve and Y-chromosomal Adam:

Mitochondrial eve is the matrilineal most recent common ancestor, estimated to have lived about 200,000 years ago. All living people's mitochondrial DNA is descended from hers. She was thought to have lived in East Africa and her discovery supported the theory that all modern humans originated in Africa and migrated from there.

Y-chromosome Adam is the patrilineal most recent common ancestor, estimated to have lived between 90,000 to 60,000 years ago. He was also believed to have originated in Africa.

The original paper supporting the Out of Africa theory was written by Cann et al in 1987. In which they found evidence that the MRCA lived in Africa about 200,000 years ago. 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, 133 were distinct from each other. Using the parsimony method they constructed a tree relating the 133 types of human mtDNA and the reference sequence:

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.

(both figure and text taken from Cann et al, 1987)

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, 'Mitochondrial Eve' 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. (Cann et al, 1987)

The Genetic Evidence:

The technique used to deduce the colonization pattern of the world is coalescence. This theory is a population genetics model based on the genealogy of gene copies and favours the Out of Africa theory. It describes the characteristics of the joining of lineages back in time to a common ancestor.This lineage joining is referred to as coalescence. The theory provides a way of estimating the expected time to coalescence and establishing the relationships of coalescence times to population size, and age of the most recent common ancestor. This theory makes use of the fact that genetic drift over time will result in the extinction of lineages. This means that any sample of DNA markers will coalesce to a common ancestor when looking backward from the present day generation. The limitation of this theory is that all genetic variation coalesces to the MRCA and as a result the population history before this MRCA is unknown. Genomic phylogenetics reconstruction is necessary to assume the dispersal routes of early modern humans.

Mitochondrial DNA evidence:

A study 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.

(Both figure and text taken from Ingman et al, 2000)

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.

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

(Both figure and text taken from Ingman et al, 2000)

The initial Homo sapiens population dynamics and dispersal routes remain poorly understood. The mtDNA phylogeny can be collapsed into two sister branches L0 and L1'2'3'4'5'6 (L1'5). The L1'5 group is more widespread and has given rise to almost all mtDNA lineages found today. The non-African genetic diversity being formed from two subclades of the L3 branch, M and N. Some of the L clades show significant phylogeographic structure in Africa, such as the localization of L1c1a to Central Africa and L0d and L0k to the Khosian people.(Behar et al, 2008)

Analysis of the complete mtDNA sequences of Khosian people suggests the divided from other modern humans no later than 90,000 years ago. This reveals evidence for the existence of an early maternal structure in the history of Homo sapiens. L0abfk split over 133,000 years ago. Since this split the expansion of L0d, L0k, L0abf and L1'5 clades have progressed in an uneven way. L0d and L0k localized in South Africa, giving rise to the Khosian people and L0abf and L1'5spread all over the world giving rise to all non-Khosian populations. These maternal southern and eastern populations remained isolated from each other for a long period of time. This isolation suggests the formation of small, independent populations in Africa instead of the previously thought uniform spread of modern humans. (Behar et al, 2008)

Mitochondrial DNA L haplogroups:

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 an HpaI site gain at nucleotide pair (np) 3592 which is found in sub-Saharan populations with a low frequency in populations which 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. These continent specific polymorphisms have a high frequency in one continental population and are specific to either European, Asian or Native American populations. These mutations took place after the genetic separation of the ancestral population that formed the modern human ethnic groups. The oldest and the largest haplogroup in each continent is usually the one that is the most divergent. All the mtDNAs associated with the HpaI site gain at np 3592 all come from the same common ancestor. These cluster in the L haplogroup. This haplogroup is subdivided into theL0, L1, L2, L3, L4, L5 and L6 sub-haplogroups by additional polymorphisms. The L haplogroup and L1 and L2 sub- haplogroups are said to be of ancient origin due to their dominance in sub-Saharan populations. The ages of these haplogroups were determined from the assumption that nucleotide substitution accumulates at a constant rate. The age of haplogroup L is between 98,000 and 130,000 years, haplogroup L1 is between 86,000 and 113,000 years and haplogroup L2 is between 59,000 and 78,000 years. Comparison of the sequence divergence of the L haplogroup determined that the African haplogroup is the most divergent. The approximate ages for the continent specific haplogroups agree with the theory that all modern humans have a common ancestor from an ancestral population in Africa. These ages also agree with the suggested times of dispersal and migration of the modern human populations into the other continents. The age of the haplogroup L could indicate that this haplogroup originated before modern humans dispersed from Africa. However, the haplogroups L1 and L2 were not carried from Africa by the modern human populations that migrated to the Middle East and Asia. Instead another haplogroup must have participated in this migration. There are mtDNAs that do not contain the HpaI site gain in np 3592. These were found in sub-Saharan populations and suggest that there were some mtDNAs without the 3592 HpaI site that originated in Africa. They are widely distributed in sub-Saharan populations and most likely have an ancient African origin. These mtDNAs are similar to mtDNAs in Europe and Asia and seem to be the only mtDNAs carried out of Africa by migration of the modern humans. They gave rise to the non-African modern human populations and are now know to be haplogroup L3. This paper exhibits data that confirms that there was a high sequence divergence within Africans compared to the rest of the world thereby supporting the Out of Africa Theory. There is less sequence divergence in Asians than in Africans. Native American populations have the lowest values of sequence divergence. (Chen et al, 1995)

