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Brief Communication: mtDNA variation in North Cameroon: Lack of Asian lineages and implications for back migration from Asia to Sub-Saharan Africa
Abstract
The hypervariable region-1 and four nucleotide positions (10400, 10873, 12308, and 12705) of the coding region of mitochondrial DNA (mtDNA) were analyzed in 441 individuals belonging to eight populations (Daba, Fali, Fulbe, Mandara, Uldeme, Podokwo, Tali, and Tupuri) from North Cameroon and four populations (Bakaka, Bassa, Bamileke, and Ewondo) from South Cameroon. All mtDNAs were assigned to five haplogroups: three sub-Saharan (L1, L2, and L3), one northern African (U6), and one European (U5). Our results contrast with the observed high frequencies of a Y-chromosome haplogroup of probable Asian origin (R1*-M173) in North Cameroon. As a first step toward a better understanding of the evident discrepancy between mtDNA and Y-chromosome data, we propose two contrasting scenarios. The first one, here termed "migration and asymmetric admixture," implies a back migration from Asia to North Cameroon of a population group carrying the haplotype R1*-M173 at high frequency, and an admixture process restricted to migrant males. The second scenario, on the other hand, temed "divergent drift," implies that modern populations of North Cameroon originated from a small population group which migrated from Asia to Africa and in which, through genetic drift, Y-chromosome haplotype R1*-M173 became predominant, whereas the Asian mtDNA haplogroups were lost.
... Under a standard neutral model, both θ π and θ W estimate the population parameter θ = 4Neμ, where Ne is the effective population size and u is the mutation rate per generation. Divergence between humans and chimpanzees were calculated as the average number of nucleotide substitutions per site, k, between one chimpanzee and 46 humans using Kimura's two-parameter model [33]. Under a neutral model, the amount of divergence, k, between sequences drawn from two species is given by k = 2μt + 4N e μ where t is the time in generations since the species have diverged, μ is the mutation rate per generation, and N e is the ancestral effective population size [34]. ...
... To compare maternally and paternally inherited patterns of variation, we re-examined 366 bp of mtDNA HVS1 sequence data compiled from a number of previous studies. 12,[31][32][33] The data set includes 39 populations from the major language groups: Khoisan (!Kung1, !Kung2, Khwe, Hadza), Nilo-Saharan (Kanuri, Songhai, Turkana, Nubian, Sudanese, Mbuti, Datoga), Afroasiatic (Moroccan Berber, non-Berber Moroccan, Egyptian, Algerian Mozabite, Tuareg, Somalian, Amhara, Hausa, Podokwo, Mandara, Uldeme, Iraqw), Niger-Congo non-Bantu (Fulbe ¼ Fulfulde, Yoruba, Serer, Wolof, Mandinka, Tupuri), and Niger-Congo Bantu (Bubi, Fang, Biaka, Kikuyu, Mozambique1, Mozambique2, Bakaka, Bassa, Mbenzele, Sukuma) ( Figure 1). Some populations represented in the original data sets 12,31 -33 were omitted because they are not found on the African mainland, are Cameroonian populations not represented in the Y chromosome data set, 33 or because linguistic designations could not be inferred. ...
... Given that levels of population differentiation can be influenced by (1) sample composition and the Y chromosomal and mtDNA data sets presented here are sampled differently, (2) the differing rates and modes of evolution characterized by the Y chromosome and mtDNA systems, and (3) the type of polymorphisms examined (eg, preascertained Y chromosome SNPs versus mtDNA HVS1 sequence data), direct comparisons between these haploid Figure 1 Map of Africa. The approximate location of 40 populations typed for Y chromosome markers in this study (K) and 39 populations surveyed for HVS1 sequence data 12,31,32,33 (J) are indicated. The distribution of the four African language families was constructed using Greenberg's 39 classifications and further refined with data from the ethnologue (http://www.ethnologue.com/). ...
... Here is another example. In the same paper (Winters, 2011) he writes on "widespread distribution of R1*-M173 in Africa, that ranges between 7% -95% and averages 39% (Coia et al., 2005)". He repeats the same "quotation" in yet another paper (Winters, 2010)-"The frequency of Y-chromosome R1*-M173 in Africa range between 7% -95% and averages 39.5% (Coia et al., 2005)". ...
... In the same paper (Winters, 2011) he writes on "widespread distribution of R1*-M173 in Africa, that ranges between 7% -95% and averages 39% (Coia et al., 2005)". He repeats the same "quotation" in yet another paper (Winters, 2010)-"The frequency of Y-chromosome R1*-M173 in Africa range between 7% -95% and averages 39.5% (Coia et al., 2005)". However, in the referenced paper Coia et al. (2005) describe the frequency of R1*-M173 only in Cameroon, "with the highest frequency in North Cameroon (from 6.7% among the Tali to 95.2% among the Uldeme". ...
... He repeats the same "quotation" in yet another paper (Winters, 2010)-"The frequency of Y-chromosome R1*-M173 in Africa range between 7% -95% and averages 39.5% (Coia et al., 2005)". However, in the referenced paper Coia et al. (2005) describe the frequency of R1*-M173 only in Cameroon, "with the highest frequency in North Cameroon (from 6.7% among the Tali to 95.2% among the Uldeme". Mr. Winters did not mention that the figures were related not to "widespread distribution in Africa", but specifically to North Cameroon, which is known since at least 2002 (Cruciani et al., 2002(Cruciani et al., , 2010. ...
... German colonials used the name "Bamileke" as a blanket referral to the various groups of people in this region (7) and a common culture unifies all the Bamileke subgroups historically, linguistically, and culturally as an ethnic group. The Bamileke samples presented in this study are compared to the Bamileke samples from Coia et al. (8). We also compare the analysis of the Fulbe by Coia et al. (8) with the HVS-1 study of Cameroonian Fulani by Cerny et al. (9). ...
... Fulani is another name for the Fulbe ethnic group, which are also referred to as Fula, Peul, Peulh, or Fulfude. For consistency in this paper, we refer to both Coia et al. (8) and Cerny et al. (9) samples as Fulbe. Historically, the Fulbe are nomadic herders who have lived across much of West Africa. ...
... Historically, the Fulbe are nomadic herders who have lived across much of West Africa. The Fulbe that reside in Cameroon live in the extreme northern regions of the country, where many neighboring ethnic groups have assimilated much of the Fulbe culture, religion, and language (5,8). The Bamileke and Fulbe are typical of many ethnic groups in Cameroon (and Africa for that matter), because of their complex history of migrations and assimilations with many major and minor ethnic groups. ...
Since the sample sizes for forensic cases, as well as studies of African ethnic groups, are usually low, and independent samples are rare, it has been difficult to determine whether small samples contain an accurate representation of a sampled population. In this study, two independent samples of the Bamileke had similar values with regard to standard and molecular diversity indices and selective neutrality. The two Fulbe samples were also similar, but they differed with respect to selective neutrality values. In both ethnic groups, shared haplotypes were present at low frequencies. However, the Fulbe had fewer exclusive matches with outside ethnic groups compared to the Bamileke. Nevertheless, in both ethnic groups, within-group matches were more common than matches to any other Cameroonian ethnic group. Only a small percentage of the observed mtDNA haplotypes have the potential for being ethnic and/or region specific. To assess this potential, sample sizes will have to be orders of magnitude larger in order to observe significant numbers of those relatively rare haplotypes. However, as database size is increased, haplotype sharing will correspondingly increase; and many haplotypes that are common in a single ethnic group will also be found in multiple ethnic groups.
... In Asia the frequency of haplotype M173 is as follows: Anatolia 0.19%, Iran 2.67%, Iraq 0.49% Oman 1.0%, Pakistan 0.57% and Oman 1.0% (Abu-Amero et al, 2009). This contrast sharply with the widespread distribution of R1*-M173 in Africa, that ranges between 7-95% and averages 39% (Coia et al, 2005); but no trace of Eurasiatic maternal lineages in West Central Africa. Y-chromosome R1 is found throghout Africa. ...
... Y-chromosome R1 is found throghout Africa. The pristine form of R1-M173 is only found in Africa (Coia et al, 2005;Cruciani et al, 2002Cruciani et al, , 2010. The age of ychromosome R is 27ky. ...
