lunes, 15 de octubre de 2012

The African Diaspora: Mitochondrial DNA and the Atlantic Slave Trade

Antonio Salas,^1,2,3 Martin Richards,^2,4 María-Victoria Lareu,¹ Rosaria Scozzari,⁵ Alfredo Coppa,⁶ Antonio Torroni,⁷ Vincent Macaulay,^3,8 and Ángel Carracedo¹

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Abstract

Between the 15th and 19th centuries ad, the Atlantic slave trade resulted in the forced movement of ∼13 million people from Africa, mainly to the Americas. Only ∼11 million survived the passage, and many more died in the early years of captivity. We have studied 481 mitochondrial DNAs (mtDNAs) of recent African ancestry in the Americas and in Eurasia, in an attempt to trace them back to particular regions of Africa. Our results show that mtDNAs in America and Eurasia can, in many cases, be traced to broad geographical regions within Africa, largely in accordance with historical evidence, and raise the possibility that a greater resolution may be possible in the future. However, they also indicate that, at least for the moment, considerable caution is warranted when assessing claims to be able to trace the ancestry of particular lineages to a particular locality within modern-day Africa.

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Introduction

Slavery has been a feature of human societies since antiquity, but the scale of the Atlantic slave trade was unprecedented. This African diaspora was the result of the enslavement in the Americas of probably ∼11 million people, and at least 2 million more died during the middle passage. The traders spread from northwestern Africa around the Atlantic coast, reaching Angola by the 17th century and Mozambique by the 19th. Historical records suggest that western Africa contributed ∼8 million people, west-central Africa (from Cameroon down to Angola) ∼4 million, and Mozambique/Madagascar in the southeast ∼1 million more, although agreement on details is lacking (Curtin 1969; Fage 1969; Thomas 1998). The scale of the displacements and the European prejudice against African populations meant that, rather than the assimilation of the imported populations, as had often been the case in antiquity (Lewis 1990), the result was often the creation of new and distinctive populations in the Americas (Sans ).

African mtDNAs fall into several distinctive paragroups (paraphyletic clusters of mtDNA lineages) and monophyletic haplogroups. The nomenclature has been amended following the suggestion of Mishmar et al. (), so that L1a, L1d, L1f, and L1k are here renamed L0a, L0d, L0f, and L0k, respectively. These haplogroups, along with L1b’c, L1e, L2, and L3A, evolved in sub-Saharan Africa (Chen et al. , ; Watson et al. ), whereas U6 is thought to have evolved in northern Africa (Rando et al. ; Macaulay et al. ). Each of these major clusters can be divided on the basis of various diagnostic mutations into subhaplogroups (Torroni et al. ; Salas et al. ), which can be used as markers of recent migrations when found in other parts of the world.

Alves-Silva et al. (), for example, found that 28% of a sample of mainly “white” subjects from Brazil were of recent African maternal ancestry, with substantial variation from region to region. Some lineages could be readily attributed to arrivals from western Africa, which had already been extensively sampled, but almost 50% belonged to haplogroups L1c and L3e, which are rare in western Africa. Their presence at much higher frequencies in small west-central African data sets suggested that the Brazilian L1c and L3e mtDNAs might be of largely west-central African origin (see also Bandelt et al. ). Indeed, major sources for Brazilian slaves are thought, on the basis of historical records, to have been Congo and Angola (e.g., Curtin 1969; Thomas 1998). Alves-Silva et al. () predicted that, when these regions were sampled for mtDNA variation, L1c and L3e would be found at high frequencies.

Brehm et al. () identified mtDNA lineages transported proximally from the western Atlantic coast to the Cabo Verde islands, many en route to the Caribbean and Brazil, and Pereira et al. () initiated work on the slave trade from southeastern Africa. They discovered numerous matches between Mozambican mtDNAs and those of America and, to a lesser extent, those of recent African ancestry in Europe (see also Salas et al. []).

There have also been several attempts, using autosomal, mtDNA, and Y-chromosomal markers, to address the question of the extent of recent African versus European and Native American ancestry in American populations (Chakraborty et al. ; Parra et al. , ; Mesa et al. ). However, attempts have not hitherto been made to trace American ancestry to particular regions within Africa. The accumulation of mtDNA data from both African populations and American populations with putative African ancestry has now reached the point where this can be pursued. In this study, we synthesize this body of evidence and attempt to quantify the contributions of the major subregions of Africa to mtDNAs in the Americas and Eurasia.

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Material and Methods

Population Samples

We compiled a database from 481 individuals carrying African mtDNAs belonging to seven available American samples harboring a major African component. The sample from North America included 101 African Americans from the United States (HvrBase database; for details, see Handt et al. ). The sample from Central America/Caribbean included 8 from Mexico (Green et al. ), 25 Carib from Belize (Monsalve and Hagelberg ), 112 from the Dominican Republic (Torroni et al. ; A.T., unpublished data), 41 Chocó from Columbia, and 37 Garífuna from Panama and Belize (A. Salas, M. Richards, M.-V. Lareu, S. Silva, M. Matamoros, V. Macaulay, and A. Carracedo, unpublished data). The sample from South America included 157 Brazilians: 29 from the study by Bortolini et al. (), 68 from the study by Alves-Silva et al. (), and 60 from the study by Santos et al. (2002). The northern African sample (650 total) included 30 Mauritanians, 25 Saharans, 60 Berbers from Morocco, and 32 Moroccans (Rando et al. ); 50 Moroccans from the Souss Valley (Brakez et al. ); 68 Egyptians (Krings et al. ); 85 Algerian Berbers (Côrte-Real et al. ); and 300 Canarians (246 from the study by Rando et al. [] and 54 from the study by Pinto et al. []).

The western African sample (694 total) included 20 Hausa, 14 Kanuri, 60 Fulbe, 10 Songhai, 23 Tuareg, and 21 Yoruba (Watson et al. ); 14 further Yoruba (Vigilant et al. ); 23 Serer, 50 Senegalese, and 48 Wolof (Rando et al. ); 119 Mandenka (Graven et al. ); and 292 individuals from the Cabo Verde islands (Brehm et al. ). The west-central African sample (179 total) included 50 individuals from the islands of São Tomé and Príncipe and 45 Bubi from the island of Bioko (Mateu et al. ); 11 Fang from Guinea (Pinto et al. ); 43 Angolans (Santos et al. 2002); 17 Biaka and 13 Mbuti (Vigilant et al. ). The eastern African sample (335 total) included 37 Turkana, 27 Somali, and 25 Kikuyu (Watson et al. ); 96 Nubians and 76 Sudanese (Krings et al. ); and 74 Ethiopians (Thomas et al. ). The southeastern African sample included 417 individuals from Mozambique (Pereira et al. ; Salas et al. ). The southern African sample (99 total) included 25 !Kung and 31 Khwe (Chen et al. ); and 43 further !Kung (Vigilant et al. ).

We also surveyed the mtDNA first hypervariable segment (HVS-I) of ∼15,000 individuals from Eurasia and found 113 mtDNAs of recent African ancestry. We excluded another 28 sequences from the database, possibly belonging to L3 but not characterized by any diagnostic sites in our data.

All sequences correspond to HVS-I of the control region; the nucleotide positions considered included at least positions 16090–16365, according to the numbering system of the Cambridge Reference Sequence (Andrews et al. ). For some purposes, we also used HVS-I information from outside the minimum segment, as well as RFLP and HVS-II data. Length variation was excluded. Transitions are indicated by the nucleotide position minus 16,000, and transversions are indicated by a suffix.

Phylogeographic Analysis

The haplogroup classification of mtDNA sequences was updated from Salas et al. (); see table 1 for HVS-I motifs (cf. Chen et al. ; Watson et al. ; Rando et al. ; Quintana-Murci et al. ; Alves-Silva et al. ; Bandelt et al. ; Pereira et al. ; Torroni et al. ). Richards et al. () discuss mtDNA haplogroups that may be regarded as of recent African ancestry.

Table 1

HVS-I Sequence Motifs Used for Haplogroup Classification

We constructed phylogenetic networks (Bandelt et al. , ) by hand, on the basis of the information from Salas et al. (), with the aid of the Network 3.0 package (Fluxus Engineering Web site). We performed principal component (PC) analysis based on haplogroup frequencies, broken down as follows: U6, M1, L0a, L0d/k, L1b, L1c, L2a, L2b, L2c, L3b, L3d, L3e, L1/L2 remainder, L3A remainder, and non-African haplogroups. The entire data sets were used in the case of Africans, whereas only mtDNAs of recent African ancestry were used in the case of Americans. We excluded some outliers from the PC analysis, as in Salas et al. (), including the Khoisan samples, with their high levels of L1d/L1k; some northern African populations, with moderate levels of U6; and the Biaka, with their very high frequency of L1c. However, it should be noted that three of the L1c HVS-I sequence types in the Biaka sample match American types (see fig. 3). We also excluded the Mexican sample because of its small size.

Figure 3

Phylogenetic network of shared mtDNA HVS-I sequence types of recent African ancestry in America, Eurasia, and Africa. The charts show: (a) the proportion in each main region of those specific haplotypes shared by >15 individuals (yellow frame ...

We estimated sequence diversity as equation M1

, where p_i is the frequency of each of the k different sequences in the sample and n is the sample size, and we evaluated the mean pairwise nucleotide difference, π, as well as the number of segregating sites, S, through use of Arlequin 2.0 (Arlequin's Home on the Web). We also computed haplotypic and segregation site mutation-drift statistics (θ_k and θ_S, respectively) (Helgason et al. ).

Admixture Analysis

To quantify the magnitude of the impact of each African region on cluster frequencies in the Americas, we fitted the following model. The number of mtDNAs in each cluster in the sample from a region of the Americas (n_i:1 [less-than-or-eq, slant]

C, the number of clusters) was assumed to be a draw from a multinomial distribution with parameters equation M2

, the sample size in the American region, and equation M3

C), where R is the number of source regions in Africa, f_ji is the frequency of the ith cluster in the jth source region (assumed to be known), and the a_j are the admixture coefficients. This model describes samples from an urn with C different kinds of ball, where the urn has been created by mixing together R other urns in proportions given by the admixture coefficients. We chose to analyze this model in a Bayesian framework, which meant that we had to explore the distribution of the admixture coefficients, given the data. The prior distribution of the admixture coefficients was taken to be uninformative—namely, uniform on equation M4

. The posterior distribution of a_j was explored with the Metropolis-Hastings algorithm, using a simple proposal, and was summarized by the posterior mean of each a_j and its root-mean-square deviation about the mean.

To assess model fit, we examined plots of standardized residuals. The analysis was first performed with all African regions present, and then, to test robustness, was repeated with those regions removed whose admixture coefficients were within 2 SDs of 0.

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Results

Data Summaries and Demography

Genetic diversity indices are shown in table 2. The haplotype mutation-drift statistic (θ_k) and haplotype diversity (H) show a distinctive pattern that is less clearly reflected in the segregating sites mutation-drift statistic (θ_S) or the mean number of pairwise differences (π). θ_k and H are similar, with eastern Africa having the highest values and southern Africa the lowest, and with minor variations in ranking. They suggest that founder effects were not important during the formation of slave communities of the Americas but that reductions in population size may have subsequently affected populations in Central America.

Table

HVS-I Diversity Indices in the African mtDNAs from North, Central, And South American Population Samples and in Africans from Different Regions in Africa

The reduction in diversity for Central American lineages is also indicated by the estimator π, but it is not reflected in this statistic for southeastern Africa (where founder effects associated with Bantu dispersals have evidently elevated the frequencies of some types in several haplogroups [Salas et al. ]). This is likely to be because, as a measure of pairwise nucleotide differences, π exaggerates the effect of the genetic divergence between haplogroups that may survive even after a substantial reduction in haplotype diversity; thus, π is a poor indicator of population size reduction (Helgason et al. ). This is evident in southeastern Africa—for example, between L0a and L3e—and is even more pronounced in west-central Africa, where, for example, L0a, L1c, and L3e are all significant. Since the haplogroup compositions of North, Central, and South America are very similar, the reduction in diversity in Central America becomes evident even with this statistic. The mutation-drift parameter based on segregating sites (θ_S), by contrast, shows a reduction in southeastern Africa but is not sensitive to the effect in Central America. In general, it therefore appears that neither of these latter two statistics is consistently sensitive to demographic processes.

Haplogroup Frequency Profiles

Haplogroup frequency profiles for the regions studied are shown in figure 1, and a scatterplot of the first two principal components is shown in figure 2. The first principal component (PC1), accounting for 30% of the variance, separates the populations into a spectrum with northern Africans at one pole, followed by northeast Africans, eastern Africans, western Africans, and west-central Africans, with Bioko at the opposite pole. Southeastern Africans and Angolans sit tightly together within the west-central African cluster. The American samples also cluster fairly tightly together in PC1, with the Brazilian and several of the Central American samples localized very closely with the southeastern Africans, whereas the African American, São Tomé, and Caribbean samples are positioned closer to the western Africans.

Figure 1

Frequency profiles of the major haplogroups in Africa and haplogroups of recent African ancestry in the Americas and Eurasia

Figure 2

Scatterplot of the first two principal components based on haplogroup frequencies. For practical reasons, the “Other-L3” and “Other non Afr” haplogroup categories, with coordinates (0.0171, 0.4210) and (0.6680, 0.0768), ...