The minimum coalescence age for modern humans has been estimated to be between 156,000 and 169,000 years before present. Analysis of the L haplogroup has been carried out in order to find those sub-haplogroups involved in the migration of modern humans out of Africa. The L0 haplogroup is the earliest descendant of mitochondrial Eve and is a sister group to the L1 haplogroup. L0 is subdivided into L0a, L0d, L0f and L0k. L0a is thought to have originated in Eastern Africa and is dominant in Ethiopia. The idea that east Africa is the most likely region for L0a variation is further supported by the phylogeny of the L0 clade. L0d and L0k originated in Southern African. L0f is rare and confined to East Africa. The relationship between L0d and L0k is still uncertain.

The first ancient split from this into L1b/c occurred over 120,000 years ago. The L1 haplogroup is divided into L1b and L1c. L1b is common in Western Africa and L1c is frequent among central African Bantu speakers. See figure__ for the relationship between these two haplogroups. FIG. 3.-Phylogenetic tree of mtDNA genomes (excluding the d-loop) obtained by maximum likelihood Bayesian analysis.

The split into the L2 lineage occurred in Africa over The L2 lineage is divided into two sub-clades L2a1 and L2b. A mutation at np12693 characterizes the L2a1 clade. Ethiopian L2a1 sequences contain mutations at the np 16189 and the np 16309. L2a1c contains mutations at np 16209, 16301 and 16354. L2a1a has a mutation at np 16286. L2a1a is found mostly in South-Eastern Africa.

The split into the L3 sub-clade occurred over 59,000 years ago in Africa. The most frequent of the L3 sub-clades is the L3f haplogroup. This haplogroup seems to be confined to East Africa. However, there is an occurrence of variations of this clade in West Africa indicating an early dispersal of the L3f1 lineages. L3f1 is characterized by two mutations in its coding region. The L3 haplogroup is subdivided into three clades, L3i, L3x and L3w. Haplogroup L3i contains a transition at np 7645. It was also found to occur within a sister group of W haplogroup lineages in Eurasia. The L3x haplogroup is characterized by transitions at nps 6401, 13708 and 16169. This haplogroup is very frequent among Ethiopians, especially among the Oromos. It can be sub divided into two clades, L3x1 and L3x2. These two clades are confined to the Horn of Africa and the Nile Valley. The L3w haplogroup contains substitutions at nps 15388 and 16260. This haplogroup is confined to East and North-eastern Africa. L3b and L3e haplogroups are found in West Africa and Bantu-speaking populations in South-east Africa. The L3d haplogroup is mostly found in Western Africa. It is divided into the two sub-clades L3d1 and L3d2. The L3d1 sub clade has a high frequency in South-East Africa. L3d2 is characterised by transcriptions at nps 15358 and 16256. These occur in Western Africa. Ethiopian L3d2 lineages contain a transition at np 16368 and this is not found anywhere else in Africa. The L3 clade is more related to Eurasian haplogroups than to African clusters of the L1 and L2 haplogroups.