... ISOGG 2010 Y-DNA haplogroup tree makes it clear that V45 is phylogenetically equivalent to M207.The most common R haplogroup in Africa is R1 (M173). The predominant haplogroup is R1b (Berniell-Lee et al,2009;Coia et al, 2005;Winters, 2010b;Wood et al, 2009). Cruciani et al (2010) discovered new R1b mutations including V7, V8, V45, V69, and V88. ...
The Eurasian y-chromosome haplogroup R is found in Africa we need to determine if its existence indicates a back migration from Asia. We analyze the varied R haplogroups in Africa to determine their distribution and clade among and within Sub-Saharan populations. Haplogroup R is found among all African populations and linguistic groups including Khoisan and Pygmies. The widespread distribution of R-V88 and R1b globally across Africa may indicate an African origin for R-M173. KEYWORDS: Y-chromosome haplogroup haplotype phylogeography. INTRODUCTION According to Underhill the geographical origin of y-chromosome R1b is situated in Eurasia. As a result, these researchers believed that the R y-chromosome haplogroup in Africa suggest a back migration from Asia to Africa (Cruciani, et al, 2010). Cruciani et al (2010), assume that the phylogeographic y-haplotype analyses suggest that Asia was probably the home for y-chromosome M173 and that the presence of haplotype M173 is due to a back migration from Asia since haplogroup R chromosomes were found in Cameroon (2002). Although this is Cruciani et al (2010), we test the hypothesis that opinion the phylogeography, diversity and widespread nature of M173 across the African continent implies that haplotype M173 probably originated in Africa, and that it expanded into Asia recently. MATERIALS AND METHODS The aggregated African populations with an R-M173 DNA profile were disaggregated to determine the distribution of R-M173 in Sub-Saharan Africa. We analyzed the y-chromosome sequences of the R haplogroup from Africa and Asia.This review of prior literature on macrohaplogroup R allowed us to critically look at the distribution of R lineages across the African continent.
... The rare L0f lineages are present and more diverse only in East Africa, where they likely arose 85-90 kya (Fig.1), with their highest incidence in Tanzanians (Knight et al., 2003;Brandstätter et al., 2004;Tishkoff et al., 2007;Behar et al., 2008;Castri et al., 2009). L0a lineages probably originated in eastern Africa in Paleolithic times at about 40-55 kya Salas et al., 2002;Behar et al., 2008;Soares et al., 2009) and are today widely spread through eastern, central and southern Africa, in some cases encompassing more than a quarter of maternal lineages there Chen et al., 2000;Salas et al., 2002Kivisild et al., 2004;Coia et al., 2005;Gonder et al., 2006;Tishkoff et al., 2007;Quintana-Murci et al., 2008;Castri et al., 2009;Coelho et al., 2009). The L0a1 sub-clade has an eastern and southeastern African distribution including Nubia, Sudan and Ethiopia, with the root type coalescing at nearly 30 kya (Salas et al., 2002;Behar et al., 2008;Soares et al., 2009). ...
... MtDNA L1 lineages are found to coalesce at about 140-150 kya (Fig.1). One of its daughter clades, haplogroup L1b, is concentrated in western-central Africa, particularly along the coastal areas Rando et al., 1998;Brehm et al., 2002;Rosa et al., 2004;Coia et al., 2005;González et al., 2006), peaking in the Senegal Mandenka and Wolof (Rando et al., 1998;Jackson et al., 2005) and Fulani people in Burkina-Faso, Chad and South Cameroon (Cerný et al., 2006) (Fig.2). The extant variation of L1b probably mirrors a clear-cut example of a bottleneck that has shaped its evolution, leaving no other progeny except a clade that began expanding at about 30 kya (Salas et al., 2002;Kivisild et al., 2004;Rosa et al., 2004;Behar et al., 2008). ...
... Its sister clade L1c occurs frequently in Central and West Africans (Rando et al., 1998;Brehm et al., 2002;Cerný et al., 2004;Coia et al., 2005;Jackson et al., 2005;González et al., 2006;Batini et al., 2007), representing over 70% of the maternal legacy of many Pygmy groups Destro-Bisol et al., 2004;Quintana-Murci et al., 2008) (Fig.2). Curiously, more recent reports state frequencies ranging 18-25% in Angola Bantu ethnic groups (Beleza et al., 2005;Coelho et al., 2009). ...
The mitochondrial DNA (mtDNA) genetic system has long proven to be useful for studying the demographic history of our species, since their proposed Southeast/East African origin 200 kya. Despite the weak archaeological and anthropologic records, which render a difficult understanding of early intra- continental migrations, the phylogenetic L0-L1'6 split at about 140-160 kya is thought to represent also an early sub-structuring of small and isolated communities in South and East Africa. Regional variation accumulated over the following millennia, with L2 and L3 lineages arising in Central and East Africa 100-75 kya. Their sub-Saharan dispersal not later than 60 kya, largely overwhelmed the L0'1 distribution, nowadays limited to South African Khoisan and Central African Pygmies. Cyclic expansions and retractions of the equatorial forest between 40 kya and the "Last Glacial Aridity Maximum" were able to reduce the genetic diversity of modern humans. Surviving regional-specific lineages have emerged from the Sahelian refuge areas, repopulating the region and contributing to the overall West African genetic similarity. Particular L1- L3 lineages mirror the substantial population growth made possible by moister and warmer conditions of the Sahara's Wet Phase and the adoption of agriculture and iron smelting techniques. The diffusion of the farming expertise from a Central African source towards South Africa was mediated by the Bantu people 3 kya. The strong impact of their gene flow almost erased the pre-existent maternal pool. Non-L mtDNAs testify for Eurasian lineages that have enriched the African maternal pool at different timeframes: i) Near and Middle Eastern influences in Upper Palaeolithic, probably link to the spread of Afro-Asiatic languages; ii) particular lineages from West Eurasia around or after the glacial period; iii) post-glacial mtDNA signatures from the Franco-Cantabrian refugia, that have crossed the Strait of Gibraltar and iv) Eurasian lineages tracing back to the Neolithic or more recent historical episodes. Finally, the non-random sub-Saharan spread of North African lineages was likely mediated by the ancestors of Fulani, nomadic pastoral communities in the Sahel.
... The R-P25* haplogroup has been found in Europe, W est and East Asia (Cruciani et al., 2010).Figure 1 shows the frequency of R1*-M173 in Africa and Eurasia. InThe frequency of Y-chromosome R1*-M173 in Africa range between 7-95% and averages 39.5% (Coia et al., 2005). The R*-M173 (haplotype 117) chromosome is found frequently in Africa, but rare to extremely low frequencies in Eurasia. ...
... remely low frequencies in Eurasia. The Eurasian R haplogroup is characterized by R1b3-M269. The M269 derived allele has a M207/M173 background. InFig. 1 we provide the frequencies of ychromosome M-173 in Africa and Eurasia. Whereas only between 8 and 10% of M-173 is carried by Eurasians, 82% of the carriers of this y-chromosome are found in Africa. Coia et al. (2005) provides substantial data that the presence of R1*-M173 did not follow the spread of the spread of mtDNA haplogroup U6 in Sub-Saharan Africa, which is found in North Africa (Coia et al., 2005). This suggest that R1*-M173 may not be the result of back migration from Asia if this theory depends on the spread of haplogroup U6 in areas wher ...
... Whereas only between 8 and 10% of M-173 is carried by Eurasians, 82% of the carriers of this y-chromosome are found in Africa. Coia et al. (2005) provides substantial data that the presence of R1*-M173 did not follow the spread of the spread of mtDNA haplogroup U6 in Sub-Saharan Africa, which is found in North Africa (Coia et al., 2005). This suggest that R1*-M173 may not be the result of back migration from Asia if this theory depends on the spread of haplogroup U6 in areas where R1*-M173 is found. ...
In this paper we discuss the role of the Kushites in the spread of R1*-M173. Human y-chromosome haplogroup R1*-M173 is mainly found in Africa. Haplogroup R1*-M173 is the pristine form of haplogroup R. In Africa researchers have detected frequencies as high as 95% among Sub-Saharan Africans. The phylogenetic, craniometric, textual, historical and linguistic evidence support the dem ic diffusion of Niger- Congo (Nilo-Saharan) carriers of R1*-M173 from Africa to Eurasia between 4-5kya.