PC2 accounts for 19% of the variance and shows an approximately east-west gradient, with northern Africans, west-central Africans, and southeastern Africans all positioned towards the eastern fringe of the western African variation. The Caribbean sample sits with the southeastern Africans, whereas the other American samples are positioned more towards the western pole. The African Americans, Brazilians, and mainland Central Americans cluster tightly together and with the São Toméan and Dominican samples, further towards the western pole.

Admixture Analysis

To quantify the proportion of ancestry from each of the major regions of Africa present in the African component of the modern American mtDNA pool, we fitted an admixture model of the haplogroup profiles in the African regions to the profiles in the Americas (table 3). The estimated admixture coefficients for all regions other than western and west-central Africa were within 2 SDs of 0, and so we repeated the analysis with a more parsimonious model by suppressing those unsupported African regions (table 4).

Table 3

Estimated Admixture Coefficients for American Samples, in Terms of the Source African Regions

Table 4

Estimated Admixture Coefficients, when Unsupported Source Regions Are Excluded

The results for the Americas overall accord broadly with the picture built up by historians, in attributing major contributions from both western and west-central Africa. The proportion of western African ancestry is not significantly greater than that of west-central Africa, and a significant southeastern African component is not detected at this level of analysis.

Again in agreement with the historical evidence—and confirming the indications from the frequency profiles—the largest component in both North and Central America appears to derive from western Africa and to be somewhat greater in Central than North America.

The southeast also seems to have left a minor signature, although the error margins are wide. South America is, however, problematic. A higher—and possibly a majority—contribution from west-central Africa is indicated, but the admixture model provides a poor description of the data, as judged from a plot of standardized residuals (not shown). For example, the frequency of L3e in South America is larger than in any of the potential source regions, an observation incompatible with the admixture model. (It is most closely approached by the frequency of L3e in Bioko, which, however, may be an unrepresentative sample, since it appears to have been subject to extensive drift [θ_k=8.4].) Several other population samples that contribute to our west-central African sample are unlikely slave sources and have also been subject to heavy drift, in particular the Mbuti (θ_k=2.5). This suggests that a major source region for South America remains unsampled; more data will be necessary to make further progress here. A further sampling issue arises because South America is represented only by Brazil (although this country bears the largest community of African descendants in America). The existing data suggest that Brazilian slaves came largely from west-central Africa rather than western Africa, but data from other parts of South America will be needed to generalize this observation.

Haplogroup Composition of American mtDNAs of African Ancestry

Frequencies of mtDNA lineages in Africa are shown in figure 1, alongside mtDNA lineages of African ancestry in North, Central, and South Americans (cf. Salas et al. ). A network of HVS-I sequence types shared between Africans, Americans, and Eurasians is shown in figure 3 (excluding U6 and one unclassified American L3* type, which matches a western African mtDNA). Eighty-eight mtDNA types from these clades are shared between the African samples and America. Although this is only 36% of the total different American sequence types of African origin in our database, it represents more than half (54%) of the total sample size of individuals, since a number of types are present in more than one individual in the database.

Remember that sequence types of Eurasian ancestry (within haplogroups M and N) are also excluded. However, in agreement with the historical evidence, the contribution of northern Africa (which includes many western Eurasian sequence types [Rando et al. , ; Macaulay et al. ]) to the American gene pool appears to be very minor. This is indicated by the low frequency of the indigenous northern African haplogroup U6 in Americans: this haplogroup is found in <2% of American lineages of African origin, which is lower than the frequency of U6 in western Africa, the likely source for most American U6 mtDNAs.

Most, but not all, of the known African subhaplogroups within L0–L3A are present in America. Overall, the continental frequency profiles of the Americas, especially those of North and Central America, are strikingly similar to those of western and west-central Africa (fig. 1), confirming that these were the major source regions for American mtDNA lineages of African ancestry. South America has a markedly higher proportion of L3e and L0a lineages, which likely reflects a relatively higher contribution of both west-central and southeastern African mtDNAs.

The great majority of haplogroup L0a mtDNAs, concentrated in South America, belong to subclusters L0a1 and L0a2, both of which are typically southeastern African. All American L0a types are shared with individuals from Mozambique, where two are elevated to extremely high frequencies (fig. 3) (Pereira et al. ; Salas et al. ). Several of the southeastern African L0a founder types and a number of derived types are also found in the Angolan sample, indicating substantial commonality between the more southerly Eastern and Western Bantu-speaking communities and pointing also to a possible west-central African contribution, especially to South America.

In contrast, American L1b sequences are most often shared with samples from western Africa, where L1b is concentrated (fig. 3; see also fig. 4 of Salas et al. ). Shared L1b types are also found in northern Africa; however, in all cases except for one, these also match western Africans, and in the one exception there is also a match with southeastern Africa. Haplogroup L1c, which is likely to be of west-central African origin, is the African mtDNA clade with the most unmatched representatives in America, particularly in South America—only ∼17% of American L1c types are shared with Africans. The Angolan sample, however, carries L1c at a frequency of ∼21%, which confirms the prediction of Alves-Silva et al. () based on the pattern of L1c lineages in Brazil, where the frequency among mtDNAs of recent African ancestry is ∼19%. One L1c3 type matches eight individuals from Bioko (mislabeled as “Bi” in figure 5 of Salas et al. ). However, it also matches a number of individuals in Mozambique, suggesting a possible origin in west-central Africa for a lineage that was probably dispersed by the Bantu expansions (Salas et al. ). This is reinforced by the discovery of a derivative of this type in Angola. L1c is rare in Mozambique (∼5%), suggesting that it may be a “west-central Bantu” marker that has been brought to southeastern Africa by interaction with western Bantu-speaking communities.

Haplogroup L2a is the most common and widely distributed sub-Saharan African haplogroup and is also frequent in the Americas (∼19%). The wide distribution of L2a in Africa makes identifying geographical origins of lineages difficult. Nevertheless, almost all of the American L2a types match with or are one-step derivatives of some western African L2a type. Several common and widespread American types are shared with eastern Africa as well, but none are shared uniquely with eastern Africans alone. A number are also shared with southeastern Africans; again, however, all of these types are also present in western Africa. A largely western African provenance, with a possible minor southeastern African contribution, seems to be the simplest explanation for this pattern. The much less frequent subhaplogroups—L2b, L2c, and L2d—are not found in eastern Africa and are again most likely to be of largely western African provenance in the Americas, although two American types are shared only with southeastern Africans and may, therefore, have their immediate origin there.

L3A types in the Americas are, again, probably of largely western African provenance, with lesser west-central and southeastern African components. L3b and L3d mtDNAs are mainly western African, with a few types shared with eastern, southeastern (and occasionally southern, through interaction between Bantu-speaking and Khoisan-speaking groups), and (for L3b) west-central Africans. The same is true of L3e2, which includes one of the most common and widespread American mtDNA types with a number of derivatives observed only in America, as well as the much less frequent L3e4. One American L3e3 type is shared with the Bubi of Bioko but is more common in Mozambique, with a one-step derived type in the Angolan sample; thus, it most likely derives from west-central or southeastern Africa. Other L3e types are also found in Bioko and neighboring São Tomé, as well as in Angola and Mozambique. American L3e1 lineages, however, largely match southeastern Africans, implying a likely origin either there or somewhere on the west-central coast of Africa, between Cameroon and Angola.

The proportion of L3e in the Angolan sample is 14%, of which 5/6 are members of L3e1, the subclade that is also particularly frequent in Mozambique, where the frequency is similar (Salas et al. ). On the basis of the phylogeographic distribution (see fig. 9 of Salas et al. ), L3e2 appears to be more northern and to have spread into western Africa, where the derived subclade L3e2b predominates, possibly accounting for its greater prevalence in the Caribbean. The minor subclade L3e4 seems to have a similar distribution. The wide distribution of L3e1 and L3e3 is likely to be due mainly to Bantu dispersals (Salas et al. ). However, the 18th-century transfer of slaves from Mozambique and Angola to work in the sugar plantations of São Tomé and probably also Bioko (Iliffe 1995) and their subsequent transfer to the Americas may also help to account for the sharing of mtDNA types across this wide area.

A few haplogroup L3f types in America match those of eastern Africans—again, however, never uniquely; they are also shared by western Africans, southeastern Africans, or both. At the same time, several L3f types are shared uniquely by western Africans only. L3f is likely of eastern African origin (Salas et al. ), but the derived subhaplogroup L3f1 is also present in western Africa, and it is this component that is most commonly found in Americans.

Some mtDNA clades are notable for their absence (or virtual absence) in the Americas. Neither of the Khoisan-specific haplogroups, L1d and L1k, are found in America, nor are the eastern African haplogroups, L1e and L1f. This supports the historical view that neither Khoisan-speaking populations nor eastern Africa contributed significantly to the Atlantic slave trade. However, the eastern African haplogroup L3g is found in several American individuals, implying either a small eastern African influence (Thomas 1998, p. 706), more recent immigration from Africa into America, or hitherto undetected gene flow into western or southeastern Africa and thence to the Americas. There is indeed evidence for low levels of transcontinental gene flow in the modern mtDNA patterns of Africa (for example, “accidental” or “erratic” lineages of western African origin in eastern and southeastern Africa [Bandelt et al. ; Salas et al. ]). Eastern African L3f types, for example, may also have had an immediate origin in the eastern African component of west-central African Bantu-speaking populations.

Some of the American U6 types (those belonging to U6b1) are most likely of Canarian ancestry and not a direct consequence of the Atlantic slave trade. They probably reflect the genetic admixture of Spanish men with Guanches women after the Spanish colonization of the Canary Islands and the subsequent movements of these admixed populations to the Caribbean islands during the process of Spanish colonization of the region.

African mtDNAs in Eurasia

Eurasian matches to African mtDNAs are also indicated in figure 3, representing <1% of Eurasian mtDNAs. More than half of Eurasian U6 lineages occur in western Iberia (Salas et al. ; Pereira et al. ), and most of the remainder occur in southwest Asia. Both Portugal and the Near East are regions with known historical gene flow from northern Africa, but both were also centers for the importation of slaves. Eurasian L0–L3A are similarly concentrated in the Near East and Iberia. Eurasian L0a types match or are one-step derivatives of eastern African L0a types and are mainly Near Eastern or southern European. The L1b types can be readily derived from western or northern Africa and are similarly distributed. As in America, it is difficult to assign a provenance to L2a types in Eurasia; two types have a likely southeastern African origin, whereas the remainder could be from either eastern or western Africa.

The precise ancestry of Eurasian L3b types is similarly difficult to trace. The eastern African–specific L3f is found mainly in the Near East and southern Europe.

African types in Eurasia, unlike those in America, can therefore be attributed to gene flow from both eastern Africa—perhaps partly via the Arab slave trade (Richards et al. )—and western and southeastern Africa, more likely as a result of the Atlantic slave trade. This latter scenario is made more probable by the surprisingly high proportion of shared types across all three continents, an observation made more remarkable by the fact that the shared types are not necessarily particularly common ones in Africa.

A contribution from the medieval Arab/Berber conquest of Iberia and Sicily is also possible (Semino et al. ; Côrte-Real et al. ). All of the Iberian L0–L3A types are shared with either western or southeastern Africans, so that it is possible that all of them might be accounted for by the Atlantic slave trade (Pereira et al. ). More than a quarter of these are, however, also shared with northern Africans, suggesting that a proportion may alternatively be attributed to the Arab/Berber conquest, especially since the northern African sample size for these types is much smaller than that for western Africa. The ratio of the frequencies of haplogroup U6 to L0–L3A in Iberia (35%) seems too small to be attributed solely to northern African immigration but too large to be accounted for by western African immigration alone (P=.0013 and P<10^-5, respectively, in a one-tailed Fisher's exact test). Therefore, it seems unlikely that the impact of mtDNAs of recent African ancestry on Iberia was the result of a single process; indeed, earlier gene flow may also have contributed some of the lineages.

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Discussion

In this study, we have identified mtDNA lineages with a recent African ancestry in contemporary American populations. Of course, all modern human mtDNAs have what is often described in the literature as “recent African ancestry.” That is to say, Eurasian mtDNAs originated in a founder effect and dispersal of haplogroup L3 lineages (rapidly differentiating into Eurasian haplogroups M and N) from sub-Saharan Africa that probably took place ∼60,000–80,000 years ago (Watson et al.; Quintana-Murci et al. ).

In this article, however, we define “recent African ancestry” as rather the result of gene flow within historical times; in the case of the Americas, this gene flow is largely (but not necessarily exclusively) due to the effects of the Atlantic slave trade.

A recent summary of the historical literature suggests that ∼62% of slaves came from western Africa to America (∼8 million slaves), ∼30% from west-central Africa (4 million), and ∼8% from southeastern Africa (1 million) (Thomas 1998, p. 806).

The North American and Central American source regions are thought likely to have been mainly in western Africa, supplemented substantially in South America by sources in west-central Africa and, to some extent, southeastern Africa.