L4 is an early branch from L3. It is divided into two sub-clades by three coding and three control region markers. Substitutions at nps 195, 198, 7376, 16207 and 16260 characterise the L4a1 haplogroup. L4g was previously named L3g but it was found to share ancestral character states at nps 769 and 1018 with haplogroup L4a. It is mostly found in Ethiopia. L4a and L4g have high haplotype frequencies and sequence diversity in Ethiopians.The L5 haplogroup is divided into L5a and L5b. L5a is found almost exclusively in East Africa. L5 b on the other hand is spread through Southern Africa.The L6 haplogroup contains six coding transitions and one control region transition. This haplogroup is thought to have originated in East Africa. It is a sister clade of the L2, L3 and L4 are all frequent there, giving support to this theory.

The mtDNA tree splits at its core layers into branches that carry exclusively African sequences and just one, L3, which the Africans share with the rest of the world. All non-African mtDNA lineages are derived from just two branches, M and N, branching from the root of the L3 haplogroup. These also give rise to a number of sub-clades specific only to African populations. The N haplogroup gives rise to a daughter clade, R, which is also a founder of extant non-African populations. The first informative split in the mtDNA tree with regards to phylogeny occurs at the level of L3/M, N, R clades. The next informative split in the mtDNA tree distinguishes all major continents excluding America beneath the M, N and R founders.

The M and N Haplogroups:

The M1 haplogroup has a high frequency in Ethiopia. It has two subclades, M1a and M1b. M1a contains a transition at np 16359. It can be found in Near Eastern, Caucasus and in European populations. The M1b group is smaller and confined to East Africa. Both M1a and M1b are rare in North Africa. Another clade, M1c, is present in Northern Africa, the Canary Islands and the Near East. This clade is characterized by a transition at np 16185.

The N (preHV) haplogroup is the most frequent in Ethiopian lineages. This lineage occurs in populations in the Near East, Southern Caucasia and North Africa.

Y-chromosomal DNA evidence:

The Y chromosome Consortium (2002) tree was updated in a paper by Karafet et al in 2008. This tree identifies the 18 major clades, A to R, in the Y chromosome tree. There are five paragroups that were not based on a derived character and they represent the interior nodes of the tree. There are 243 different mutational events that give rise to 153 non recombining Y chromosome haplogroups. The C and FT haplogroups were united by the P143 mutation. These haplogroups contain lineages that are not usually found in sub-Saharan Africa. The C-FR chromosome must have been carried out of Africa early on in the dispersal out of Africa. The IJ clade is joined by seven mutations and the NO clade is joined by six mutations. The M lineage is joined to two K haplogroups by the P256 marker into the M super clade.

Diagram p4 from the revised Y chromosome haplogroup tree.

Two mutations, M91 and P97, identify Clade A. This clade is one of the most base haplogroups on the Y-chromosome tree and is almost entirely confined to Africa, being most frequent in Khosian, Ethiopian and Sudanese populations. Clade B is characterized by four mutations and is also almost completely restricted to Africa, mostly confined to sub-Saharan Africa with the highest frequencies in Pygmy populations. The C haplogroup is identified by five mutations. It has not been found in African populations and may have an originated in Asia after the dispersal of modern humans out of Africa. Haplogroup D is defined by two mutations. This haplogroup is also thought to have originated in Asia as it has not been found anywhere else. These lineages are found almost completely in Central Asia and Japan with a low frequency in Southeast Asia and the Andaman Islands. Clade E is identified by 18 mutations and is the most mutationally diverse Y chromosomal haplogroup. These are found mostly in Africa with moderate frequencies in the Middle East and low frequencies in Central and South Asia. The FT clade is defined by 25 mutations. The F* paragroups has a low frequency in India. The G clade is identified by two mutations and is divided into two subclades, G1 and G2. This clade is mostly present in the Middle East, the Mediterranean and the Caucasus Mountains. Haplogroup H is characterized by one mutation and is divided into two subclades, h1 and H2. This group is almost exclusive to the Indian subcontinent. Clade I is characterised by six mutations and is sub-divided into two subclades, I1 and I2. This clade represents two of the major European Y chromosome haplogroups with clade I1 being found mostly in Northern Europe and clade I2 is widespread in Eastern Europe and the Balkans. Clade J is defined by three mutations and is divided into two major subclades, J1 and J2, and also contains a paragroup J*. These lineages are found at high frequencies in North Africa, the Middle East, Europe, Central Asia, Pakistan and India. Haplogroup K is defined by the derived state at four sites and the ancestral state at the mutations that characterize the L, M, NO, P, S and T lineages. There is a paragroup K* and four different lineages characterized by five mutations. The K1 haplogroup is found at a low frequency in India and the K2, K3 and K4 haplogroups are found in Oceania, Indonesia and Australia. The L haplogroup is characterized by six mutations and the majority of this haplogroup is found in India, with the L haplogroup also being present in the Middle East, Asia, Northern Africa and along the Mediterranean coast. The M superclade contains 19 internal mutations. This lineage is confined to Oceania and eastern Indonesia. The N haplogroup is defined by 10 mutations and is restricted to Northern Eurasia. Clade O is defined by four mutations and is a major haplogroup in East Asia. It is also found at a low frequency in Central Asia and Oceania. Haplogroup contains the Q and R lineages. Clade Q is characterized by the M242 mutation and is distributed in North Eurasia with a high frequency in some Siberian groups. It is also found in Europe, East Asia and the Middle East and is the major lineage in native Americans. Cade R is defined by eight mutations and is the major y chromosomal lineage of Europeans. Clade S is defined by three mutations and is mostly found in Oceania and Indonesia. Clade T is identified by six mutations and is divided into two subclades found at a low frequency in Africa, Europe and the Middle East.