... The most frequent haplotype (n = 10), corresponding to the U5b1b1b clade, is one mutational step away (np 16320) from a node with equal amount of samples from Crete, Austria, and Germany (see Supplementary Figure S2). Clade U5b1b1b is regarded as specifijic to West Africa, associated to the Serer, Wolof, and Fulani populations from Senegal and northern Cameroon (Rando et al. 1998;Achilli et al. 2005;Coia et al. 2005;Cerny et al. 2006). The scarcity of HVR2 sequences of samples from these populations explains why this most frequent U5b control region haplotype in Puerto Rico fijinds a match only with a Spanish sample. ...
... The latter connection is likely due to back-migration. U5b1b1b is common among the nomad Fulani of West Africa and the Wolof and Serer populations of Senegambia (Rando et al. 1998;Rosa et al. 2004;Achilli et al. 2005;Coia et al. 2005). Its ancestral clade U5b1b (control region motif 16189-16192-16270-73-150-263) has been proposed together with haplogroups H1, H3, and V to represent hunter-gatherer migrations from the Franco-Cantabrian refuge to North Africa during the Ice Age (Achilli et al. 2005). ...
Maternal lineages of West Eurasian and North African origin account for 11.5% of total mitochondrial ancestry in Puerto Rico. Historical sources suggest that this ancestry arrived mostly from European migrations that took place during the four centuries of the Spanish colonization of Puerto Rico. This study analyzed 101 mitochondrial control region sequences and diagnostic coding region variants from a sample set randomly and systematically selected using a census-based sampling frame to be representative of the Puerto Rican population, with the goal of defining West Eurasian–North African maternal clades and estimating their possible geographical origin. Median-joining haplotype networks were constructed using hypervariable regions 1 and 2 sequences from various reference populations in search of shared haplotypes. A posterior probability analysis was performed to estimate the percentage of possible origins across wide geographic regions for the entire sample set and for the most common haplogroups on the island. Principal component analyses were conducted to place the Puerto Rican mtDNA set within the variation present among all reference populations. Our study shows that up to 38% of West Eurasian and North African mitochondrial ancestry in Puerto Rico most likely migrated from the Canary Islands. However, most of those haplotypes had previously migrated to the Canary Islands from elsewhere, and there are substantial contributions from various populations across the circum-Mediterranean region and from West African populations related to the modern Wolof and Serer peoples from Senegal and the nomad Fulani who extend up to Cameroon. In conclusion, the West Eurasian mitochondrial ancestry in Puerto Ricans is geographically diverse. However, haplotype diversity seems to be low, and frequencies have been shaped by population bottlenecks, migration waves, and random genetic drift. Consequently, approximately 47% of mtDNAs of West Eurasian and North African ancestry in Puerto Rico probably arrived early in its colonial history.
... There has been some discussion of the degree of genetic isolation of these groups from one another (MacEachern, 2001;Spedini et al., 1999Spedini et al., , 2001), but by 2006 their extensive interactions with neighbouring populations was not really in doubt. Moreover, genetic research demonstrates significant connections between these Chadic-speaking populations and populations in West Asia, the Nile Valley and Northern/Northeastern Africa ( Cerny et al., 2004;Coia et al., 2005;Cruciani et al., 2002), as well as with other, sub-Saharan populations ( Sansonetti et al., 1992;Spedini and Destro-Bisol, 1988;Spedini et al., 1999). These relationships exist in mtDNA, non-recombining Y-chromosomal (NRY) and autosomal genetic features, but again these relations are complex. ...
... Thus, NRY data indicate substantial frequencies of a West Asianderived haplogroup (R1*-M173 [haplotype 117]) among Chadic-speaking populations (especially the Uldemé, where the frequency of this haplogroup approaches 95%), implying a significant male contribution from ultimately West Asia (or possibly North Africa) to the local gene pool ( Cruciani et al., 2002; Figure 3). There is less evidence in the mtDNA data for such a contribution by immigrant women, and the limited evidence that does exist indicates a North African origin for such a contribution ( Coia et al., 2005). It is not uncommon to find significant differences in mtDNA and NRY characteristics of the same population, as the two systems are inherited independently of one another. ...
For the most part, the boundaries of African Studies remain fixed at the shores of that continent, with periodic excursions into diasporic communities across the seas. The northern limits of this enquiry into `Africa' are, however, more vaguely located, placed somewhere in the Sahara when they are thought of at all. This imprecision in the northern frontiers of `Africa' is closely related to traditional conceptions of race on the continent, and especially of a distinction between `Negroid' and `Caucasoid' peoples and histories. Recent genetic research in and to the south of the Sahara suggests that such distinctions are false, and that human biological variability in these regions does not accord with racialized models. Nevertheless, such models continue to be widely used in popular interpretations of events in these regions — most strikingly, today, in Darfur.
... In particular, many studies have demonstrated that continental origin can be readily inferred by classification into known mtDNA haplogroups (24)(25)(26). In Africa, these haplogroups appear to be differentially distributed across the continent (27)(28)(29)(30)(31)(32)(33)(34)(35)(36)(37). Some recent mtDNA studies have shown differential regional African admixture in African Diaspora from North America, Central ⁄ Caribbean America, and South America, with the first two showing higher west African percentages and the latter higher West-Central African (26,38,39). ...
... When performing genetic comparisons with other published data, a shorter range was used to accommodate those data sets. The following African mtDNA data were used for comparisons: a total of 1661 from West Africa that include 240 from Senegal (44)(45)(46), 204 from Mali (31,47), 372 from Guinea-Bissau (48), 393 from Sierra Leone (32,49), 160 from Nigeria ⁄ Niger (46,50), and 292 from Cabo Verde (51); a total of 1132 from West-Central Africa includes 673 from Cameroon (29,30,52), 74 from Central African Republic (46,50,53), 153 from Sao Tome (54,55), 55 from Equatorial Guinea (54,56), 23 from Democratic Republic of Congo (39,46,50), 110 from Cabinda (27), and 44 from Angola (36); a total of 659 from East Africa include 65 from Sudan (57), 289 from Ethiopia ⁄ Eritrea (33,58), 161 from Kenya (28,46), 27 from Somalia (46), and 117 from Tanzania (34,50); a total of 416 from Southeast Africa mostly from Mozambique (35,37). Also, published data from African Diaspora included 1065 African-Americans (59), 73 Gullah-speaking African-Americans (47), 168 Dominicans (3,4), eight Mexicans (60), 25 Belize (61), 41 Choco from Columbia, 37 Garifuna from Panama ⁄ Belize (62), and 298 Brazilians (24,39,63). ...
Very little genetic data exist on Haitians, an estimated 1.2 million of whom, not including illegal immigrants, reside in the United States. The absence of genetic data on a population of this size reduces the discriminatory power of criminal and missing-person DNA databases in the United States and Caribbean. We present a forensic population study that provides the first genetic data set for Haiti. This study uses hypervariable segment one (HVS-1) mitochondrial DNA (mtDNA) nucleotide sequences from 291 subjects primarily from rural areas of northern and southern Haiti, where admixture would be minimal. Our results showed that the African maternal genetic component of Haitians had slightly higher West-Central African admixture than African-Americans and Dominicans, but considerably less than Afro-Brazilians. These results lay the foundation for further forensic genetics studies in the Haitian population and serve as a model for forensic mtDNA identification of individuals in other isolated or rural communities.
... and have settled in distant and environmentally different areas. This expectation is met by genetic evidence based mainly on unilinear markers, which showed that the Podokwo and Uldeme probably experienced a back migration from Asia and some genetic influence from North Africa (Cruciani et al., 2002;Coia et al., 2005;Wood et al., 2005), whereas the Ewondo and Bamileke had been influenced by neighbouring Bantu populations (Spedini et al., 1999;Cruciani et al., 2002;Coia et al., 2005). Our HLA data support the genetic diversity between the two population pairs and also highlights the similarity between neighbouring populations. ...
... and have settled in distant and environmentally different areas. This expectation is met by genetic evidence based mainly on unilinear markers, which showed that the Podokwo and Uldeme probably experienced a back migration from Asia and some genetic influence from North Africa (Cruciani et al., 2002;Coia et al., 2005;Wood et al., 2005), whereas the Ewondo and Bamileke had been influenced by neighbouring Bantu populations (Spedini et al., 1999;Cruciani et al., 2002;Coia et al., 2005). Our HLA data support the genetic diversity between the two population pairs and also highlights the similarity between neighbouring populations. ...