The mtDNA composition in America, although indicating only the female line of descent, broadly corroborates historical research. In particular, and unsurprisingly, our admixture estimates, PC plots, and phylogenetic networks all stress the overwhelming impact of western and west-central Africa on the composition of American mtDNAs with recent African ancestry, with a likely small southeastern African component.

Western Africa appears to have been the most important source for North and Central America, although, perhaps surprisingly, North America appears to harbor the larger (but probably still a minority) west-central African component. The results from South America are more problematic, but the likely picture appears to be of a large, possibly majority west-central African contribution, with a substantial western African component as well, at least for Brazil. However, the west-central African contribution most likely derives largely from an area that so far has not been sampled for mtDNA variation, such as the Congo basin. A contribution in Brazil from southeastern Africa also seems likely, as suggested by the high level of matching between Brazilian and Mozambican lineages within L3e1 (fig. 3).

The contributions of northern, eastern, and southern Africa to the American mtDNA gene pool appear to be very small, which, again, is in good agreement with the historical picture. Eastern Africa is, by contrast, an important donor of mtDNAs to the Near East. This may be the result, at least in part, of more ancient movements of slaves, such as the Arab trade through Red Sea and Indian Ocean ports (Richards et al. ). However, there are also discernible western and southeastern African components to the (relatively few) mtDNAs of recent African ancestry within Europe, which are likely to be mainly attributable to the more recent Atlantic trade. Portuguese western, southwestern, and southeastern Africa were the main sources for the Atlantic slave trade to Europe (Thomas 1998, p. 805). A striking finding of this study is the high number of three-way sequence matches between African, American, and European mtDNAs.

Almost all of these are of likely western African (such as those in L1b) or southeastern African (such as those in L0a) origin. These matches are particularly prevalent in Portugal, which was indeed the principal destination for slaves within Europe. Nevertheless, the composition of Iberian mtDNAs of recent African ancestry suggests that other processes, such as the medieval Arab/Berber conquest, must also have been influential.

Overall, these results show that mtDNAs in America and Eurasia can, in many cases, be traced to broad geographical regions within Africa. This raises the possibility that a greater resolution may be possible in the near future. However, there are many difficulties with such an endeavor. A major problem at the moment is the poor sampling coverage in some parts of the continent, especially central Africa. Nevertheless, even when this is resolved, there are many features of African mtDNA variation that will persist to confound such an undertaking. In the first place, some of the major African mtDNAs, such as haplogroup L2a, seem to have been widely distributed within the continent in prehistoric times, and individual mtDNA types are often difficult to localize geographically.

Another important factor is the effect of the Bantu dispersals, which resulted in a fairly small number of mtDNA types from various haplogroups being widely dispersed quite recently throughout subtropical Africa. Further confounding influences for phylogeographic analyses result from the large-scale and widespread movements of people within the continent itself during the period at which the slave trade was in operation. It is likely that improved phylogenetic resolution, with the aid of more complete mtDNA sequences, will increase the phylogeographic resolution to some extent, but the problems of recent widespread movements will remain. The implication is that, although great progress can be made towards understanding the broad pattern of human dispersals using mtDNA, tracking the lineages of individuals is fraught with problems. Considerable caution is warranted when assessing claims of being able to trace the ancestry of certain American or European lineages to a particular region or population within modern-day Africa.

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Acknowledgments

We thank James Walvin for a critical reading of the text. This work was supported by Ministerio de Ciencia y Tecnología grant DGCYT-P4. BIO2000-0145-P4-02 and by Ministerio de Sanidad y Consumo (Fondo de Investigación Sanitaria, Instituto de Salud Carlos III) grant PI030893; SCO/3425/2002. Financial support was also provided by the Italian Ministry of the University (Progetti Ricerca Interesse Nazionale 2002 and 2003) (to A.T., R.S., and A.C.), Progetto CNR-MIUR Genomica Funzionale-Legge 449/97 (to A.T.), Grandi Progetti di Ateneo (to R.S.), and the Instituto Pasteur Fondazione Cenci Bolognetti (to R.S.). A.S. is supported by the Isidro Parga Pondal program (Xunta de Galicia). V.M. was partly supported by a Research Career Development Fellowship from the Wellcome Trust.

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Electronic-Database Information

The URLs for data presented herein are as follows:

Arlequin's Home on the Web, http://lgb.unige.ch/arlequin/ (for Arlequin 2.0: a software for population genetic data analysis)

Fluxus Engineering, http://www.fluxus-engineering.com/ (for Network 3.0: software for median network constructions)

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Mutations
	HVR1	HVR2
1.	16223T	00073G
2.	16278T	00146C
3.	16294T	00152C
4.	16309G	00195C
5.	16368C	00263G
6.	16390A	00315.1C
7.	16519C

Mutations
	HVR1	HVR2
1.	16188C	00063T
2.	16278C	00199G
3.	16320T	00207A
4.	16172C	00246A
5.	16171C	00262G
6.	16178T	00299C
7.	16222T	00468G
8.	16229G	00749G
9.	16310C	00235C
10.	16319T	00263G
11.	16391A	00185G
12.	16179C	00236C
13.		00146T

Haplogroup L0 (mtDNA)

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Haplogroup L0
Possible time of origin	112,200 to 188,000 YBP^[1]
Possible place of origin	East Africa
Ancestor	Mitochondrial Eve
Descendants	L0a'b'f'k, L0d
Defining mutations	263!, 1048, 3516A, 5442, 6185, 9042, 9347, 10589, 12007, 12720^[2]

In human mitochondrial genetics, Haplogroup L0 is a human mitochondrial DNA (mtDNA) haplogroup.

Origin

The region in Africa where Tishkoff found the greatest level of mitochondrial diversity (green) and the region Behar et al. postulated the most ancient division in the human population began to occur (light brown)

L0 is one of two branches from the most recent common ancestor, MRCA, for the shared human maternal lineage. This ancestor is estimated to have lived in East Africa approximately 150,000 to 170,000 years ago.^{[citation needed]} Haplogroup L0 consists of five main branches (L0a, L0b, L0d, L0f, L0k). Four of them were originally classified into haplogroup L1 as L1a, L1d, L1f, and L1k.

MRCA (mtDNA)

	L0a

	L0b

L0f

L0k

L0d

L1-6

	L1

	L2-6

Distribution

It is found most commonly in the Sub-Saharan Africa. It reaches its highest frequency in the Khoisan people at 73%.^[3] Some of the higher frequencies are: ^[4] Namibia (!Xun) 79%, South Africa (Khwe/!Xun) 83% and Botswana (!Kung) 100%.

Haplogroup L0d is the most divergent ("ancient") haplogroup of global mitochondrial DNA haplogroups. It is found at highest frequencies in the Khoisan groups of Southern Africa.^[5] ^[6] ^[7] ^[8] L0d is also commonly found in the Coloured population of South Africa and frequencies range from 60% ^[9] to 71%.^[10] This illustrates the massive maternal contribution of Khoisan people to the Coloured population of South Africa.

Haplogroups L0k is the second most common haplogroup in the Khoisan groups (following L0d) and is largely restricted to the Khoisan.^[11] ^[12] ^[13] ^[14] Interestingly, while the Khoisan associated L0d haplogroup were found in high frequencies in the Coloured population of South Africa, L0k were not observed in two studies involving large groups of Coloured individuals.^[15] ^[16]

Haplogroup L0f is present in relatively small frequencies in Tanzania, East Africa.

Haplogroup L0a is most prevalent in South-East African populations (25% in Mozambique).^[3] Among Guineans, it has a frequency between 1% and 5%, with the Balanta group showing increased frequency of about 11%. Haplogroup L0a has a Paleolithic time depth of about 33,000 years and likely reached Guinea between 10,000 and 4,000 years ago. It also is often seen in the Mbuti and Biaka-pygmies.

Haplogroup L0b Ethiopia.

Subclades

Tree

This phylogenetic tree of haplogroup L0 subclades is based on the paper by Mannis van Oven and Manfred Kayser Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation^[2] and subsequent published research.

Most Recent Common Ancestor (MRCA)
- L0
  - L0d
    - L0d3
    - L0d1'2
      - L0d1
        L0d1a
        L0d1b
        L0d1c
        L0d1c1
      - L0d2
        L0d2a'b
        L0d2a
        L0d2a1
        
        L0d2b
        
        L0d2c
  - L0a'b'f'k
    - L0k
      - L0k1
      - L0k2
    - L0a'b'f
      - L0f
        L0f1
        L0f2
        L0f2a
        L0f2b
      - L0a'b
        L0a
        L0a1
        L0a1a
        L0a1a2
        
        L0a1b
        L0a1b1
        L0a1b1a
        
        L0a1b2
        
        L0a1c
        L0a1d
        
        L0a2
        L0a2a
        L0a2a1
        L0a2a1a
        L0a2a1a1
        L0a2a1a2
        
        L0a2a2
        L0a2a2a
        
        L0a2b
        L0a2ba
        
        L0a2c
        L0a2d
        
        L0a3
        L0a4
        
        L0b
        =====================
        See also:
      - Genealogical DNA test
      - Genetic Genealogy
      - Human mitochondrial genetics
      - Population Genetics
      - Human mitochondrial DNA haplogroups
      - http://oldesthumandna.blogspot.co.uk/

Adam was African, but perhaps barely

The figure to the left comes from a short paper in The American Journal of Human Genetics, A Revised Root for the Human Y Chromosomal Phylogenetic Tree: The Origin of Patrilineal Diversity in Africa. The paper is interesting because of two factors: 1) they sequenced more of the Y chromosome 2) their African data set of individuals was very large, in excess of 2,000. The weird thing about the results is that it upends one of the truisms in human phylogenetics: that African Pygmies and Khoisan are basal to other human lineages. By this, I mean that they “split off” first (this is why people say these are the “oldest” human populations). This is not what these researchers found. Rather, the basal Y chromosomal haplogroups were concentrated in Central West Africa and Northwest Africa! The map below shows the distributions of the two most divergent Y chromosomal lineages, red being the outgroup, and green being the second most divergent:

A second major point in this paper is that they recalculated the coalescence back to the last common ancestor of these Y chromosomal lineages, and doubled that value, to ~140,000 years. I don’t know the technical details of the calibration well here, last I checked the dates for Y chromosomal lineages were a total mess. So I’m not going to express confidence in this specific value, but, it does align well with a suspicion among many people that the idea of modern humans all tracing back to ancestors on the order of ~50,000 years B.P. just isn’t tenable any longer (this excludes the issue of possible admixture with other lineages such as Neandertals).

Dienekes has a lot more to say. I’m kind of left scratching my head. Remember that this is the male lineage of humanity. Who knows what peculiarities there are here?

Here’s their conclusion:

In conclusion, we present here a Y chromosome phylogenetic tree deeply revised in its root and earliest branches. Our data do not uphold previous models of Y chromosomal emergence…and demand a reevaluation of some fundamental ideas concerning the early history of the human genetic diversity we find today….Our phylogeny shows a root in central-northwest Africa. Although this point requires further attention, we think that it offers a new prospect from which to view the initial development of our species in Africa.

Y-chromosomal Adam

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Y chromosome in descendants of one human male

In human genetics, Y-chromosomal Adam (Y-MRCA) is the most recent common ancestor (MRCA) from whom all living people are descended patrilineally (tracing back only along the paternal lines of their family tree). Recent studies report that Y-chromosomal Adam lived as early as around 142,000 years ago.^[1] Older studies estimated Y-MRCA as recent as 60,000 years ago.^[2] All living humans are also descended matrilineally from Mitochondrial Eve who is thought to have lived earlier, about 190,000–200,000 years ago. Y-chromosomal Adam and Mitochondrial Eve need not have lived at the same time.

Hypothesis

The existence of a Y-chromosomal Adam was determined by applying the theories of molecular evolution to the Y chromosome. Unlike the autosomes, the human Y chromosome does not recombine with the X chromosome but is transferred intact from father to son. Mutations periodically occur within the Y chromosome and these mutations are passed on to males in subsequent generations. These mutations can be used as markers to identify shared patrilineal relationships. Y chromosomes that share a specific mutation are referred to as haplogroups. Y chromosomes within a specific haplogroup share a common patrilineal ancestor who was the first to carry the defining mutation. A family tree of Y chromosomes can be constructed, with the mutations serving as branching points along lineages. Y-chromosomal Adam is positioned at the root of the family tree as the Y chromosomes of all living males are descended from his Y chromosome.

Researchers can reconstruct ancestral Y chromosome DNA sequences by reversing mutated DNA segments to their original condition. The most likely original or ancestral state of a DNA sequence is determined by comparing human DNA sequences with those of a closely related species, usually non-human primates such as chimpanzees and gorillas. By reversing known mutations in a Y-chromosome lineage, a hypothetical ancestral sequence for the MRCA, Y-chromosomal Adam, can be inferred.

Determining Y-chromosomal Adam's DNA sequence, and the time when he lived, involves identifying the human Y-chromosome lineages that are most divergent from each other—the lineages that share the least unique mutations with each other when compared to a non-human primate sequence in a phylogenetic tree. The common ancestor of the most divergent lineages is therefore the common ancestor of all lineages.