The two primary splits in this tree lead to the A and B haplogroups, both of which are restricted to Africa. These are genetically diverse and have sub-haplogroups geographically distinct from each other. The remainder of the deep structures of the phylogeny are characterized by three sub-clusters that coalesce at the root of the CR-M168 node. These represent all the African haplogroups and all the non African haplogroups. There is a shared presence of the De haplogroup in Africa and Asia. The C haplogroup is a non African haplogroup and is widely distributed in East Asia, Oceania and North America. The haplogroup F-M89 is another non African cluster that is distributed all around the world. The F* and H haplogroups are restricted to Asia, the I haplogroup in Europe and the J haplogroup in the Middle East.

Apart from the A and B haplogroups all other Y chromosome haplogroups descend from one ancestral node, CDEF which is defined by the mutations M168 and M294. This node is split into the C, DE and F haplogroups and these make up the majority of African and non African affiliated chromosomes. Due to the fact that the A and B haplogroups originate in Africa it was proposed the CDEF node also originated in Africa. An African origin of the DE haplogroup was supported with the detection of the DE* chromosome in Nigeria and by the recognition of the D-M174 haplogroup.

See figure8d page 555 from Underhill

It was proposed that two independent founder types D and CF evolved out of Africa (see figure above) The common ancestry of C and F founder types was supported by a single mutation, implying the diversification of CF from DE was shortly followed by they split of C from F. Although the D and E haplogroups share a common ancestry there is a geographic distance existing between the two of them. The D haplogroup is widely distributed in Asia and the E haplogroup is frequent in Africa. This suggests long term isolation and extinction of descendants in the area between Africa and Asia.

Upon analysis of the Y chromosome it is clear that North Africa is genetically similar to the Middle East and there is a clear genetic difference between North-Western Africa and Sub-Sahara Africa and Europe. The lineages most prevalent to North Africa are absent in both Europe and sub-Saharan Africa. E3b2 is most common in North Africa, R1b is common in Europe and E3a is common in many sub-Saharan areas. This suggests that there was limited gene flow between North Africa and Sub-Saharan Africa and Europe. E3b2 is rare outside of North Africa and the other dominant haplogroup J* in North Africa reaches its highest frequency in the Middle East indicating that there was gene flow between these two populations. It has been proposed that the J haplogroup originated in the Middle East. The M35 lineage is thought to have originated in East Africa due to its high frequency and diversity there. It is thought to have given rise to the M81 lineage, E3b2, that is found in North Africa. (Arredi et al, 2004)

Exodus from Africa:

The migration out of Africa is thought to have occurred over 100,000 years ago and is believed to have led to the later colonization of the rest of the world. The first evidence of the existence of modern humans outside of Africa has been dated to over 80,000 years ago. However, this was an isolated incidence and is thought to represent an early offshoot that has since died out. Successful migrations are believed to have occurred between 45,000 and 75,000 years ago. There are two scenarios describing modern human's dispersal from Africa. The first suggests a single migration event took place. This theory proposes that only about 150 people left Africa crossing the red sea. This is because only the descendants of one lineage, L3, are found outside Africa. The M and N haplogroups are rare in Africa and seem to have arrived recently. This may be a result of mutations in the L3 haplogroup arising in East Africa just before the dispersal out of Africa or may have arisen shortly after the migration from Africa. The second scenario suggests a multiple dispersal model. This indicates that the M haplogroup crossed the Red Sea, travelled along the coast and arrived in India and the N haplogroup headed North, trailing the Nile and crossed into Asia through the Sinai Peninsula in Egypt. This group divided and went in several different directions. Some went east into Asia and others went to Europe. This scenario might clarify why the N haplogroup is predominant in Europe and the M haplogroup is absent.