HLA class I diversity (loci A, B and C) was analysed in four populations, two from North Cameroon (Podokwo and Uldeme) and two from South Cameroon (Ewondo and Bamileke). Northern and southern Cameroon populations show a substantial genetic diversity in terms of haplotype sharing and genetic distances, even despite the low percentage of variance due to differences among populations evidenced by analysis of molecular variance. The signals of differentiation among populations are consistent with their linguistic affiliation, and support previous evidence, based on autosomal microsatellites and protein loci, which has shown that the complex pattern of genetic variation of Cameroon can in part be described by contrasting the northern and southern part of the country. Looking at our results in the more general framework of HLA diversity in sub-Saharan Africa, it turns out that the Podokwo and Uldeme show some genetic links to populations of the southern western branch of the Sahel corridor, while their high frequency of A*02 and C*04 alleles is congruent with previously hypothesised introgression of non-sub-Saharan alleles. On the other hand, signals of shared ancestry between the Bamileke and Ewondo and the Bantu speakers from central and southern Africa were detected.
... This has been presented as evidence for a possible back migration from Asia to sub-Saharan African through the Levantine corridor. However, mtDNA showed no such signal, suggesting that admixture of the immigrating group was primarily male-mediated, at least once they reached their destination ( Coia et al. 2005). ...
... However the mtDNA data are still very heterogeneous with many different types showing a mostly Central African connection but with possible gene flow from East Africa and from West Africa ( Cerny et al. 2004;Cerny et al. 2007) as well as a small North African influence ( Coia et al. 2005), demonstrating that the Sahel along which the Chad Basin lies has been a major corridor for human migration in Africa. ...
Sub-Saharan Africa is believed to possess more human genetic diversity than any other region of the world, a likely consequence of it being the probable place of origin of anatomically modern man. Despite its evolutionary importance studies into the distribution of this genetic variation have been somewhat limited in comparison to Europe, Asia and the Americas, especially with respect to fine-scale studies that would help elucidate local histories and the consequences of ethnic and linguistic interactions. Another possible consequence of knowledge of genetic diversity is that much information of functionally important genetic variants that are potentially relevant to pharmacogenetic research is not available. This lack of information can add to an already prevalent Eurocentric ascertainment bias in current knowledge of genetic variation, depriving sub-Saharan Africa communities of the potential medical benefits pharmacogenetics has to offer. This thesis describes three case studies that form part of an investigation into human genetic variation in sub-Saharan Africa.
Chapter 2 uses sex-specific genetic systems to successfully differentiate between two alternative oral histories of the ethnogenesis of the Nso’ people of Cameroon. Chapter 3 establishes that substantial male and female gene flow has occurred among the peoples of the Cross River region of Nigeria, a region that includes multiple ethnic groups speaking distinct languages that appear to have separated hundreds and thousands of years ago. Chapter 3 demonstrates that the drug metabolising enzyme Flavin-containing Monooxygenase 2, which has been shown to be non-functional in all Europeans and Asian individuals collected to date, has a putative functional allele in approximately one third of sub-Saharan Africans, a finding that may have important implications for therapeutic intervention strategies and xenobiotic exposure. This thesis demonstrates inter alia the value of conducting genetic studies in sub-Saharan Africa using large datasets of well known provenance.
... Meanwhile, human haplogroup U5b1b frequencies in the Saami (47.6%) (Tambets et al., 2004) are comparable to sub-haplogroup D1 frequencies in their associated dogs (Swedish Lapphund: 100%, Finnish Lapphund: 64.7%, and Lapponian Herder: 75%) (Klütsch et al., 2011). Further, U5b1b occurs in low frequencies in West Africa, such as 2.7% in Senegambia (Rosa et al., 2004) and Cameroon (Coia et al., 2005), similar to frequencies of D1 in indigenous dogs (about 2.0% in Nigeria). Thus, the synthesis of our discoveries and previous analyses reveals similar genographic patterns for human U5b1b and dog D1. ...
Domestic dogs have an ancient origin and a long history in Africa. Nevertheless, the timing and sources of their introduction into Africa remain enigmatic. Herein, we analyse variation in mitochondrial DNA (mtDNA) D-loop sequences from 345 Nigerian and 37 Kenyan village dogs plus 1530 published sequences of dogs from other parts of Africa, Europe and West Asia. All Kenyan dogs can be assigned to one of three haplogroups (matrilines; clades): A, B, and C, while Nigerian dogs can be assigned to one of four haplogroups A, B, C, and D. None of the African dogs exhibits a matrilineal contribution from the African wolf (Canis lupus lupaster). The genetic signal of a recent demographic expansion is detected in Nigerian dogs from West Africa. The analyses of mitochondrial genomes reveal a maternal genetic link between modern West African and North European dogs indicated by sub-haplogroup D1 (but not the entire haplogroup D) coalescing around 12,000 years ago. Incorporating molecular anthropological evidence, we propose that sub-haplogroup D1 in West African dogs could be traced back to the late-glacial dispersals, potentially associated with human hunter-gatherer migration from southwestern Europe.
... Meanwhile, human haplogroup U5b1b frequencies in the Saami (47.6%) (Tambets et al., 2004) are comparable to sub-haplogroup D1 frequencies in their associated dogs (Swedish Lapphund: 100%, Finnish Lapphund: 64.7%, and Lapponian Herder: 75%) (Klütsch et al., 2011). Further, U5b1b occurs in low frequencies in West Africa, such as 2.7% in Senegambia (Rosa et al., 2004) and Cameroon (Coia et al., 2005), similar to frequencies of D1 in indigenous dogs (about 2.0% in Nigeria). Thus, the synthesis of our discoveries and previous analyses reveals similar genographic patterns for human U5b1b and dog D1. ...
Domestic dogs have an ancient origin and a long history in Africa. Nevertheless, the timing and sources of their introduction into Africa remain enigmatic. Herein, we analyse variation in mitochondrial DNA (mtDNA) D-loop sequences from 345 Nigerian and 37 Kenyan village dogs plus 1530 published sequences from dogs from other parts of Africa, Europe and West Asia. All Kenyan dogs can be assigned to one of three haplogroups (matrilines; clades): A, B, C, while Nigerian dogs can be assigned to one of four haplogroups A, B, C, and D. None of the African dogs exhibits a matrilineal contribution from the African wolf (Canis lupus lupaster). The genetic signal of a recent demographic expansion is detected in Nigerian dogs from West Africa. The analyses of mitochondrial genomes reveal a maternal genetic link between modern West African and North European dogs indicated by sub-haplogroup D1 (but not the entire haplogroup D) coalescing around 12,000 years ago. Incorporating molecular anthropological evidence, we propose that sub-haplogroup D1 in West African dogs could be traced back to the late-glacial dispersals, potentially associated with human hunter-gatherer migration from southwestern Europe.
... The final major dispersion of human groups was into the Americas and is estimated to have occurred 30,000 to 15,000 years ago [25]. In addition to movement out of Africa, mitochondrial data also support back migrations to Africa from different regions of the world [26,27]. ...
Within genetic anthropology, mitochondrial DNA (mtDNA) has garnered a prominent if not enduring place within the anthropological toolkit. MtDNA has provided new and innovative perspectives on the emergence and dispersal of our species, interactions with extinct human species, and illuminated relationships between human groups. In this paper, I provide a brief overview of the major findings ascertained from mtDNA about human origins, human dispersal across the globe, interactions with other hominin species, and the more recent uses of mtDNA in direct to consumer ancestry tests. Relative to nuclear DNA, mtDNA is a small section of the genome and due to its inheritance pattern provides a limited resolution of population history and an individual’s genetic ancestry. Consequently, some scholars dismiss mtDNA as insignificant due to the limited inferences that may be made using the locus. Regardless, mtDNA provides some useful insights to understanding how social, cultural, and environmental factors have shaped patterns of genetic variability. Furthermore, with regard to the experiences of historically marginalized groups, in particular those of African descent throughout the Americas, mtDNA has the potential to fill gaps in knowledge that would otherwise remain unknown. Within anthropological sciences, the value of this locus for understanding human experience is maximized when contextualized with complementary lines of evidence.