The existence of Y-chromosomal Adam was confirmed by a worldwide sample of Y chromosomes that included individuals from all continents. A number of Y-chromosome lineages, or haplogroups, from Africa were found to be the most divergent from each other, and non-African lineages were determined to be subsets of a few lineages found in Africa. This suggested Africa was the most likely home of Y-chromosomal Adam.

Variable Adam

Different MRCA's

The title "Y-chromosomal Adam" is not permanently fixed on a single individual. Because knowledge of human Y chromosomes is still incomplete, Y-chromosomal Adam's DNA sequence, his position in the family tree, the time when lived, and his place of origin, are all subject to future revisions. In addition, demographic changes during the course of human evolution would have frequently caused the title of Y-chromosomal Adam to change hands.^[3] The following events would change the individual designated Y-chromosomal Adam:

Further sampling of Y chromosomes could uncover previously unknown divergent lineages. If this happens, Y-chromosome lineages would converge on an individual who lived further back in time.
The discovery of additional deep rooting mutations in known lineages could lead to a rearrangement of the family tree.
When deep rooting haplogroups are permanently lost from the world's population, living human Y chromosomes converge on a more recent common ancestor. A Y-chromosome lineage is halted when a male dies without leaving any male offspring (although this individual may or may not have had daughters). Phenomena such as bottlenecks and genetic drift during human evolution would have caused the total extinction of several basal haplogroups. Because of these factors, the title "Y-chromosomal Adam" has changed hands numerous times.^[3]

Family tree

The revised y-chromosome family tree by Cruciani et al. 2011 compared with the family tree from Karafet et al. 2008

Y-chromosomal Adam had at least two sons and two of his sons have unbroken lineages that have survived to the present day. Initial sequencing of the human Y chromosome suggested that two most basal Y-chromosome lineages were Haplogroup A and Haplogroup BT. Haplogroup A is found at low frequencies in parts of Africa, but is common among certain hunter-gatherer groups. Haplogroup BT lineages represent the majority of African Y-chromosome lineages and virtually all non-African lineages.^[4] Y-chromosomal Adam was represented as the root of these two lineages. Haplogroup A and Haplogroup BT represented the lineages of the two sons of Y-chromosomal Adam.

However, a recent paper^[1] places this event around 142,000 years ago. Cruciani et al. 2011, determined that the deepest split in the Y-chromosome tree is found between two previously reported subclades of Haplogroup A, rather than between Haplogroup A and Haplogroup BT. Subclades A1b and A1a-T, now descend directly from the root of the tree and now represent the lineages of Y-chromosomal Adam's two sons. The rearrangement of the Y-chromosome family tree implies that lineages classified as Haplogroup A do not necessarily form a monophyletic clade.^[5] Haplogroup A therefore refers to a collection of lineages that do not possess the markers that define Haplogroup BT, though Haplogroup A includes the most distantly related Y chromosomes.

The M91 and P97 mutations distinguish Haplogroup A from Haplogroup BT. Within Haplogroup A chromosomes, the M91 marker consists of a stretch of 8 T nucleobase units. In Haplogroup BT and chimpanzee chromosomes, this marker consists of 9 T nucleobase units. This pattern suggested that the 9T stretch of Haplogroup BT was the ancestral version and that Haplogroup A was formed by the deletion of one nucleobase. Haplogroups A1b and A1a were considered subclades of Haplogroup A as they both possessed the M91 with 8Ts.^[4]^[5]

But according to Cruciani et al. 2011, the region surrounding the M91 marker is a mutational hotspot prone to recurrent mutations. It is therefore possible that the 8T stretch of Haplogroup A may be the ancestral state of M91 and the 9T of Haplogroup BT may be the derived state that arose by an insertion of 1T. This would explain why subclades A1b and A1a-T, the deepest branches of Haplogroup A, both possess the same version of M91 with 8Ts. Furthermore Cruciani et al. 2011 determined that the P97 marker, which is also used to identify Haplogroup A, possessed the ancestral state in Haplogroup A but the derived state in Haplogroup BT.^[5]

Origin

Initial studies implicated East Africa and Southern Africa as the likely sources of human Y-chromosome diversity. This was because the basal lineages, Haplogroup A and Haplogroup B achieve their highest frequencies in these regions. But according to Cruciani et al. 2011, the most basal lineages have been detected in West, Northwest and Central Africa. In a sample of 2204 African Y-chromosomes, 8 chromosomes belonged to either haplogroup A1b or A1a. Haplogroup A1a was identified in two Moroccan Berbers, one Fulbe and one Tuareg from Niger. Haplogroup A1b was identified in three Bakola pygmies from Southern Cameroon and one Algerian Berber. Cruciani et al. 2011 suggest a Y-chromosomal Adam, living somewhere in Central-Northwest Africa, fits well with the data. However they suggest that this interpretation is still very preliminary due to the incomplete sampling of African Y chromosomes, and incomplete knowledge of past demographic events.^[5]

Nomenclature

Y-chromosomal Adam is named after the Biblical Adam. This may lead to a misconception that he was the only living male of his times, even though he co-existed with plenty of men around,^[6] including his own father who was not the "most recent". However, all his other male contemporaries failed to produce a direct unbroken male line to the present day.

Time frame

The time when Y-chromosomal Adam lived is determined by applying a molecular clock to human Y-chromosomes. In contrast to mitochondrial DNA, which has a short sequence of 16,000 base pairs, and mutates frequently, the Y chromosome is significantly longer at 60 million base pairs, and has a lower mutation rate. These features of the Y chromosome have slowed down the identification of its polymorphisms and as a consequence, reduced the accuracy of Y-chromosome mutation rate estimates.^[7] Initial studies, such as Thomson et al. 2000,^[7] proposed that Y-chromosomal Adam lived about 59,000 years ago. This date suggested that Y-chromosomal Adam lived tens of thousands of years after his female counterpart Mitochondrial Eve, who lived 150,000–200,000 years ago.^[8] This date also meant that Y-chromosomal Adam lived at a time very close to, and possibly after, the migration from Africa which is believed to have taken place 50,000–80,000 years ago.

One explanation given for this discrepancy in the dates of Adam and Eve was that females have a better chance of reproducing than males due to the practice of polygyny. When a male individual has several wives, he has effectively prevented other males in the community from reproducing and passing on their Y chromosomes to subsequent generations. On the other hand, polygyny doesn't prevent most females in a community from passing on their mitochondrial DNA to subsequent generations. This differential reproductive success of males and females can lead to fewer male lineages relative to female lineages persisting into the future. These fewer male lineages are more sensitive to drift and would most likely coalesce on a more recent common ancestor. This would potentially explain the more recent dates associated with Y-chromosomal Adam.^[9]^[10]

The 2011 study by Cruciani et al. found that Y-chromosomal Adam lived about 142,000 years ago, significantly earlier than previous estimates, such as the 59,000 years ago estimate proposed by Thomson et al. 2000. The older TMRCA was due to the discovery of additional mutations and the rearrangement of the backbone of the y-chromosome phylogeny following the resequencing of Haplogroup A lineages. According to the study, determining the precise date when Y-chromosomal Adam lived depends on the accuracy of the mutation rate used. But the repositioning of the MRCA from the root of Haplogroups A and BT to the root of Haplogroups A1b and A1a still entails that Y-chromosomal Adam is older than previously thought. According to Cruciani et al., the much older date is easier to reconcile with models of human origins.^[5]

Cradle of Humankind

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For other uses, see Cradle of Humankind (disambiguation).

Coordinates: 25.96716°S 27.66245°E

Fossil Hominid Sites of Sterkfontein, Swartkrans, Kromdraai, and Environs *
UNESCO World Heritage Site
Cradle of Humankind
Country	South Africa
Type	Cultural
Criteria	iii, vi
Reference	915
Region **	Africa
Inscription history
Inscription	1999 (23rd Session)
Extensions	2005
* Name as inscribed on World Heritage List ** Region as classified by UNESCO

The Cradle of Humankind is a World Heritage Site first named by UNESCO in 1999, about 50 kilometres northwest of Johannesburg, South Africa in the Gauteng province. This site currently occupies 47,000 hectares (180 sq mi);^[1] it contains a complex of limestone caves, including the Sterkfontein Caves, where the 2.3-million year-old fossil Australopithecus africanus (nicknamed "Mrs. Ples") was found in 1947 by Dr. Robert Broom and John T. Robinson. The find helped corroborate the 1924 discovery of the juvenile Australopithecus africanus skull, "Taung Child", by Raymond Dart, at Taung in the North West Province of South Africa, where excavations still continue.

The name Cradle of Humankind reflects the fact that the site has produced a large number, as well as some of the oldest, hominid fossils ever found, some dating back as far as 3.5 million years ago.^[2] Sterkfontein alone has produced more than a third of early hominid fossils ever found.^[3]

Mitochondrial Eve

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Haplogroup Modern humans
Possible time of origin	152,000 - 234,000 BP ^[1]
Possible place of origin	East Africa
Ancestor	n/a
Descendants	Mitochondrial macro-haplogroups L0, L1, and L5
Defining mutations	None

In the field of human genetics, Mitochondrial Eve refers to the matrilineal most recent common ancestor (MRCA) of modern humans. In other words, she was the most recent woman from whom all living humans today descend, on their mother's side, and through the mothers of those mothers and so on, back until all lines converge on one person. Because all mitochondrial DNA (mtDNA) is generally passed from mother to offspring without recombination, all mitochondrial DNA (mtDNA) in every living person is directly descended from hers by definition. Mitochondrial Eve is the female counterpart of Y-chromosomal Adam, the patrilineal most recent common ancestor, although they lived thousands of years apart.

Each ancestor (of people now living) in the line back to the matrilineal MRCA had female contemporaries such as sisters, female cousins, etc. and some of these female contemporaries may have descendants living now (with one or more males in their descendancy line). But none of the female contemporaries of the "Mitochondrial Eve" has descendants living now in an unbroken female line.

Mitochondrial Eve is estimated to have lived around 200,000 years ago,^[2] most likely in East Africa,^[3] when Homo sapiens sapiens (anatomically modern humans) were developing as a population distinct from other human sub-species.

Mitochondrial Eve lived later than Homo heidelbergensis and the emergence of Homo neanderthalensis, but earlier than the out of Africa migration.^[4] The dating for 'Eve' was a blow to the multiregional hypothesis, and a boost to the hypothesis that modern humans originated relatively recently in Africa and spread from there, replacing more "archaic" human populations such as Neanderthals. As a result, the latter hypothesis became dominant.

Female and mitochondrial ancestry

Further information: Genetic genealogy (matrilineal), Mitochondrial DNA, and Human mitochondrial molecular clock

Through random drift or selection the female-lineage will trace back to a single female, such as Mitochondrial Eve. In this example over 5 generations colors represent extinct matrilineal lines and black the matrilineal line descended from mtDNA MRCA.

Simplified Human mitochondrial phylogeny

Without a DNA sample, it is not possible to reconstruct the complete genetic makeup (genome) of any individual who died very long ago. By analysing descendants' DNA, however, parts of ancestral genomes are estimated by scientists. Mitochondrial DNA (mtDNA) and Y-chromosome DNA are commonly used to trace ancestry in this manner. mtDNA is generally passed un-mixed from mothers to children of both sexes, along the maternal line, or matrilineally.^[5]^[6] Matrilineal descent goes back to our mothers, to their mothers, until all female lineages converge.

Branches are identified by one or more unique markers which give a mitochondrial "DNA signature" or "haplotype" (e.g. the CRS is a haplotype). Each marker is a DNA base-pair that has resulted from an SNP mutation. Scientists sort mitochondrial DNA results into more or less related groups, with more or less recent common ancestors. This leads to the construction of a DNA family tree where the branches are in biological terms clades, and the common ancestors such as Mitochondrial Eve sit at branching points in this tree. Major branches are said to define a haplogroup (e.g. CRS belongs to haplogroup H), and large branches containing several haplogroups are called "macro-haplogroups".

The mitochondrial clade which Mitochondrial Eve defines is the species Homo sapiens sapiens itself, or at least the current population or "chronospecies" as it exists today. In principle, earlier Eves can also be defined going beyond the species, for example one who is ancestral to both modern humanity and Neanderthals, or, further back, an "Eve" ancestral to all members of genus Homo and chimpanzees in genus Pan. According to current nomenclature, Mitochondrial Eve's haplogroup was within mitochondrial haplogroup L because this macro-haplogroup contains all surviving human mitochondrial lineages today, and she must predate the emergence of L0.

The variation of mitochondrial DNA between different people can be used to estimate the time back to a common ancestor, such as Mitochondrial Eve. This works because, along any particular line of descent, mitochondrial DNA accumulates mutations at the rate of approximately one every 3,500 years.^[7]^[8]^[9] A certain number of these new variants will survive into modern times and be identifiable as distinct lineages. At the same time some branches, including even very old ones, come to an end, when the last family in a distinct branch has no daughters.

Mitochondrial Eve is the most recent common matrilineal ancestor for all modern humans. Whenever one of the two most ancient branch lines dies out, the MRCA will move to a more recent female ancestor, always the most recent mother to have more than one daughter with living maternal line descendants alive today. The number of mutations that can be found distinguishing modern people is determined by two criteria: firstly and most obviously, the time back to her, but secondly and less obviously by the varying rates at which new branches have come into existence and old branches have become extinct. By looking at the number of mutations which have been accumulated in different branches of this family tree, and looking at which geographical regions have the widest range of least related branches, the region where Eve lived can be proposed.