Mitochondrial evidence for the dispersal from Africa:

Mitochondrial DNA analysis of present day African lineages points to a rapid population growth in the ancestral African population. Studies revealed a peak in African populations about 80,000 years ago with similar peaks in Asia and Europe somewhere between 60,000 and 40,000 years ago. This evidence shows a rapid increase in the African population much earlier than in Europe or Asia indicating expansion in Africa due to dispersion from a small population to other parts of the continent. There was an expansion of the L2 and L3 mitochondrial lineages about 80,000 and 60,000 years ago.

Population diversity among African populations:

There seems to be limited haplotype sharing among northern, eastern and Sub-Saharan Africans. Some haplotypes are common in one area but missing from the others. Chromosomes with the PN2 T and DYS271 A alleles are common in both northern and eastern Africa. These have been divided into different haplotypes, one of which bears the M81 mutation and is present in some Northern African populations and absent in Eastern African populations. There has been a population expansion in Northern Africa suggested by the age and the high frequency of the M81 haplotypes in north-western Africa. The spread of haplotypes 22 and 24, both of which contain the DYS271 allele, has erased pre-existing genetic differences among different regions in sub-Saharan Africa. Haplotypes 22, 24 and 41 have an extremely high frequency in Sub-Saharan Africans. It is thought that haplotype 41 was involved in the expansion of Bantu-speaking populations from western Africa into southern Africa. This is supported by the fact that the variance of haplotype 41 is much higher in the central western Africa than in southern Khosians. This is also true for the 22 and 24 haplotypes.

An Eastern African origin:

The oldest remains of modern humans were found in eastern and southern Ethiopia and have been dated to over 160,000 years ago. Eastern Africa is thought to be the origin of the earliest migrations of modern humans out of Africa. The M haplogroup has been found in high frequencies in Ethiopia and Asia. The presence of the 'Asian' mtDNA haplogroup M is unique to Ethiopia. These two regions have a different variation of the M haplogroup and seem to have divided over 50,000 years ago. The Eastern African group is named M1 and shows a more recent coalescence time than the M haplogroup in Asia. The M haplogroup is thought to have originated in eastern Africa about 60,000 years ago and was then carried to Asia where the haplogroup founder group went through a demographic and geographic expansion. The M haplogroup in East Africa did not expand until about 10,000 to 20,000 years ago. The M haplogroup is the first indicator of the migration route out of Africa through Eastern Africa toward South East Asia, Australia and the Pacific islands.

Tanzania contains high mtDNA genetic diversity compared to the level of diversity in sub-Sahara African populations. This diversity is divided among ancient mtDNA haplogroups such as L0d, L0f and L5 which are rare in other parts of Africa. This suggests that in order for these lineages to be preserved Tanzania must have had a large population size or large degree of long-term population structure. It also suggests that eastern Africa may have been the origin for many of the African mtDNA lineages. The time of the most recent common ancestor for the L3, M and N lineages is half that of the TMRCA for all modern humans indicating modern humans spent a significant amount of time in Africa before their dispersal to the rest of the world.

The strongest evidence from mtDNA indicates the possibility that modern humans expanded from Ethiopia via the mouth of the Red Sea and then dispersed either northward through Arabia or eastward along the South Asian coast as the most probable possibility and points to the fact that there was only a single dispersal event out of Africa. This was represented by members of the L3 lineage. Two independent lineages spread out of Africa, the M and N lineages. The M derivatives that spread out of Africa have been found in India and Eastern Asia. There is genetic evidence from the presence of the M1 sub-clade in Eastern Asia supporting the idea that the M haplogroup spread out of Africa through Ethiopia and the Arabian Peninsula along South Asia. However, this may be explained by a back migration from Asia to Africa due to the fact that genetic diversity of the M haplogroup is more diverse in Asia than in Africa. The N haplogroup is thought to have migrated out of Africa through the Levant over 43,000 years ago.