... , Banhu (1), Beafada(19), Bijagò(22), Brame(8), Cassanga(6), Diola(29), Landoma (1), Lebou (4), Manjaco(32), Mankanya(20), Mansonca(18), Nalu(26), Papel (23), Sahalle (1), Serer (30), ‡ Songhai/Sonrhai -Nilo-Saharan speakers of Nigeria and Mali (10+6) -were left out of the analysis MDS clustering of W/WC Africa divided by geography. We first divided our mtDNA dataset of non-Bantu speaking and non-Pygmy populations of NW/W/WC/C Africa based on geographical location/political clusters into 10 countries: Burkina Faso, Cameroon "other", Chad, Guinea-Bissau, Mali, Mauritania + Western Sahara, Niger, Nigeria, Senegal, and Sierra Leone. ...
This file contains Tables S1–S8, Figures S1–S7, Text S1, and References S1.
(2.96 MB PDF)
... Overall, the results indicate that K1f has been lost from present-day populations, rather than being a rare haplotype undetected due to inadequate sampling. With a binomial distribution 13,14 given the size of our dataset, we estimated (with a 95% of probability) that the K1f lineage should not occur with a frequency above 0.3%. In addition, the most parsimonious phylogenetic tree showed that there exist no intermediate haplotypes connecting the Tyrolean Iceman's lineage to the main root of K1 (Fig. 2). ...
The Tyrolean Iceman is an extraordinarily well-preserved natural mummy that lived south of the Alpine ridge ~5,200 years before present (ybp), during the Copper Age. Despite studies that have investigated his genetic profile, the relation of the Iceman´s maternal lineage with present-day mitochondrial variation remains elusive. Studies of the Iceman have shown that his mitochondrial DNA (mtDNA) belongs to a novel lineage of haplogroup K1 (K1f) not found in extant populations. We analyzed the complete mtDNA sequences of 42 haplogroup K bearing individuals from populations of the Eastern Italian Alps - putatively in genetic continuity with the Tyrolean Iceman-and compared his mitogenome with a large dataset of worldwide K1 sequences. Our results allow a re-definition of the K1 phylogeny, and indicate that the K1f haplogroup is absent or rare in present-day populations. We suggest that mtDNA Iceman´s lineage could have disappeared during demographic events starting in Europe from ~5,000 ybp. Based on the comparison of our results with published data, we propose a scenario that could explain the apparent contrast between the phylogeographic features of maternal and paternal lineages of the Tyrolean Iceman within the context of the demographic dynamics happening in Europe from 8,000 ybp.
... Most previous genetic studies of sub-Saharan Africa have mainly focused either on speakers of click-languages and other hunter-gatherer populations (Batini et al. 2007;Behar et al. 2008;Gonder et al. 2007), or on the Bantu dispersals (e.g. Batai et al. 2013;Beleza et al. 2005;Castri et al. 2009;Coia et al. 2005;Gonder et al. 2007;Plaza et al. 2004;Quintana-Murci et al. 2008;Richards et al. 2004;Salas et al. 2002;Scozzari et al. 1994). Several also studied populations speaking Nilo-Saharan languages (Krings et al. 1999;Poloni et al. 2009;Tishkoff et al. 2007Tishkoff et al. , 2009Watson et al. 1996;Wood et al. 2005) and Afroasiatic languages (Boattini et al. 2013), and a substantial genome-wide dataset from Ethiopia points to significant differentiation amongst speakers of the different language phyla (Pagani et al. 2012). ...
The Great Lakes lie within a region of East Africa with very high human genetic diversity, home of many ethno-linguistic groups usually assumed to be the product of a small number of major dispersals. However, our knowledge of these dispersals relies primarily on the inferences of historical, linguistics and oral traditions, with attempts to match up the archaeological evidence where possible. This is an obvious area to which archaeogenetics can contribute, yet Uganda, at the heart of these developments, has not been studied for mitochondrial DNA (mtDNA) variation. Here, we compare mtDNA lineages at this putative genetic crossroads across 409 representatives of the major language groups: Bantu speakers and Eastern and Western Nilotic speakers. We show that Uganda harbours one of the highest mtDNA diversities within and between linguistic groups, with the various groups significantly differentiated from each other. Despite an inferred linguistic origin in South Sudan, the data from the two Nilotic-speaking groups point to a much more complex history, involving not only possible dispersals from Sudan and the Horn but also large-scale assimilation of autochthonous lineages within East Africa and even Uganda itself. The Eastern Nilotic group also carries signals characteristic of West-Central Africa, primarily due to Bantu influence, whereas a much stronger signal in the Western Nilotic group suggests direct West-Central African ancestry. Bantu speakers share lineages with both Nilotic groups, and also harbour East African lineages not found in Western Nilotic speakers, likely due to assimilating indigenous populations since arriving in the region ~3000 years ago.
... Les études des différentes souches du rétrovirus HTLV-I montrent en effet que le sous-type A, fréquent chez les Noirs Marrons, est étroitement similaire à la souche décrite en Afrique de l'Ouest (Van Dooren et al., 1998;Tortevoye et al., 2000;Kazanji et Gessain, 2003). Enfin, le récent travail prédoctoral de Razafindrazaka (2006) Černý et al., 2004;b Coia et al., 2005;c Brehm et al., 2002;d Rosa et al., 2004;e Graven et al., 1995;g Trovoada et al., 2003;h Jackson et al., 2005;i Watson et al., 1997;j Salas et al., 2005b;k Salas et al., 2004;l Graven et al., 1995;Mateu et al., 1997;Watson et al., 1997;Brehm et al., 2002;Trovoada et al., 2003;Černý et al., 2004;Rosa et al., 2004;Coia et al., 2005et Jackson et al., 2005 ...
To better understand the Amerindian peopling of French Guiana, six populations (Palikur, Emerillon, Kaliña, Wayampi, Apalaí and Matsiguenga) were analysed in relation to mtDNA and Y-chromosome genetic markers, and three of them tested for seven autosomal loci. Genetic material (DNA) has been extracted from serum or red-cell samples and DNA analysis were performed using the PCR-RFLP method coupled with sequencing of the HVS-I region of the mtDNA to detect the major Amerindian genetic components. The present work demonstrates that genetic drift does not act as the principal evolutive force. Furthermore, it strenghtens the importance of an interdisciplinary approach in any anthropological study. Finally, the role of recent historical events in the Amerindian settlement of French Guiana is to be considered, notably those involving non-Amerindian populations.
... Mbenzele Central African Republic 57; 46 Destro-Bisol et al. 2004b; Coia et al. 2004 Bantu farmers Bakaka Cameroon 50; 49 Destro-Bisol et al. 2004b; Coia et al. 2004 Bassa Cameroon 47; 49 Destro-Bisol et al. 2004b; Coia et al. 2005 Bateke (northern) Congo 50; 38 Montano et al. 2013; Montano et al. 2011 Ewondo Cameroon 53; 39 Destro-Bisol et al. 2004b; Coia et al. 2005 Ngoumba Cameroon 44; 36 Batini et al. 2007; Montano et al. 2011 size, migration, and mutation) applying the formula Nν = (1/F ST ) – 1 under an island model (Wright 1931; Cavalli-Sforza and Bodmer 1971). Because the contribution of mutation rate to the Nν parameter in our genetic systems may be considered negligible (Wjisman 1984; Seielstad et al. 1998), its fluctuations have been assumed to be dependent only on migration rate and/or effective population size among populations. ...
In a previous study, we proposed a model for genetic admixture between African hunter-gatherers and food producers, in which we integrated demographic and genetic aspects together with ethnographic knowledge (Destro-Bisol et al. 2004b). In that study it was possible to test the model only using genetic information from widely dispersed and genetically heterogeneous populations. Here we reevaluate the congruence between the model and patterns of genetic variation using an anthropologically and geographically more homogeneous data set that includes Pygmies and farmers from Cameroon, Congo, and the Central African Republic. As implied by the model, the ratios of mtDNA to Y chromosome Nm estimates (effective population size, N, times the migration rate, m; 0.154 in Pygmies and 6.759 in farmers), support an asymmetric gene flow, with a higher Bantu-to-Pygmy gene flow for paternal than for maternal lineages, and vice versa for farmers. Analyses of intra- and interpopulation genetic variation further support the above observation, showing a prevailing effect of genetic drift on maternal lineages and gene flow on paternal lineages among Pygmies, and an opposite pattern among farmers. We also detected differences between patterns for classical and molecular measures of Y chromosome intrapopulation variation, which likely represent signatures of the introgression of Bantu lineages into the gene pool of Pygmy populations. On the whole, our results seem to reflect differences in the demographic history and the degree of patrilocality and polygyny between the two population groups, thus providing further support to our microevolutionary model in an anthropologically coherent framework.