The date when Mitochondrial Eve lived is estimated by determining the MRCA of a sample of mtDNA lineages. In 1980, Brown first proposed that modern humans possessed a mitochondrial common ancestor that may have lived as recently as 180,000 years ago. In 1987, Cann et al. suggested that mitochondrial Eve may have lived between 140-280 thousand years ago.

Common misconceptions

Not the only woman

One of the misconceptions of mitochondrial Eve is that since all women alive today descended in a direct unbroken female line from her that she was the only woman alive at the time.^[10]^[11] Nuclear DNA studies indicate that the size of the ancient human population never dropped below tens of thousands. Other women alive at Eve's time have descendants alive today, but sometime in the past, each of their lines of descent included at least one male, thereby breaking the mitochondrial DNA lines of descent. By contrast, Eve's lines of descent to each person alive today includes precisely one purely matrilineal line.^[10]

Not a contemporary of "Adam"

Sometimes mitochondrial Eve is assumed to have lived at the same time as Y-chromosomal Adam, perhaps even meeting and mating with him. Like mitochondrial "Eve", Y-chromosomal "Adam" probably lived in Africa; however, this "Eve" lived much earlier than this "Adam" – perhaps some 50,000 to 80,000 years earlier.^[12] However, studies conducted in 2011 by Cruciani et al.^[13] found that Y-chromosome Adam lived about 142,000 years ago, significantly earlier than previous estimates. This can reconcile with dates for human origins.

Not the most recent ancestor shared by all humans

Main article: Most recent common ancestor

Mitochondrial Eve is the most recent common matrilineal ancestor, not the most recent common ancestor (MRCA). Since the mtDNA is inherited maternally and recombination is either rare or absent, it is relatively easy to track the ancestry of the lineages back to a MRCA; however this MRCA is valid only when discussing mitochondrial DNA. An approximate sequence from newest to oldest can list various important points in the ancestry of modern human populations:

The Human MRCA. All humans alive today share a surprisingly recent common ancestor, perhaps even within the last 5,000 years, even for people born on different continents.^[14]
The Identical ancestors point. Just a few thousand years before the most recent single ancestor shared by all living humans was the time at which all humans who were then alive either left no descendants alive today or were common ancestors to all humans alive today. In other words, "each present-day human has exactly the same set of genealogical ancestors" alive at the "Identical ancestors point" in time. This is far more recent than Mitochondrial Eve.^[14]
"Y-chromosomal Adam", the most recent male-line common ancestor of all living men, was much more recent than Mitochondrial Eve, but is also likely to have been long before the Identical ancestors point.
Mitochondrial Eve, the most recent female-line common ancestor of all living people.

Implications of dating and placement of Eve

Further information: Out of Africa hypothesis, Multiregional evolution hypothesis, Recent African origin of modern humans

Initially there was a lot of resistance against the Mitochondrial Eve hypothesis. This resistance was due, in part, to the popularity of the Multiregional Evolution hypothesis amongst some leading paleoanthropologists such as Milford Wolpoff. This prevailing theory held that the evolution of humanity from the beginning of the Pleistocene 2.5 million years BP to the present day has been within a single, continuous human species, evolving worldwide to modern Homo sapiens. More resistance came from those who argued that there was too little time between Homo erectus and modern Homo sapiens to allow for another new species, and others who argued that for regional evolution from archaic hominin forms into modern ones. Consequently, the finding of a recent maternal ancestor for all humans in Africa was very controversial.

Cann, Stoneking & Wilson (1987)'s placement of a relatively small population of humans in sub-saharan Africa, lent appreciable support for the recent Out of Africa hypothesis. The current concept places between 1,500 and 16,000 effectively interbreeding individuals (census 4,500 to 48,000 individuals) within Tanzania and proximal regions. Later, Tishkoff et al. (2009) using data from many loci (not just mitochondrial DNA) extrapolated that the Angola-Namibia border region near the Atlantic Ocean is likely to be near the geographical point of origin of modern human genetic diversity. In its relatively southern origin proposals, this autosomal study was considered by the authors to be broadly consistent with a previous mitochondrial DNA studies, including one by some of the same authors which associated the origins of mitochondrial haplogroups L0 and L1 with "click languages" in southern and eastern Africa.^[15]

To some extent the studies have already revealed that the presence of archaic homo sapiens in Northwest Africa (Jebel Irhoud) were not likely part of the contiguous modern human population. In addition, the older remains at Skhul and Qafzeh are also unlikely part of the constrict human population, evidence currently indicates humans expanded in the region no earlier than 90,000 BP.^{[citation needed]} Tishkoff argues that humans might have migrated to the Levant before 90 Ka, but this colony did not persist in SW Asia.^{[citation needed]} Better defined is the genetic separation among Neanderthals, Flores hobbit, Java man, and Peking man. In 1999 Krings et al., eliminated problems in molecular clocking postulated by Nei, 1992 when it was found the mtDNA sequence for the same region was substantially different from the MRCA relative to any human sequence. Currently there are 6 fully sequenced Neanderthal mitogenomes, each falling within a genetic cluster less diverse than that for humans, and mitogenome analysis in humans has statistically markedly reduced the TMRCA range so that it no longer overlaps with Neandertal/human split times. Of all the non-African hominids European archaics most closely resembled humans, indicating a wider genetic divide with other hominids.

Since the multiregional evolution hypothesis (MREH) revolved around a belief that regional modern human populations evolved in situ in various regions (Europe: Neandertals to Europeans, Asia: Homo erectus to East Asians, Australia: Sumatran erectines to indigenous Australians), these results demonstrated that a pure MREH hypothesis could not explain one important genetic marker.

Nomenclature

Mitochondrial Eve is named after mitochondria and the Biblical Eve.^[16] The reference to Eve may lead to the misconception that she was the only living female of her time, even though she co-existed with other females. However, all of her other female contemporaries failed to produce a direct unbroken female line to the present day.

In popular science

Newsweek reported on Mitochondrial Eve based on the Cann et al. study in January 1988, under a heading of "Scientists Explore a Controversial Theory About Man's Origins". The edition sold a record number of copies.^[17]
The Seven Daughters of Eve presents the theory of human mitochondrial genetics to a general audience.^[18]
In River Out of Eden, Richard Dawkins discusses human ancestry in the context of a river of genes and shows that Mitochondrial Eve is one of the many common ancestors we can trace back to via different gene pathways.^[19]
The Discovery Channel produced a documentary entitled The Real Eve: 6 Billion People ... from ONE Woman (or Where We Came From in the United Kingdom), based on the book The Real Eve: Modern Man's Journey Out of Africa by Stephen Oppenheimer.^[20]

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Grimaldi

(The First Homo-Sapien-Sapien in Europe)

The First Modern Humans in Europe

Khoisan (Khoi + San) - Is the name for the two original ethnic groups of Southern Africa. From the beginning of the Upper Paleolithic period, a hunting and gathering culture known as the Sangoan occupied this area. Today's San and Khoi people resemble their ancient skeletal remains and are believed to be their descendants. The Khoisan people were the inhabitants of much of southern Africa before the southward Bantu expansion, and later European colonization. Both Khoi and San people share physical and linguistic characteristics, and it seems clear that the Khoi branched forth from the San when they adopted the practice of herding cattle and goats from neighboring Bantu speaking groups.

Culturally they are divided into the hunter gatherer San people (commonly known as Bushmen) and the pastoral Khoi. In the Khoisan language, consonants are pronounced with a clicking sound. This prompted their Dutch invaders to call them “Hottentots” – a derogatory word meaning "stutterer" or "stammerer" in the language of the Dutch invaders; Who, together with British and German settlers, would eventually exterminate them with the Herero and Namaqua Genocides.

One of the great ironies of Human History, is that this marks the second time, that these very same peoples – the British, Dutch, and Germans - would exterminate Khoisans and seize their lands. It is a repeat of what happened (ca. 500 B.C.), when the ancestors of today's British, Dutch, and Germans: The Celts and Germans who migrated into Europe from the place of their evolution, (the Eurasian Plains): exterminated the Khoisan inhabitants of Europe and seized their lands. It appears that unfortunately, word never got back to those in Africa, as to what the Caucasians were likely to do.

Khoisan: The worlds oldest human group
According to Knight et al. (2003) Y-haplogroup A, the most diverse or oldest-diverging Y haplogroup transmitted purely by patrilineal descent, is today present in various Khoisan groups at frequencies of 12-44%, and the other Y-haplogroups present have been formed by recent admixture of Bantu male lineages E3a (18-54%), and in some groups, noticeable Pygmy traces are visible (B2b). The Khoisan also show the largest genetic diversity in matrilineally transmitted mtDNA of all human populations. Their original mtDNA haplogroups L1d and L1k are one of the oldest-diverging female lineages as well.

Khoisan imagination and artistry
Around 75,000 years ago, in a cave near the southern Cape shoreline in South Africa, a human drilled tiny holes into the shells of snails and strung them as beads to make the oldest known jewelry. The shells are marked with traces of red ochre, suggesting they were either decorated with iron oxide pigment or; they were worn by someone wearing primitive makeup with iron oxide pigment. They are the first evidence of artistic creativity and symbolism in Modern Man. This artistic creativity in the Khoisan; would be continued and improved upon.

Steatopygia Females
Steatopygia - is a high degree of fat accumulation in and around the buttocks extending to the outside and front of the thighs, forming a thick layer reaching sometimes to the knee. This constitutes a genetic characteristic of some Khoisan females. It has also been noted among the Pygmies of Central Africa and the Andamanese Negritos of the Andaman Islands. Among the Khoisan, it is regarded as a sign of beauty: it begins in infancy and is fully developed by the time of the first pregnancy. While the Khoisan afford the most noticeable examples of its development, it is by no means rare in other parts of Africa, and occurs even more frequently among male Basters than among Khoikhoi women. The Khoisans admiration for steatopygia females, together with his great artistic ability, will provide artifacts that are a great aid in tracking their migrations across Europe and Asia.

Migration to Europe
Sometime about 45,000 B.C. The Great Glacial Ice Sheets that covered most of Europe, started to melt and a group, or groups of these Khoisan peoples walked across the Gibraltar straits and entered Europe. This marks the first time in Human History that modern Humans have crossed over into the formally frozen wilderness of Europe. Once in Europe, Grimaldi Man continued his migrations, and came to eventually inhabit all of Europe and Northern Asia. The Easternmost limit of his range, appears to have been the settlement known as Mal'ta in Siberia Russia, just north of Mongolia.

Please note: One of the sad, and unfortunate facts of life, is that many Anthropologists, Researchers and Academics, still refuse to acknowledge that Africans were the first Human colonizers of Europe. To hide this fact, they prefer to use the terms Aurignacian and Gravettian cultures; which is fine, it still means Grimaldi. However, the current fad of attributing Grimaldi artifacts to the Humanoid Cro-Magnon is in all ways, mystifying. After all, thought different, Cro-Magnon like Grimaldi, was a Black African.

One of the first evidences of this historic journey of Grimaldi, was found at the caverns of Grimaldi (Baousse-Rousse), between Mentone and Ventimiglia and on the Italian side of the international boundary, these caverns form one of the most compact groups of paleolithic caverns in all Europe. Counting two small rock-shelters, the group includes nine stations, the most important being the Grotte des Enfants, La Barma Grande, Grotte du Cavillon and the Grotte du Prince. General attention was first called to this region many years ago by Dr. Paul Riviere's discovery of a human skeleton in the Grotte du Cavillon, the so-called homme de Menton, now in the Natural History Museum, Paris. Here Rivière demonstrated the presence of deliberate burials and ornamented clothing in 1872.

Later five skeletons in all were found at La Barma Grande, and two of children, in the Grotte des Enfants, whence its name. Interest in archeology and ownership of one of the caverns (Grotte du Prince), led the Prince of Monaco, Prince Albert I Grimaldi (1848-1922), to provide for a systematic exploration of the caverns: thus the fossils became known as "Grimaldi" in his honor. Fossil remains of these ancient Africans have also been found in France, Switzerland, Central Europe, Bulgaria, Russia, and as Far East as Siberia. The African Khoisan nature of the Fossils was first documented by Boule, Marcellin & Vallois, in their book "Fossil Men" The Dryden Press (1957).

One of the most exciting Grimaldi finds of the 19th century, was made by a Spanish nobleman: Sr. Don Marcelino de Sautoula, on his estate on the northern coast of Spain. An amateur prehistorian, he partially excavated a cave on a hill called Altamira. He found stag, horse, bison bones, oyster shells, numerous implements and bone tools characteristic of the Magdalenian culture. Exploring deeper into the cave, he encountered cave bear bones and extensive ashes. On one of his excavation trips, he took his 12-year-old daughter, Maria, with him into the cave. While he sat digging in damp darkness under the light of a lantern, the girl suddenly cried out, "Papa, papa.