Moving into East Asia:

A paper from Shi et al clarifies migration routes and times of settlements for East Asia. It is suggested that modern humans reached East Asia about 60,000 years ago and spread northward from here. They looked at the distributions of the Y chromosome lineage for the sub haplogroup D-M174. (yellow dot in figure__) The earliest modern human settlers from Africa are said to be people who live in remote islands in the Indian Ocean. There is a high frequency of D-M174 in this population. The populations with the highest frequency of D-M174 are located at the edge of mainland Asia with a divergent dispersal. They sampled over 5,000 males from east and Southeast Asia and suggested that there was an independent northward migration of modern humans from East Asia. Africans have the highest frequency of YAP+(haplogroup D/E). All of these are in the same haplogroup E-M40. In order to deduce the sub clades of the Haplogroup D-M174, M15, M57 and p47 (yellow, green and orange dots respectively) were treated to further typing. They named the subsequent clades D1, D2 and D3.D1-M15 is present in Tibeto-Burman and Daic speaking populations. D2-M47 is restricted to Japan and D3-p47 is present in Tibet, areas beside Tibet, in Daic speaking populations and Central Asia. D-2 lineage is the youngest and D*, D1 and D3 are the oldest. D-M174 is rare in Central Asia thereby disproving a northern origin. The idea of an Indian origin is also disproved because there was no D-M174 found in the individuals tested from India across India. In respect of their Y-chromosome haplotypes, the natives of the Andaman Islands are genetically isolated. They have East Asian specific Y chromosome lineages. A Southern origin of D-M174 can be determined. This is consistent with the idea that modern humans settled in mainland Southeast Asia and is also consistent with other Y-chromosome lineages. Tibet and Japan are in two geographically distant areas and their D-M174 lineages have two different sub-haplogroups. The finding of two DE* in Tibet suggests that the D-M174 lineage is among the earliest modern human settlers in East Asia. If D-M174 moved with other Y chromosome lineages, such as O3-M122, during northern migration then there would have had to have been recurrent mutations or independent random enrichment of D-M174 in Tibet and Japan. This is very unlikely. Instead the trace of D-M174 migration was possibly wiped out by the much larger migration of O3-M122. The divergence time of haplogroup D is about 60,000 years ago. This would be the first modern human migration after their settlement in southern East Asia.

Southern route out of Africa:

Recently there has been a suggestion of a southern route of dispersal out of Africa. This route, from the Horn of Africa along the coast of the Indian Ocean to Southeast Asia and Australasia, took place about 60,000 to 75,000 years ago. The presence of populations, which were once widespread but are now living in isolated localities, in Southern India and Southeast Asia indicate that these may be the descendants of a much earlier dispersal than was suggested. Analysis of mtDNA restriction enzyme data from New Guinea and control region sequences from mainland Asia and the Andaman Islands support the existence of a Southern route. A maximum likelihood analysis of complete mtDNA genomes from Orang Asli tests the possible dispersal routes out of Africa. This analysis yielded a result for the time of the most recent common ancestor to about 200,000 years ago. Haplogroup L3 is about 84,000 years old and haplogroups M and N are both about 63,000 years old. If modern non-Africans are descendents of populations that dispersed along both, Northern and Southern routes, then mtDNA lineages belonging to surviving populations should diverge from founder types that are distinct from those leading to main continental Eurasian groups. If there was just a single dispersal then all non-African populations should diverge from the same set of founders which would come together about 50,000 years ago if the Levantine corridor model is correct or to about 75,000 years ago if they were all the result of the proposed earlier Southern route. Most of the mtDNA from the Orang Asli population are unique to that population suggesting that the mtDNA lineages they posses are about 60,000 years old. This means that these lineages, very likely, diverged around that time within mainland Southeast Asia. Studies of complete mtDNA genomes from Papuans and Aboriginal Australians show an analogous situation in which the lineages are mostly unique to Australasia but diverge from the base of all three haplogroups. The mtDNA of indigenous Malaysians and of Australasians are derived from all three haplogroups M, N and R. The similar ages of all three of these haplogroups suggest that they were all part of the same colonization process. The presence in each region of the same three founder haplogroups indicates that there was rapid coastal dispersal about 65,000 years ago around the Indian Ocean and onto Australasia. This coastal route was likely the only route taken during the Pleistocene settlement of Eurasia by the ancestors of modern humans and suggests that the primary route from India to Australasia was very rapid. By assuming a distance, between India and Australasia, of about 12,000km it could be estimated from point estimates that the dispersal rate was about 4km/year. In contrast, Eurasians have a high level of haplogroup diversity within haplogroups N and R and lack haplogroup M almost entirely. The colonization of Eurasia was thought to be from the Northern route dispersal out of Africa but because of the similarity of the mtDNA founder age to that if India it is suggested that Eurasia's colonization was a result of an early offshoot from colonies along the Southern route.