... In and around the Mandara Mountains, along the basin's southern peripheries, ethnic diversity is greater than almost anywhere else in Africa, especially among Chadic-speaking montagnard populations that have been one focus of genetic investigations for more than two decades (e.g. Spedini et al. 1999 ; Cruciani et al. 2002 Cruciani et al. , 2010 Coia et al. 2005 ; Cerny et al. 2009 ; Tishkoff et al. 2009 ). Th e region's location and cultural characteristics have also encouraged signifi cant ethnographic , archaeological, and linguistic research during the last sixty years, making it one of still identifi ed Mandara montagnard populations as paléonigritique , an entirely obsolete designation dating to before the Second World War implying more or less unchanged remnants of an ancient stratum of African culture, pushed into refuge areas by more advanced societies and accompanied by assumptions about the historical isolation of populations that, in some cases, lived only kilometres apart. ...
... The paléonigritique concept was used by some geneticists working in the Mandara Mountains at the end of the twentieth century to describe montagnard populations (Spedini et al. 1999: 146). We now have a significant number of studies on mtDNA, NRYand autosomal 2 genetic variation amongst a number of different southern Lake Chad Basin populations (Spedini & Destro-Bisol 1988; Rossi et al. 1991; Spedini et al. 1999; MacEachern 2001a; Spedini et al. 2001; Cruciani et al. 2002 Cruciani et al. , 2010 Coia et al. 2005; Cerny et al. 2007 Cerny et al. , 2009 Tishkoff et al. 2009a; Cerezo et al. 2011). It is certainly the case that many regional populations have never been sampled at all, and in many instances, comparable data for these different genetic systems are not available for the same populations. ...
Archaeological evidence indicates a complex history of settlement of the southern Lake Chad Basin from the mid-Holocene onward, in parallel with the gradual desiccation of the Sahara and reduction of lake and river systems in the region. These archaeological data can be compared with a growing body of data from historical linguistics and genetics, and the southern Lake Chad Basin is one of few areas in Africa where such comparisons can be undertaken. This paper will serve as a preliminary consideration of some of the issues generated by an initial comparison of archaeological, genetic and linguistic evidence for the peopling of the Lake Chad Basin. It focuses on the contexts of initial encounters between ancestral Nilo-Saharan and Chadic populations south of Lake Megachad and subsequent population expansions and diversifications around the Mandara Mountains.
... From its distribution in current African populations, one could hypothesize that some mtDNA sub-clades of haplogroup L1c1a entered Bantu-speaking populations through admixture with central African pygmy groups: it is found in exceedingly high frequencies in western pygmies, as noted above, and is otherwise restricted to Bantu-speaking groups, with the exception of the Chadicspeaking Mandara (Coia et al., 2005) (5 %) as well as the Yoruba, whose language is part of the Benue-Congo branch of Niger-Congo (6 % of the sequences reported by Watson et al., 1996 andVigilant et al., 1991). However, contrary to this hypothesis of admixture between the ancestors of the Bantuspeaking groups and the ancestors of modern-day pygmy groups, Quintana-Murci et al. (2008) propose that L1c was already present in the shared ancestor of agricultural groups (in their study represented by Bantu-speaking groups from Gabon and Cameroon) and pygmy groups; in addition, they suggest gene flow to have taken place over a long period of time after an extended period of initial isolation. ...
The expansion of Bantu-speaking peoples over large parts of sub-Saharan Africa is still a matter of debate—not only with respect to the propelling force behind it and the route(s) taken, but, also, in terms of the question whether there actually was a demographic expansion of peoples, rather than just a cultural expansion involving the spread of languages and technologies. In this paper, we provide a critical review of the extant linguistic and molecular anthropological data on Africa and discuss the insights they provide concerning the expansion itself as well as the demographic processes involved in it. Contrary to some assumptions by historians and cultural anthropologists, the genetic data speak in favor of an actual movement of peoples during the expansion of the Bantu languages over Africa, rather than a spread through language and culture shift. Furthermore, the molecular data indicate that sociocultural practices such as patrilocality and possibly even polygyny played a role in shaping the genetic diversity of Bantu-speaking peoples. These sociocultural practices might explain why, in Africa, there is a correlation between Y-chromosomal (i.e., paternal) lineages and linguistic affiliation, but not between mtDNA (maternal) lineages and language.
... Such biological relationships, if accurate, would probably originate in the early Holocene, when higher levels of rainfall would have facilitated movements across the Sahara and along the Nile Valley. On the other hand, mtDNA research has found (1) low frequencies of the mtDNA U6 haplogroup in Podokwo and Ouldemé populations (Coia et al. 2005), which might indicate North African origins dissimilar to those of the R-P25* Y-chromosomal subclade , but also (2) somewhat higher frequencies of a L3f3 mtDNA sub-haplogroup found almost exclusively among Chadic-speaking populations (including Ouldemé, Podokwo and Wandala), but with affinities to eastern African populations, including Afroasiatic-speaking Cushites (Cerny et al. 2007, 2009). Finally, in a recent and much larger-scale genome-wide survey of African genetic affinities, Tishkoff et al. (2009) suggest (1) very close genetic relations between Chadic-and Nilo-Saharan-speaking populations of the region (the Chadic speakers including Ouldemé, Podokwo, Mada, Zulgo, Giziga and Wandala groups from the Mandara area) and (2) more ancient affinities of these Lake Chad Basin groups with Nilo-Saharan populations in Northeast and East Africa. ...
... Based on available data haplogroup L4 seems more abundant within East Africa [44] but only scarcely present in West Africa (Nigeria and Ghana [20]). Haplogroup L5 also seems to show higher frequencies in East Africa [24,26,45,46] with traces in the Congo [36] as well as in Cameroon [21] while haplogroup L6 seems to be more frequent north of the equator [20,24]. ...
West Africa is characterized by a migration history spanning more than 150,000 years. Climate changes but also political circumstances were responsible for several early but also recent population movements that shaped the West African mitochondrial landscape. The aim of the study was to establish a Ghanaian mtDNA dataset for forensic purposes and to investigate the diversity of the Ghanaian population sample with respect to surrounding populations. We sequenced full mitochondrial control regions of 193 Akan people from Ghana and excluded two apparently close maternally related individuals due to preceding kinship testing. The remaining dataset comprising 191 sequences was applied as etalon for quasi-median network analysis and was subsequently combined with 99 additional control region sequences from surrounding West African countries. All sequences were incorporated into the EMPOP database enriching the severely underrepresented African mtDNA pool. For phylogeographic considerations, the Ghanaian haplotypes were compared to those of 19 neighboring populations comprising a total number of 6198 HVS1 haplotypes. We found extensive genetic admixture between the Ghanaian lineages and those from adjacent populations diminishing with geographical distance. The extent of genetic admixture reflects the long but also recent history of migration waves within West Africa mainly caused by changing environmental conditions. Also, evidence for potential socio-economical influences such as trade routes is provided by the occurrence of U6b and U6d sequences found in Dubai but also in Tunisia leading to the African West Coast via Mauritania and Senegal but also via Niger, Nigeria to Cameroon.
... Africa. Only four African lineages were shared between the black and white Porto Alegre groups, with all four occurring in Africa and/or other Brazilian populations (Salas et al., 2002; Plaza et al., 2004; Rosa et al., 2004; Beleza et al., 2005; Coia et al., 2005; Jackson et al., 2005; Gonçalves et al., 2008). The four major Amerindian haplogroups were detected among Porto Alegre whites (A = 28%; B = 22%, C = 47%, D = 3%), whereas haplogroup A was absent among blacks (B = 19%, C = 69% and D = 12%). ...