Mira. Toros pintados." (Father, father, Look Painted bulls.) Maria showed her astonished father that the roof of the cavern was covered with a superb fresco of red and black bison. Lantern light gave them three-dimensional form since the artist had incorporated the natural projections of the ceiling with great skill into his art. Sautuola was deeply moved as he and his daughter explored the cavern roof and saw marvelous polychrome animals, executed in three-dimensional skill, all painted by an artist who had known the animals before they became extinct from Spain in the distant past.

Grimaldi skeletons as displayed in the Musée d'Anthropologie in Monaco

The Black mans art: 35,000 years before Mona Lisa

Altamira is the name of the Cave of Altamira, and other Paleolithic Cave Art of Northern Spain, under which are grouped 18 caves located in different regions of northern Spain. These represent the apogee of Paleolithic cave art developed in Europe between 35,000 and 11,000 D.C.

Don Marcelino was later to explore chamber after chamber of extraordinary drawings: polychrome horses in flight, painted prints of human hands, outlines of human hands. Here again was extraordinary evidence of the humanness and artistic skills of these Paleolithic Grimaldi artists. Don Marcelino hired a French painter to make sketches of the artwork so that he could publish them. This well-written paper, An Account of Certain Prehistoric Discoveries in the Province of Santander (1880), included the paintings and a detailed description of the archeology of the cave.

Just as exciting as the fossil finds, were the artifact finds at the Balzi Rossi, or Red Rocks (also known as the Grimaldi Caves), were Louis Alexandre Jullien, carried out the excavations that led, at the end of the last century, to the discovery of fifteen figurines, called the Balzi Rossi Venuses. Many other sites across Europe and Asia have also produced Grimaldi Venuses: many of them Steatopygia Females, and many of normal proportion females. Notable of these are the Venus of Willendorf: found near Krems, Austria. The Venus of Brassempouy, found in France in 1892. It should be noted; that though all Grimaldi figures are not of Steatopygia Females, that style of figure, is the signature of Grimaldi.

As demonstrated by the Venuses, Bust reproductions of Skulls, and other artifacts: The Grimaldi people, like modern day Africans, show great variation in facial features, hair styles, clothing and adornment. They show a particular liking for bracelets, necklaces, and pendants.

When Grimaldi Man entered Europe, he encountered the Humanoid, Neanderthal man: who had migrated to Europe thousands of years earlier, and had become physically adapted to the cold. Grimaldi was followed into Europe: perhaps 15,000 years later, by the Humanoid Cro-Magnon man. Nothing is known of their relationships, or even if they intermingled. But it is generally believed that at some point, there had to have been some crossbreeding.

Thought Grimaldi Man is known to have established settlements as far south as Catal Huyuk in Anatolia. There is uncertainty as to whether it was Grimaldi descendants, or a different group, such as those Africans who settled North Africa and the Middle East, that can be credited with the creation of the original Southern European civilizations, especially those in Italy, Greece, and Anatolia (modern Turkey).

/

The Mother of Mothers !

It has been well known for about 20 years now that the mother of all Non-Africans, and indeed a lot of Africans, was an East African woman, in more recent nomenclature this woman has been called L3, so what do geneticists recently say about this woman, mother to greater than six and a half billion people on Earth, including many who still inhabit her original homeland?

The most recent study conducted to uncover the story behind L3 and her compatriots was one from the end of last year entitled “The Expansion of mtDNA Haplogroup L3 within and out of Africa”.

This important study capped the timing of the out of Africa migrations, which all contemporary men and women outside of Africa are descended from, to no earlier than Seventy Thousand Years Ago.

The basis for this reasoning can be found in this paragraph from the text:

“The time window for the out-of-Africa migration on the basis of mtDNA lies between the emergence of haplogroup L3 in Eastern Africa and its derivative non-African haplogroups M and N, which most likely arose during the departure or outside Africa (Richards et al. 2006).”

Meaning, since all Non-Africans are descended from this woman, the timing of the out of Africa migration can not be any older than when she lived and can not be any younger than when here descendant daughters M and N lived, although there still remains a possibility that M and N emerged in Africa, albeit increasingly unlikely.

The expansion of L3 however has been linked in the past to not only the Out of Africa expansion but also Expansions within Africa, generally in association with two different episodes:

With the spread of Pastoralism in the Sahara of the early Holocene
With the Bantu Expansion/s

To this end, the samples for this study were said to come from:

“We collected a total of 102 Sudanese, 77 Ethiopian (both emigrants in Dubai), and 148 Somali (refugees in Yemen) samples, belonging to unrelated individuals, who gave appropriate informed consent for their biological samples to be used for mtDNA characterization.”

Where a set of identified L3 lineages from above (plus other previous papers) were then selected for complete mtDNA sequencing:

“We selected for complete mtDNA sequencing a total of 21 Sudanese, 16 Ethiopian, and 20 Somali samples chosen from the sequences characterized in this work, and 11 from Chad and 2 from Soqotra belonging to haplogroup L3 from data sets published previously (Cerny´ et al. 2007; Cerny´, Pereira, et al. 2009).”

So what were the main results of the extensive statistical analysis done on this lineage?

A) Complete mtDNA phylogeny for Haplogroup L3:

Schematic tree of haplogroup L3. Age estimates are respectively rho estimates from the complete mtDNA genome (black font), rho estimates using the synonymous clock (gray font), and ML estimates using the complete mtDNA genome (black font underlined). Color scheme for each clade indicates the probable geographic origin. Haplogroups M and N are indicated and age estimates are according to Soares et al. (2009). MSA refers to Middle Stone Age and LSA to Late Stone Age.

B) Reaffirmation of what was known in the past with respect to the origins of L3:

“L3 most likely had an origin in Eastern Africa (Torroni et al. 2006). This is supported by the presence of all major branches, with L3a and L3h virtually specific to the region and L3eikx and the L3f haplogroups having a probable origin there as well, whereas for L3bcd, the region of origin is less clear and will be discussed in more detail below. The other two main branches of L3, M and N, exist only outside Africa, except for some back-migrations into Africa around 50–30 ka in the form of haplogroups U6 and M1 (Olivieri et al. 2006; Pereira et al. 2010) and some more recent intrusions (Cherni et al. 2009; Ottoni et al. 2010). Since there is strong evidence that the dispersal out of Africa was via the Horn, soon after L3 arose (Macaulay et al. 2005), the distribution of M and N also points to Eastern Africa as the center of gravity for L3.”

C) Temporal analysis of the sampled L3 lineages with origins bracketed within 60 – 70 thousand years ago:

"It seems likely that L3 dates somewhere between 60 and 70 ka, as the TMRCA estimates vary between 58.9 ka (using rho and the complete genome) and 70.2 (using ML), with the synonymous clock providing a value between the two (63.1 ka). We checked if the L3 tree rejected a strict molecular clock by running the ML analysis without stipulating a molecular clock and performing a likelihood ratio test that clearly did not reject the clock hypothesis (P 5 0.9899). These results led us to consider an age of 65 ka (varying between 60 and 70 ka in the 95% percentile) in the internal calibration of BEAST, as there was no other reliable calibration point we could use. The ages using the complete genome and the synonymous clock were 1.04 and 0.97 times the BEAST estimates, respectively, indicating that the BSPs were calculated using a similar rate to the other analyses, as we intended.”

D) Identification of 3 main episodes of population growth/expansion within Africa:

i) Approximately 40 thousand years ago corresponding with the emergence of the various intra-African subclades of L3.

ii) Around the Holocene, associated mainly with L3bd and L3e (Central Africa)

iii) The largest increase of the expansions detected around four thousand years ago and most pronounced in the Central African Bayesian Skyline Plots.

E) L3f and L3eikx both implied to have an origin in Eastern Africa. Where L3f was carried into the Sahel and Central Africa, with L3f3 specifically expanding into the Sahel 8 to 9 thousand years ago.

F) The most frequent clade of L3, i.e. L3e implied to have an origin in Central/Western Africa. With Eastern African L3e discounted as more recent introgression from there.

G) An ambiguous interpretation for the origin of L3bcd, a tentative east African origin is however suggested:

“L3bcd has three main subclades, with L3b and L3d tentatively united by a transition at control region position 16124 to form the putative subclade L3bd. The great age of L3bcd and its wide distribution across Africa makes phylogeographic inferences difficult. Furthermore, L3c is extremely rare: Only two samples have been detected so far, one in Eastern Africa and the other in the Near East. This might echo an early origin of L3bcd in Eastern Africa, before moving west, but its rarity makes this conclusion extremely tentative. In a scenario of an early origin of L3bcd in Eastern Africa, M and N would be the only subclades of L3 to have most likely originated outside of Eastern Africa (although an origin in Eastern Africa remains possible: Richards et al. 2006).

H) A virtual exclusion of a scenario in which the ancestors of contemporary people outside of Africa migrated out of Africa before the eruption of Toba.

I) And finally the most interesting part of this paper's conclusion, a unified demographic process that led to both the out-of-Africa and within Africa primary expansion of L3:

“Furthermore, since the age of the M and N Eurasian founders of ;50 to 65 ka (Soares et al. 2009) is close to the age of their ancestral L3 clade in Africa, the out of-Africa dispersal may have been of a piece with the initial diversification and expansion of L3, so that the L3 expansions in Eastern Africa and the exit of modern humans from Africa;60 ka were all part of a single demographic process.

It seems likely that the moister climate after;70 ka in Eastern Africa allowed dramatic human population growth (Scholz et al. 2007), perhaps associated with improved hunting, marine exploitation, exchange networks, and possibly even plant food management strategies as suggested by Mellars (2006). This generated the oldest major signal of expansion in the human mtDNA tree, the radiation of L3, leading rapidly to the spread of H. sapiens toward the rest of the world. It is worth stressing that this signal is not reflected in other mtDNA lineages at this time (Behar et al. 2008). Within Africa, the Pleistocene migrations detected in the L3 pool were responsible for the introduction of L3bd and L3e into Central Africa in the period between 60 and 35 ka (fig. 5A), but none reached Southern Africa at that time.”

Interestingly, the previous explanations that the Out of Africa expansion of modern humans being linked with behavioral modern thinking is largely dismissed by these authors for the sole explanation of Environmental factors, their main reasoning being that there is evidence for behavioral modernity of humans in Africa (Both in South and North Africa) long before their proposed timing of the OOA migrations.

“Thus, as suggested by Basell (2008), the demographic expansions that led to the first successful dispersal out of Africa seem better explained by the play of palaeoenvironmental forces than by recourse to the advantages of ‘‘modernity."

More interesting figures from the paper:

“Frequency maps based on HVS-I data for haplogroups L3a, L3i, L3h, and L3x combined (A), L3f (B), L3e (C), L3b (D), and L3d (E).”

“Outline of the main dispersals detected in this work during the Pleistocene (A) and the Holocene (B).”

** Sketches on top of page depicting contemporary women that still live in the putative land of L3's origin. Credit goes to Ethiopian Artist Adis Gebru and taken from this blog.

23 comments:

MajuJanuary 19, 2012 11:21 PM
A very interesting study, even if I have to disagree with the age estimates, which are probably (based on the archaeology of Arabia and India) more c. 90 Ka or even maybe 125 Ka., within the Abbassia Pluvial surely in any case.

I have reblogged this (in my own style but with due credit) at FWTWWA.

I must also say that your choice of portraits is surely not too accurate as those women are obviously influenced by genetic back-flow from Asia. I'd rather pick tribal women from the SW as more likely representatives (the centroid of L3 certainly falls over there, right at the border with South Sudan, although its precursors L3'4'6 and L4'3 look more centered towards Eritrea instead).
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EtyopisJanuary 20, 2012 11:15 AM
I am beginning to sense some sort of a romantic fixation that you have with 'South Western' Ethiopia Maju. I clearly and explicitly said that those sketches, and I emphasize sketches instead of the random pictures that you took the liberty to post, represented women that inhabit the area of the putative origin of L3 as outlined in the subject of the paper, that does off course not mean that the original L3 bearer exactly looked like them, since nobody really knows what they looked like.

The Area outlined in this paper for L3's origin is approximately bounded in the North by Khartoum, North Sudan, in the East by Awash, Ethiopia, in the South by around the middle of Lake Turkana, Kenya and in the West by Agok, Abyei South Sudan. This is a large area with numerous types of people living in it, but mostly just Nilotes , that is Nhilo Saharan speakers and Afroasiatics. You can not simply just say these people are 'white' looking or 'black' looking as likely all 'black' and 'white' looking people originated in this region, there is nothing surprising about finding people who have a 'white' morphology in this area. As for your back migration hypothesis as to why the pictures I selected are unjustified, you first have to prove what the people who back migrated looked like, you also have to quantify what physical divergence these people had to the people of the area they back migrated to, and remember that it is not called back migration for no reason, those people went back to whence they came from, so in essence they were the same people.

In addition, before you nonchalantly throw around terms like 'Oromia', and 'Semitics', the woman in the middle of my selected sketches is an oromo lady, have you any clue as to the numerous type of people that live in these regions? They are not monolithic, have been cross pollinating with each other for millenia upon millenia, and the languages they speak bear little to no witness to the genesis of their physical types. Please cease with your tourist-like romantic fixation of certain African peoples that you pick and choose at whim.
Now as to the paper, I'm glad you found it interesting, to me also it was one of the best genetic papers done on Africa that I have read in quite some time, besides Tishkoff and some of the Cruciani papers. It was well sourced, with tones of references and a great read.