Back Migration from Asia into Africa:

It is unsure whether the M and N haplogroups were present in Africa before the migration of modern humans out of Africa took place. The M1 clade from East Africa has been suggested to support the theory of a single origin of halpogroup M in Africa. The coalescent age of this haplogroup is much younger than those for other M clades and most of the M1 lineages have been found in Northwest Africa and in the Near East, not in East Africa. A study by Gonzalez et al suggests that M1 or it's ancestor originated in Asia and that there was migration back into Africa of this clade. There are numerous different M haplogroups present in Asia suggesting the origin of the M haplogroup here and the possibility the M1 lineage in Africa arose through a black flow from Asia. India was first proposed to be the region where M1 originated as this lineage is very rich here. However, recent studies of mitochondrial DNA sequences of Indians show no evidence of this. The M2 Indian lineage shows support for an M haplogroup origin in Asia. The origin of M1 in Africa is uncertain based on comparison of eastern and western African sequences. The ancestor of the M haplogroup, L3, originated in Africa, the macrohaplogroup migrated out of Africa and M1 is considered a branch that has migrated back into Africa.

There is also evidence from Y chromosome analysis of a back migration from Asia into sub-Saharan Africa. In sub-Saharan Africa the majority of haplotypes are within one of three groups, all containing an ancestral allelic site at the M89 locus. The derived form of this allele is carried by most non-Africans. Sub-Saharan Africans, on the other hand, contain a set of chromosomes that carries the M207 and M173 mutations. These characterise all the members of the group IX chromosomes. All group IX chromosomes from Europe and the Middle East contain either the M269 mutation or the SRY10831 and M17 mutations which are frequent in western Eurasia but in opposite extremes. Haplotypes containing the SRY10831 mutation are also present in central, Northern and eastern Asian populations. The IX chromosome group containing the M73 mutation are confined to Asia and the group containing the 117 haplotype is found in the Cameroons. The latter group represents a paternal back migration from Asia to Africa. The majority of the M9 haplotypes (haplogroups VII-X) are only present in Asia. Asia is thought to be the source for the migration of modern humans into Europe, America and Oceania. Chromosomes containing the M173 mutation show an expansion from Asia into Europe about 30,000 years ago and it is thought that Asia is the origin for the M173 chromosome in both Europe and the Cameroons. However, the 117 haplotype (Cameroon M173 chromosome) is very rare in Asia suggesting that this diversity accumulated after the back migration into Africa from Asia. (Cruciani et al, 2002)

The M1 clade occurs at a high frequency in the Horn of Africa and appears to be predominantly African specific suggesting that M could have arisen in East Africa before the migration out of Africa or that M1 represents a back migration into East Africa from Asia. The N haplogroup includes the R haplogroup which in turn includes the U haplogroup. The U6 clade is found mainly in northern Africans but is also present in East Africa. M1 is frequent in East Africans but also present in Northern Africans. The coalescence age for M1 and U66 supports the scenario that M1 and U6 could have been involved in the same population expansion and dispersal events. The fact that that none of the M haplogroups in Asia contain M1 mutations supports the idea that there was an ancient arrival of M1 into Africa. It is suggested that the populations containing M1, U6 and U5 all lived in the broad area of southern Asia and we all affected by some event that led to their dispersal and relocation. It is possible that the population bearing M1 and U6 did not return to Africa along the southern coastal root but instead from the Mediterranean area where U5 took part in the population of Europe. The M1b and the majority of the U6 clades are only present in the Mediterranean suggesting that these two haplogroups diverged into their major subclades in this area before M1a and U6a2 migrated to East Africa.(Gonzalez et al, 2007)

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