Two hundred and three individuals classified as white were tested for 11 single nucleotide polymorphisms plus two insertion/deletions in their Y-chromosomes. A subset of these individuals (n = 172) was also screened for sequences in the first hypervariable segment of their mitochondrial DNA (mtDNA). In addition, complementary studies were done for 11 of the 13 markers indicated above in 54 of 107 black subjects previously investigated in this southern Brazilian population. The prevalence of Y-chromosome haplogroups among whites was similar to that found in the Azores (Portugal) or Spain, but not to that of other European countries. About half of the European or African mtDNA haplogroups of these individuals were related to their places of origin, but not their Amerindian counterparts. Persons classified in these two categories of skin color and related morphological traits showed distinct genomic ancestries through the country. These findings emphasize the need to consider in Brazil, despite some general trends, a notable heterogeneity in the pattern of admixture dynamics within and between populations/groups.
... Despite its potential, Y chromosome variation has been scantily explored in sub-Saharan Africa and has been studied even less than the other unilinearly transmitted marker, mitochondrial DNA (mtDNA) (Salas et al. 2002; Pakendorf & Stoneking 2005; Destro-Bisol et al. 2010). In fact, previous Y-chromosomal studies have been carried out on a local geographic scale or have investigated a limited number of geographically dispersed Bantu-speaking populations (Beleza et al. 2005; Coia et al. 2005; Berniell-Lee et al. 2009), and even the broadest datasets do not contain certain areas of primary importance to test the hypotheses concerning the Bantu expansion (Hammer et al. 2001; Underhill et al. 2001; Wood et al. 2005; De Filippo et al. 2011). Nonetheless, there is a substantial convergence concerning the hypothesis that specific paternal lineages , defined using single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs), could be a genetic legacy of the Bantu expansion. ...
The current distribution of Bantu languages is commonly considered to be a consequence of a relatively recent population expansion (3-5kya) in Central Western Africa. While there is a substantial consensus regarding the centre of origin of Bantu languages (the Benue River Valley, between South East Nigeria and Western Cameroon), the identification of the area from where the population expansion actually started, the relation between the processes leading to the spread of languages and peoples and the relevance of local migratory events remain controversial. In order to shed new light on these aspects, we studied Y chromosome variation in a broad dataset of populations encompassing Nigeria, Cameroon, Gabon and Congo. Our results evidence an evolutionary scenario which is more complex than had been previously thought, pointing to a marked differentiation of Cameroonian populations from the rest of the dataset. In fact, in contrast with the current view of Bantu speakers as a homogeneous group of populations, we observed an unexpectedly high level of interpopulation genetic heterogeneity and highlighted previously undetected diversity for lineages associated with the diffusion of Bantu languages (E1b1a (M2) sub-branches). We also detected substantial differences in local demographic histories, which concord with the hypotheses regarding an early diffusion of Bantu languages into the forest area and a subsequent demographic expansion and migration towards eastern and western Africa.
... This maternal African ancestry showed a low divergence with 41% of African groups (Fst < 0.05). Many of them are located in West Africa and South West Africa, such as Senegal [52], Cabo Verde [53], Sierra Leone [54], Guinea-Bissau [55], Mali [41], Ivory Coast (present study), Burkina Faso [56], Benin [57] (present study), Niger [56], Cameroon585960616263, Chad [59], Gabon [62], Equatorial Guinea [64], Angola [65] and Cabinda [66]. However, inside this large area, three clusters of high genetic divergence from the mtDNA gene pool were observed identifying the Pygmy communities of Camer- oon [61,62], Gabon [62] and Central African Republic [63,67], the Fang from Equatorial Guinea [68] and the Mbuti from the Democratic Republic of Congo [69]. ...
Retracing the genetic histories of the descendant populations of the Slave Trade (16th-19th centuries) is particularly challenging due to the diversity of African ethnic groups involved and the different hybridisation processes with Europeans and Amerindians, which have blurred their original genetic inheritances. The Noir Marron in French Guiana are the direct descendants of maroons who escaped from Dutch plantations in the current day Surinam. They represent an original ethnic group with a highly blended culture. Uniparental markers (mtDNA and NRY) coupled with HTLV-1 sequences (env and LTR) were studied to establish the genetic relationships linking them to African American and African populations.
All genetic systems presented a high conservation of the African gene pool (African ancestry: mtDNA = 99.3%; NRY = 97.6%; HTLV-1 env = 20/23; HTLV-1 LTR = 6/8). Neither founder effect nor genetic drift was detected and the genetic diversity is within a range commonly observed in Africa. Higher genetic similarities were observed with the populations inhabiting the Bight of Benin (from Ivory Coast to Benin). Other ancestries were identified but they presented an interesting sex-bias. Whilst male origins spread throughout the north of the bight (from Benin to Senegal), female origins were spread throughout the south (from the Ivory Coast to Angola).
The Noir Marron are unique in having conserved their African genetic ancestry, despite major cultural exchanges with Amerindians and Europeans through inhabiting the same region for four centuries. Their maroon identity and the important number of slaves deported in this region have maintained the original African diversity. All these characteristics permit to identify a major origin located in the former region of the Gold Coast and the Bight of Benin; regions highly impacted by slavery, from which goes a sex-biased longitudinal gradient of ancestry.
... It is also clear that the Fulani language is genetically related to languages in the Niger-Congo Superfamily and has no relationship to any languages spoken in Eurasia. Granted, analyses of the Fulani mtDNA and Y chromosome markers include some Eurasian genetics, but African genetic markers predominate among the Fulani (4,5). The archaeogenetic and linguistic data make it clear that the Fulani are not of Eurasian origin as suggested by Scheinfeldt et al. (1). ...
In a recent issue of PNAS, Scheinfeldt et al. (1) maintained that, although Fulani mtDNA is consistent with a West African origin, the linguistic and nonrecombinant portion of the Y chromosome (NRY) supports a Middle Eastern origin for this population. Although this is their opinion, the linguistic and genetic evidence fails to support this conclusion.
... Notre base de données rassemble les fréquences des haplogroupes mitochondriaux de 41 populations (Figure 1) : 20 du nord de l'Afrique (Maroc, Algérie, Tunisie, Egypte, Mauritanie), 5 des régions sub-sahariennes (Cameroun, Angola, Kenya, Mozambique, Ethiopie), 6 du Proche-et Moyen-Orient (Yémen, Iraq, Israël, Jordanie, Turquie, Syrie) et 10 du sud de l'Europe (Grèce, Italie, Espagne, Portugal). Les références de chaque population sont : Asni, Bouhria, (Dugoujon et Torroni, non publié), Figuig (Dugoujon, non publié), Souss (Brakez et al., 2001), Arabes Maroc (Rando et al., 1998 ; Plaza et al., 2003), Saharaouis (Plaza et al., 2003), Ghardaïa (Macaulay et al., 1999), Algérie (Plaza et al., 2003), Douiret-Chenini, Sened, Matmata (Fadhlaoui-Zid et al., 2004), Berbères Jerba, Arabes Jerba (Loueslati et al., 2006), Arabes Tunisie (Plaza et al., 2003), Siouah (Dugoujon et Torroni, non publié), Gurna (Stevanovitch et al., 2004), Adaïma (Dugoujon, non publié), Mauritanie (Rando et al., 1998), Cameroun (Coia et al., 2005), Angola (Plaza et al., 2004), Kenya (Brandstatter et al., 2004), Mozambique (Pereira et al., 2001 ; Salas et al., 2002), Ethiopie, Yemen (Kivisild et al., 2004), Iraq, Israel, Jordanie (Richards et al., 2000), Syrie (Richards et al., 2000 ; Vernesi et al., 2001), Turquie (Richards et al., 2000 ; Di Benedetto et al., 2001 ; Quintana-Murci et al., 2004), Grèce (Richards et al., 2000 ; Vernesi et al., 2001), Italie (Torroni, non publié), Sardaigne, Sicile (Richards et al., 2000 ; Torroni, non publié), Basques (Richards et al., 2000), Espagne, Andalousie (Crespillo et al., 2000 ; Richards et al., 2000 ; Larruga et al., 2001 ; Plaza et al., 2003), Portugal (Pereira et al., 2000 ; Richards et al. 2000 ; González et al., 2003). Pour les comparaisons entre populations, nous avons réalisé différentes Analyses en Composantes Principales (ACP). ...