CC: For what they were... we are
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MajuJanuary 20, 2012 8:56 PM
What happens is that when I have in the past estimated the origin of L3 and other lineages (L5 and possibly mtDNA "Eve" herself) the area between the SNNPR and South Sudan almost systematically shows up as natural geometric centroid. I already said that L3'4'6 and L3'4 look more towards Eritrea or Djibouti, so there's room for debate (and indeed I meant to stir up some debate - healthy and in good mood).

Also the Omo river, considered to be (on archaeological grounds) a most likely urheimat (notice that I do not say "the urheimat" but "an urheimat") of Homo sapiens drains the SNNPR and West Oromia, so the data accumulates in that area, with permission of Herto and Irhoud, of course.

Call it a fetish if you wish but, if anything, it is a fetish fed in its specificity by data. When I was younger my anthropological "fetish" was surely more like the Kalahari and not long ago I was fascinated with the Hadzabe but it's good that the mind wanders a bit... as long as it is justified. Too much of the same thing gets boring.

But anyhow the ethnic diversity of that area, including tribes that, while not anymore huntergather (isn't there one or two that used to be so till recently?), have extremely traditional and often exotic and thought-provoking ways of life.

"the woman in the middle of my selected sketches is an oromo lady"

I though that she's the less "white" of the three. Some Semitic Ethiopians have very narrow noses, even more than the most narrow-nosed Europeans. Maybe that's an ancestral trait of the L3 clan but it may also be the product of back-flow and the fact that the trait is concentrated among Semitic speakers, who concentrate most of the genetic back-flow from Asia, makes it somewhat suspicious.

... "there is nothing surprising about finding people who have a 'white' morphology in this area".

Not but yes when it happens to be concentrated among ethnicities who are known to have important apportions of lineages that have back-migrated from Eurasia. You cannot obviate that. It'd be like defining Europeans in relation to Saami (who have notable Siberian ancestry) or the Bantu based on Xosha (who have lots of Khoisan genetics). You must look for populations which retain the original brew in the best possible way.

I sincerely thought that those portraits have a "Bollywood" feeling to me: Bollywood actresses and actors are indeed Indian types but almost invariably of the whitest-looking variants. This is not imported (colonial) racism but a type of somewhat more subtle racism brewed mostly inside South Asia with deep historical roots. I assume (although I do not know for sure) that something like that may happen in Ethiopia, where the Amhara and other Semitic groups have held for long primacy and may have looked upon other ethnicities with some pretense of superiority. I am assuming that you are of Amhara or otherwise Semitic (Tigray?) ethnicity, right?

(continues)
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MajuJanuary 20, 2012 9:08 PM
(...)

"you first have to prove what the people who back migrated looked like"

I cannot prove anything, the closes to evidence I may wield is the well known Herto man (Idaltu) reconstruction, who certainly does not have that narrow nose. But of course it is a reconstruction and hence arguable.

But I do have an opinion and it disagrees with your choice, which I find shockingly bollywoodian (because even for Amharas, those women look whitey, in the "whitest" possible range - just google "Amhara woman" as image, please).

Consider also that the ancestral L3 types eventually evolved not just in European or West Asian "Caucasoid" types but also South Asian, East Asian, Australian Aboriginal, Melanesian, Native American types. And that only considering the M and N sublineages, with other five basal lineages expanding to Africa (including North Africa and probably in part Arabia pen.) So the prototypes would have to account for most of the phenotype diversity on Earth right now, what makes impossible to discern how they might have looked.

"Please cease with your tourist-like romantic fixation of certain African peoples that you pick and choose at whim".

Of course my selection is arbitrary but not any more arbitrary than yours. I remain persuaded that my selection includes less back-migrant genetics in any case and therefore most likely reflects the phenotype reality of the past in that area (up to a point).

Whatever the case I did not mean to offend you but I was really struck by the choice of portraits, which is not any less romantic than mine, just that in a different direction of preference.

...

"Now as to the paper, I'm glad you found it interesting"...

It is a very interesting paper in principle (I do not have a copy so I'm relying on what you wrote 100%). It fits very well with what Behar (and separately myself on his data) have concluded on the patterns of human expansion in Africa based on mtDNA lineages (as you know Y-DNA and autosomal DNA are contradictory however).

Specially it seems true for L3. I for one tend to be more inclined for the Upper Nile region rather than The Horn as such (for the human and L3 homeland) but whatever.

... "to me also it was one of the best genetic papers done on Africa that I have read in quite some time, besides Tishkoff and some of the Cruciani papers".

There has been growing interest in Africa, even if it is yet patchy. I have mentioned before the Behar 2008 paper and I'm a bit surprised that you did not mention it, nonetheless because he also has some nice maps that "show" (?) that Ethiopia is the mother of humankind (at least mtDNA wise). As said, I'm rather more inclined for the Upper Nile are in general including much of Sudan and maybe Uganda and such, but it's almost demonstrated (at least mtDNA-wise) that that are is the urheimat of not just the L3 clan but probably all modern humankind.
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EzeJanuary 22, 2012 9:28 AM
A large portion of the 'Somalis' they sampled in this study living in Yemen are not ethnically Somali at all. They possessed way too many blatantly foreign lineages (HV1b, L1c, L3e, M51a just to name a few ..heck even Khoisan L0d and Austronesian B4a1a!). I suspect many of them were from the southern coastal Swahili Afro-Arab origin groups who were ousted after the civil war and mainly fled to Yemen. Another Y-DNA study which sampled Somalians in Yemen had very strange haplogroup frequencies (too high J1) as well. It's a pity they didn't check for ethnicity. Too many non-natives were included here, because this looks like very bad sampling.
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MajuJanuary 22, 2012 10:25 PM
"Almost all genetic data points to the fact that there is none to minimal difference as far as genetics between the Cushitic and Semitic speakers of Ethiopia"...

Alright. You seem correct in that, however I'd take more the "unspecified Ethiopians" group, whatever they are because they have much less back-migrant Eurasian Y-DNA F (incl. J and T) than the rest (30% back-migrant blood is too pretend being ultra-aboriginal at the level we are discussing here).

Maybe I've gone too far in some of my conclusions: I stand corrected re. the Semitic/Cushitic issue (though I still have some doubts) and I apologize for whatever unfair statement I made.

However I still think it's more correct to search, as much as possible, for the peoples of more neatly non-migrant African stock - i.e. with less West Eurasian back-flow, which can only be misleading.
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EzeJanuary 23, 2012 8:54 AM
Etyopis,

Check out this new study about adaptation to high altitude in Ethiopians. It might be of interest to you.

http://genomebiology.com/2012/13/1/R1/abstract
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MajuJanuary 23, 2012 1:03 PM
Languages apart, they are almost all from the SNNPR (the two exceptions are from nearby areas). While I may have been wrong by establishing the divide in the linguistic realm, the intuition I had was not that bad.

On the other hand it can be hard to exclude migration from other parts of Africa. In any case I can't but notice the high diversity the SW Ethiopians have in African specific Y-DNA lineages, with important amounts of E2, E* and B, lacking in other Ethiopians.

They are an interesting bunch. And I imagine that there is also interesting stuff the other side of the border in South Sudan (and maybe also North Sudan). It's not fetish as much as knowledge that there is a lot to dig in that area, which looks very much like the ancestral homeland of Humankind (or something close to that).
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andrewMarch 5, 2012 7:26 PM
The pre-Toba data and Horn source for Out of Africa is a bit hard to swallow given the mounting evidence for older dates out of Africa and archaeological links between the Nile Valley and points South to internal Arabian sites (as opposed to coastal ones).

Maybe there was replacement during the roughly 25,000 year gap in Levantine modern humans, but it would have to be pretty complete replacement given the mtDNA makeup of Eurasia.

I'm less skeptical of relative mtDNA dates than for Y-DNA or autosomal DNA, but color me skeptical on the accuracy of the calibration and the accuracy of the demographic models. A +/-4% accuracy assumption seems wildly optimistic given the systemic uncertainties.

In the larger African context, certainly, it seems like every other mtDNA hg but L2 did get pretty much swamped by L2 and L3. But, our pre-Bantu models of what was going on with African populations are pretty fuzzy, and I'm skeptical that the population structure observed is really as old as claimed.

70kya does stick in my mind as close to the oldest harpoon fishing evidence.
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EtyopisMarch 6, 2012 8:50 PM
"and archaeological links between the Nile Valley and points South to internal Arabian sites (as opposed to coastal ones)."

I suppose you are talking about the African Middle Stone Age industry found in Southern Arabia dubbed as the 'Nubian Complex' ~100KY old, well no skeletal evidence has been found in connection with those technologies, even-though one could speculate that they were made by modern humans, nevertheless, if they were modern humans, they could have just as easily carried older lineages of L3 or other types of L that was wiped either to extinction or near extinction with more recent migrations from Eastern Africa that soon gave rise to M and N, or simply, the 'Nubian Complex' could have just fizzled out and not made it beyond Dohfar, and subsequently met its demise sometime in the Late Pleistocene in the Arabian Peninsula, whereby later migrants from Eastern Africa not only took over that landscape, but also made it to migrate beyond the Peninsula and then some.....
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MajuMarch 7, 2012 6:36 AM
Yes, the main OoA flow was probably not based on the Nubian techno-complex, even if these are part of the wider picture. The characterization of Petrarglia 2007 for the Indian late MP toolkits is one of "Southern African MSA". This does not only exclude a Nubian but probably most East African cultures in fact - even if we know from genetics that the Eurasian gene pool has unmistakable East African origins.

Petraglia seems to favor a late (c. 90 Ka.) OoA via the interior of Arabia, while an alternative early (c. 125 Ka.) chronology is proposed by Armitage (I contrasted both options here).

I'm personally most sympathetic with the Armitage option because it is the only one that (taken as it is, the Petraglia model may need revision anyhow) fits with the genetic evidence but the evidence from South Asia (see Petraglia 2010, fig. 4) lacks data between c. 105 Ka and c. 80 Ka., rather not supporting an early exit.

In any case, the people of the Nubian and all other cultures involved were practically certain H. sapiens ("moderns") because there are no other remains so late in all the area except a few Neanderthals from West Asia, invariably with Mousterian tech.
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Mitochondrial "Eve" Theory
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The world is a diverse place. People come in all shapes and sizes, with obvious differences in abilities and appearances. There are many 'faces of Man' found throughout the world. Yet, although the faces are different, the genetic structure, the DNA, is not so different as most people believe. Over 99% of the DNA in all people is identical. This is not an accident. Most of the proteins that carry out the biochemical functions of a human body are made exactly the same from one person to the next. The remaining one percent, however, accounts for people's diversity. It can also be used as a tool to determine how genetically "related" people are.

This 'sameness' has been of great interest to scientists ever since the discovery of DNA and its function in inheritance patterns. These scientists thought that perhaps the study of DNA could provide essential clues in the long-standing quest for an understanding of the evolution of Homo sapiens sapiens.

By comparing mutations in the DNA of people who live in different parts of the world, geneticists are developing new theories about how humans populated the Earth. The evidence points to a common African origin. Much of the work has been based upon maternal lines. The DNA of present-day Africans is more diverse than that of people of other continents, indicating that humans have lived there the longest. Traces of ancient African genes can be found in everyone living today.

Who were our ancestors? A stumbling block for this research has been the basic process of meiosis--the recombination of genetic factors from both the male and female of the species. Within this genetic mixing bowl, genetic clues could be lost. However, there is one form of DNA that is inherited from only the female; this DNA could be traced back in time, to perhaps the ancestor of us all! (Eve?)

Modern technologies, much like those used in the OJ Simpson trial, have made this quest possible. Research the "Eve Theory", match your wits with scientists and supercomputers, and decide whether or not you believe!

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The Basics
Cells are the fundamental working units of every living system. All the instructions needed to direct their activities are contained within the chemical DNA (deoxyribonucleic acid).

DNA from all organisms is made up of the same chemical and physical components. The DNA sequence is the particular side-by-side arrangement of bases along the DNA strand (e.g., ATTCCGGA). This order spells out the exact instructions required to create a particular organism with its own unique traits.

The genome is an organism’s complete set of DNA. Genomes vary widely in size: the smallest known genome for a free-living organism (a bacterium) contains about 600,000 DNA base pairs, while human and mouse genomes have some 3 billion. Except for mature red blood cells, all human cells contain a complete genome.

DNA in the human genome is arranged into 24 distinct chromosomes--physically separate molecules that range in length from about 50 million to 250 million base pairs. A few types of major chromosomal abnormalities, including missing or extra copies or gross breaks and rejoinings (translocations), can be detected by microscopic examination. Most changes in DNA, however, are more subtle and require a closer analysis of the DNA molecule to find perhaps single-base differences.

Each chromosome contains many genes, the basic physical and functional units of heredity. Genes are specific sequences of bases that encode instructions on how to make proteins. Genes comprise only about 2% of the human genome; the remainder consists of noncoding regions, whose functions may include providing chromosomal structural integrity and regulating where, when, and in what quantity proteins are made. The human genome is estimated to contain 30,000 to 40,000 genes.

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Although genes get a lot of attention, it’s the proteins that perform most life functions and even make up the majority of cellular structures. Proteins are large, complex molecules made up of smaller subunits called amino acids. Chemical properties that distinguish the 20 different amino acids cause the protein chains to fold up into specific three-dimensional structures that define their particular functions in the cell.

The constellation of all proteins in a cell is called its proteome. Unlike the relatively unchanging genome, the dynamic proteome changes from minute to minute in response to tens of thousands of intra- and extracellular environmental signals. A protein’s chemistry and behavior are specified by the gene sequence and by the number and identities of other proteins made in the same cell at the same time and with which it associates and reacts. Studies to explore protein structure and activities, known as proteomics, will be the focus of much research for decades to come and will help elucidate the molecular basis of health and disease.

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YOUR TASK (whether you choose to accept it or not!):

In your research, 'surf the net' in a quest for the answer to the essential question, "Does the inheritance pattern of mitochondrial DNA justify the Eve Theory?". In order to conduct an appropriate search, several questions must be answered. Those questions are:

1. What is a mitochondrion?
2. Where are mitochondria located?
3. What is mitochondrial DNA?
4. Is mitochondrial DNA different from nuclear (or other forms) of DNA?
5. What is the inheritance pattern of mitochondrial DNA?
6. Is the inheritance pattern of mitochondrial DNA different from the inheritance patterns of other forms of DNA?
7. Who is (or was) Eve?
8. What is the Eve Theory?

You may want to use the following sources, but you will want to search beyond these links to discover additional information to aid you in your conclusion.

Check these sources:

DNA From the Beginning

A comprehensive overview, organized around key concepts. The science behind each concept is explained by: animation, image gallery, video interviews, problem, biographies, and links.

The Great DNA Hunt

This abstract from 'Archaeology', a professional journal, offers information of a 'mitochondrial eve'. In addition, inheritance questions concerning the origins of the Japanese people are discussed. This site offers an interesting human migratory graphic.

The Debate over Human Origins

Information regarding the research question, as well as data concerning basic primate evolution, is contained in this site. The computer program used in the construction of the "Eve Theory" is discussed. A site well worth visiting, especially for those students concerned with the validity of the use of statistical analysis in the development of scientific theory.

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Tracking Down Mitochondrial "Eve" and Y Chromosomal "Adam"

Mitochondrial Eve - An Explanation
Mitochondrial Eve represents one of the most poorly understood scientific ideas of the 20th century. In its time it has been feted and condemned, frequently by the same parties at different times. The premise of the idea is that we can all be traced back to a single woman living in Africa.

What are Mitochondria?
Mitochondria are the powerhouse of the cell. Technically 'organelles', mitochondria are essentially symbiotes1 – they consume the sugars that our bodies have converted from food, and in return produce electricity with which to power the cell. But why is it considered separate from the cell? This is an important distinction. The reason why mitochondria are considered separate is because they have their own DNA – DNA which is unaffected by other genetic exchanges.

Why is Mitochondrial DNA important?
Well, put it this way. You are a genetic mix of your parents, each of which contributed half of your genetic material. They, of course, have gone through the same process and share an equal split of their parent's DNA. This means if you stop this back-tracking process with your grandparents, you are already a genetic mix of six distinct individuals who may have come from different regions of the planet.

But one factor remains constant – the mitochondrial DNA hasn't altered at all – it remains intact through the female line. Male sperm contains only enough mitochondria to power the sperm to the surface of the egg – it does not enter the egg. The egg, however, contains mitochondria that have been passed from mother to daughter for countless generations. The only way for mitochondrial DNA to alter is by natural mutations, which occur very slowly when compared with the almost frantic gene mixing we and our parents take part in.

How Does This Relate to an 'Eve' Concept?
Because the rate of mitochondrial genetic mutation is slow, it can be used as a clock to turn back time to a period before the mutations had crept in. When mitochondrial DNA from certain populations in Africa are sampled, they can be compared with European mitochondrial DNA. The mutation difference between the two populations can then be compared, and a 'clock' can be produced, enabling the rate of mutation in mitochondria to be established. This produces a time-scale which indicates when modern Europeans first left Africa.

The genetic survey that produced the whole Mitochondrial Eve scenario didn't just sample Africans and Europeans – it sampled genes from people all over the planet. When mitochondrial DNA was compared, the survey discovered a startling result. Fundamental similarities in mitochondrial DNA in living humans suggested that we all contain genetic material from a single woman who was living in Africa.

That's Ridiculous – How Could a Single Being Populate a Planet?
And this is where the confusion sets in. A single organism can't populate a planet (arguments about amoeba aside). The evidence didn't suggest a single woman living in isolation from members of her own species. What it suggested was a genetic bottleneck – a period in human history when the population was so small that the genetic expressions of a single woman could have an impact on all humans living on the planet today.

She didn't live alone – she would have lived within a community. She didn't just pump babies out, either. There is no reason to suppose that she had more than one female child. But there is reason to suppose that whatever female children she had, they contained specific advantages for survival over the rest of the population.

But How Would the Population Become So Depleted?
Truth is, nobody knows the causes of the population crash. It could have been due to environmental pressures or a raging plague. The other important thing to consider is why did Eve survive and prosper where so many others died? Isolation is a tempting route to go down. She missed what-ever happened to everyone because she and her people where somehow isolated from the general population. Perhaps her people lived in a geographically remote valley, emerging when the threat had passed. Perhaps her people had access to food when starvation was rife – it is almost certain we will never know the cause for the depletion of the general population. A more fruitful line of inquiry is to question which traits made her progeny so successful.

Why Was She So Successful?
The reasons are all around you. What makes us so successful? An ability to share ideas, to help one another in dire circumstances, a certain creative flair to overcome everyday problems. Or perhaps she introduced the ability to slaughter those who came between us and required resources. We, as her children, display all of these traits. It could have been something as simple as wanderlust – a yearning to see what lay over the horizon. They were perhaps more fertile, were more agile, more resistant to disease, or could throw missiles more accurately than anyone else around at that time. If you want to find out, then next time you're on a bus, or train, or walking down the street, look around you – look at the behavior of your extended family.

Is Any of This True?
Well, yes and no. To get a completely accurate result the tests would have to be performed on every single person living on the planet today. The dates are in dispute, but the date is perhaps the least important point. Broadly speaking, populations do pass through bottlenecks. Eve had many ancestors – it helps if you think about her as an hourglass – she was the pinch in the glass through which our genes ran. There had been many more Eves before her, she is just our most recent common ancestor. There will probably be more population bottlenecks and more Mitochondrial Eves in the future.

Locating "Adam" and "Eve"

The rate at which polymorphisms develop though generations is known. Scientists can determine the number of polymorphisms in a certain population, as well as how many polymorphisms exist between different populations. In 1987, Mark Stoneking and Allan Wilson at the University of California, Berkeley, announced they had tracked down mitochondrial "Eve". By examining polymorphisms contained in the mitochondria, they were able to construct a global family tree. At its top branch was a woman who lived in Africa many years ago.

The next place to start looking for patterns of heredity was on the Y chromosome. Y chromosomal "Adam," the ancestor of all men, was determined in 1997. Two different research groups, led by Peter Underhill at Stanford University and Mike Hammer at the University of Arizona, each announced that Y chromosomal "Adam" had also lived in Africa many years ago. This is the most recent common male ancestor to all men in the world.

Strutting DNA

Anthropologists now commonly use mitochondrial and Y chromosomal DNA to track different populations. Recent studies of the Y chromosome from the lab of Nestor Bianchi in Argentina suggests that there is a common male ancestor to most of the Native American males of both North and South America. Two other research groups, led by Fabricio Santos in Brazil and Tatyiana Karafet at the University of Arizona, have shown evidence that this Native American "Adam" lived in Siberia.

There have also recently been studies on the relative migration rates of men and women. Mark Seielstad at Harvard University has determined that between different populations, there is much more similarity in mitochondrial DNA than in the Y chromosomal DNA. This means that women moved and migrated more often than men, a view dissimilar to the common "Man the Conqueror" idea.

It is clear that analysis of DNA polymorphisms has become a very powerful tool for anthropologists and historians. It should be noted, however, that the history of population migrations is not simple. Although "Adam" and "Eve" lived in Africa, scientists believe that their offspring migrated to Asia only to eventually return again. DNA analysis, however, provides a useful tool for anthropologists trying to determine how we got where we are now. Here is a collection of websites for further information on this exciting new technique.

* DNA Learning Center Solving the Mystery of the Romanovs

* Related Articles "America's Founding Fathers May Have Siberian Roots" - Daily InScight - May 1999

* Offline References Gibbons, Ann. 1997. "Y Chromosome Shows That Adam Was an African." Science October 31; 278: 804-805.
* Braginski, Ricardo, and Diego Hurtado de Mendoza. 1999 "Y Chromosomes Point to Native American Adam." Science March 5; 283: 1439-1440.
* Stoneking, Mark. 1998 "Women on the move." Nature Genetics November 20; 20:219-220.

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A Different Twist: Mitochondria can be inherited from both parents

23 August 23, 2002 -- NewScientist.com news service

Mitochondria may not be inherited solely through the maternal line, according to new research that promises to overturn accepted biological wisdom.

If confirmed by other researchers, the findings could have huge implications for evolutionary biology and biochemistry.

Robert Sanders Williams, from Duke University Medical Center in North Carolina, says the findings are "remarkable and unanticipated. This is more than a mere curiosity. It asserts the principle that it can occur in humans. It could have significant implications for the study of human evolution and the migrations of populations," he says.

For decades biologists have assumed that mitochondria - the cells' power stations - are inherited solely through the maternal line.

Mitochondria in the sperm from the father were presumed to be destroyed immediately after conception, leaving behind only those from the mother. But Marianne Schwartz and John Vissing from the University Hospital Rigshospitalet in Copenhagen, have discovered that one of their patients inherited the majority of his mitochondria from his father.

"Even with very sensitive methods, paternal mitochondrial DNA has never been detected in man before," Schwartz told Reuters. "There are many examples of family pedigrees that follow mitochondrial diseases through the maternal line."

Little oxygen

The pair made the discovery while trying to discover why one of their patients suffered extreme fatigue during exercise. The 28-year-old man had an entirely normal heart and lungs and his muscles appeared healthy. But on closer inspection, Schwartz and Vissing discovered that his muscles absorbed very little oxygen.

This led them to examine the genetic sequence of his mitochondria. They discovered two mutations in his mitochondrial DNA - one of which was responsible for his extreme fatigue.

To try and investigate the mutations further, they also sequenced the DNA of his mother, father and uncle. To their surprise, the sequence matched those of his father and uncle.

Spontaneous mutation

Muscle biopsies showed that about 90 per cent of his mitochondria came from his father. However, the mitochondria in his blood, hair roots and fibroblasts came entirely from his mother.

The two mutations appear to have arisen spontaneously during, or shortly after, conception.

The researchers think inheritance of paternal mitochondrial DNA is probably very rare. But the findings will have implications for a number of branches of biology. Evolutionary biologists often date the divergence of species by the differences in genetic sequences in mitochondrial DNA. Even if paternal DNA is inherited very rarely, it could invalidate many of their findings. It will also have implications for scientists investigating inherited metabolic diseases.

Journal reference: New England Journal of Medicine (vol 347, p576)

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The use of mitochondrial mtDNA to investigate human history is not without drawbacks.

The rate of mtDNA mutation is not well known. A study by Parsons et al. (1997) found a rate 20 times higher than that calculated from other sources. In an article reviewing mtDNA research, Strauss (1999a) reports that mtDNA mutation rates differ in some groups of animals, and can even vary dramatically in single lineages. Although there are many agreements, some divergence dates for modern animals calculated from mtDNA do not match with what is known from the fossil record. There are suggestions from a few sources that paternal mtDNA can sometimes be inherited, which could affect analyses based on mtDNA.

In 1999 Awadalla et al. published a study suggesting that mtDNA could sometimes be inherited from fathers. If mtDNA is inherited only from mothers, the correlation between different mutations should not depend on how far apart on the genome they were. Instead, their measurements showed that mutations at distant sites on the mtDNA genome were less likely to be correlated than nearby mutations, suggesting that mtDNA from mothers and fathers could sometimes get mixed. However, there is no explanation so far as to how this recombination could be occurring, and the possibility that other phenomena could be causing this effect has not yet been disproved. If it occurs, mixing would mean that the dates from current mtDNA studies would be too old. If mixing is common enough, it could even mean that there was no mitochondrial Eve, because different parts of the mtDNA molecule would have different histories. (Awadalla et al. 1999, Strauss 1999b) Other studies, however, have contradicted these results and argued for strictly maternal mtDNA inheritance (Elson et al. 2001).

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lunes, 15 de octubre de 2012

The African Diaspora: Mitochondrial DNA and the Atlantic Slave Trade

Abstract

Introduction

Material and Methods

Population Samples

Phylogeographic Analysis

Admixture Analysis

Results

Data Summaries and Demography

Haplogroup Frequency Profiles

Admixture Analysis

Haplogroup Composition of American mtDNAs of African Ancestry

African mtDNAs in Eurasia

Discussion

Acknowledgments

Electronic-Database Information

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