Various molecular markers can be used to study the genetic diversity of human populations. Here, we present our work on the mitochondrial diversity of Berberspeakers from North Africa. Analyses were done after control region sequencing (HVSI and HVSII) and coding region RFLPs of the mitochondrial DNA (mtDNA) from various Berber populations from Morocco and Egypt. Through comparison with geographically related populations (in particular from south-western Europe, the Middle East and sub-Saharan areas), our objective is to understand how this diversity was set up in North Africa in connection with the several migrations of different populations. Our results show that North-Africans have, in the total mitochondrial diversity, an intermediate position between European and sub-Saharan populations. We also see a genetic differentiation between North-Western and North-Eastern African groups: populations from Maghreb are related to European and Middle Eastern populations whereas High Egyptians share more affinities with sub-Saharans and East Africans. Our data also reveal a clear and significant genetic differentiation between Berbers from Maghreb and Egyptian Berbers, the latter sharing more affinities with East- African populations. Divers marqueurs moléculaires peuvent être utilisés pour retracer la diversité génétique des populations humaines. Nous présentons ici nos travaux sur la diversité mitochondriale des populations berbérophones du nord de l�Afrique. Les analyses portent sur le séquençage de la région contrôle (HVS-I et HVS-II) et sur des RFLPs dans la région codante de l�ADN mitochondrial (ADNmt) de différentes populations berbères du Maroc et d�Egypte. Au travers de comparaisons avec des populations géographiquement proches (notamment du sud-ouest de l�Europe, du Proche-Orient et des régions subsahariennes), notre objectif est de comprendre comment cette diversité a pu se mettre en place au nord de l�Afrique en rapport avec les divers mouvements de populations. Nos résultats montrent que les populations nord-africaines occupent, dans la diversité mitochondriale globale, une position intermédiaire entre les populations européennes et sub-sahariennes et qu�il apparaît une différenciation génétique entre le nord-ouest et le nord-est du continent africain, les populations du Maghreb se rapprochant des populations européennes et du Moyen-Orient alors que les populations de Haute Egypte montrent plus d�affinités avec les populations subsahariennes et d�Afrique de l�Est. Nos travaux révèlent également une nette et significative différenciation génétique entre les Berbères du Maghreb et les Berbères égyptiens, ces derniers présentant plus d�affinités avec les populations est-africaines.
... However, neither the difference between the Bisa and the Turu, nor that between the Bisa and Mozambican populations is significant after the conservative Bonferroni correction for multiple tests is applied (P-values [ 0.22). Haplogroup L1c, which is generally found with very high frequencies (55–100%) in ''pygmy'' groups and with moderate frequency (6–36%) in farmers of central Africa (Vigilant et al., 1991; Destro-Bisol et al., 2004a,b; Coia et al., 2005; Batini et al., 2007; Tishkoff et al., 2007; Quintana-Murci et al., 2008), was detected in both the Bisa (19%) and the Kunda (8%). The frequency of L1c in the Bisa and Kunda is higher than that found in Bantuspeaking populations of east Africa (cf.Table 1 ). ...
The transformation from a foraging way of life to a reliance on domesticated plants and animals often led to the expansion of agropastoralist populations at the expense of hunter-gatherers (HGs). In Africa, one of these expansions involved the Niger-Congo Bantu-speaking populations that started to spread southwards from Cameroon/Nigeria approximately 4,000 years ago, bringing agricultural technologies. Genetic studies have shown different degrees of gene flow (sometimes involving sex-biased migrations) between Bantu agriculturalists and HGs. Although these studies have covered many parts of sub-Saharan Africa, the central part (e.g. Zambia) was not yet studied, and the interactions between immigrating food-producers and local HGs are still unclear. Archeological evidence from the Luangwa Valley of Zambia suggests a long period of coexistence ( approximately 1,700 years) of early food-producers and HGs. To investigate if this apparent coexistence was accompanied by genetic admixture, we analyzed the mtDNA control region, Y chromosomal unique event polymorphisms, and 12 associated Y- short tandem repeats in two food-producing groups (Bisa and Kunda) that live today in the Luangwa Valley, and compared these data with available published data on African HGs. Our results suggest that both the Bisa and Kunda experienced at most low levels of admixture with HGs, and these levels do not differ between the maternal and paternal lineages. Coalescent simulations indicate that the genetic data best fit a demographic scenario with a long divergence (62,500 years) and little or no gene flow between the ancestors of the Bisa/Kunda and existing HGs. This scenario contrasts with the archaeological evidence for a long period of coexistence between the two different communities in the Luangwa Valley, and suggests a process of sociocultural boundary maintenance may have characterized their interaction.
... This is the case of the work by Wood et al. (2005), in which they intended to establish the association between genetic markers for both sexes and linguistic and geographic variation in Africa. With this objective, they genotyped 50 SNPs in the Y chromosome in 40 African populations and compared their results with those of several previous mtDNA publications (Salas et al. 2002; Knight et al. 2003; Destro-Bisol et al. 2004; Coia et al. 2005). Their results suggested that the patterns of migration inside Africa have been different for males and females. ...
ResumLestudi de la variació genòmica ens pot ajudar a entendre la història demogràfica de lespoblacions i els events de selecció que hi han influït. Normalment això es fa mitjançant elstests de neutralitat, una eina estadística que permet detectar desviacions de la neutralitatmitjançant la comparació dels resultats empírics obtinguts per un estadístic a partir dunamostra dADN, contra una distribució neutra simulada daquest estadístic. Tot i això, aquestametodologia té algunes limitacions, principalment relacionades amb (a) la variació a partir dela que treballa el test, (b)la metodologia dús dels estadístics de neutralitat, i (c) la tecnologiaemprada per obtenir informació de les seqüències dADN. En els quatre articles presentats enaquesta tesis he abordat tots aquests problemes. Respecte a la primera limitació he analitzatlefecte que les desviacions de la neutralitat, com ara la recombinació i la demografia, tenensobre el poder dels estadístics de neutralitat. Pel que fa a la metodologia, he estudiat si laincertesa en la reconstrucció de les dades de resequenciació té algun efecte en el poder delstests quan aquests es comparen contra dades simulades. Finalment, els dos darrers treballsaborden els problemes que sorgeixen quan sutilitzen genotips en lloc de dades deresequenciació, i proposen alternatives per a lanàlisi daquestes dades.AbstractThe study of the genomic variation can give us insights into the demographic history of thepopulations and of the selective events acting upon them. This is usually approached by meansof the neutrality tests, a statistical tool that can detect departures from neutrality bycomparing the empirical results for a given statistic obtained from DNA samples againstneutral, simulated distribution of this statistic. However, this methodology has somelimitations, mainly related to (a) the variation the tests rely upon, (b) the methodology of theuse of neutrality tests, and (c) the technology used to obtain information from DNA sequences.In the four papers included in this thesis I approach all these issues. For the first of thementioned concerns, I have analysed how the power of neutrality statistics is affected bydepartures of neutrality such as recombination or demographic events. As for themethodology, I have estudied whether uncertainity in the reconstruction of resequencing datahas any effect on the power of the tests when it is compared with simulation data. Finally, thelast two works address the problems of using genotyping instead of resequencing data andpropose alternatives to the analysis of such data.
... We compared the data obtained in the course of this study with previously published results regarding mtDNA (hypervariable region-1, np 16024-16390; Destro-Bisol et al., 2004; Coia et al., 2005). Furthermore, specifically for correlation and inter-population diversity analyses we considered the data from 10 polymorphisms of protein coding loci (PCL) (6-PGD, ACP, CAII, ESD, GLO, GPX1, PGM1, A1-AT, GC and TF published by Spedini et al. (1999) , which represents to date the reference study of genetic variation in Cameroon on a regional scale. ...
In this study, we report the genetic variation of autosomal and Y-chromosomal microsatellites in a large Cameroon population dataset (a total of 11 populations) and jointly analyze novel and previous genetic data (mitochondrial DNA and protein coding loci) taking geographic and cultural factors into consideration. The complex pattern of genetic variation of Cameroon can in part be described by contrasting two geographic areas (corresponding to the northern and southern part of the country), which differ substantially in environmental, biological, and cultural aspects. Northern Cameroon populations show a greater within- and among-group diversity, a finding that reflects the complex migratory patterns and the linguistic heterogeneity of this area. A striking reduction of Y-chromosomal genetic diversity was observed in some populations of the northern part of the country (Podokwo and Uldeme), a result that seems to be related to their demographic history rather than to sampling issues. By exploring patterns of genetic, geographic, and linguistic variation, we detect a preferential correlation between genetics and geography for mtDNA. This finding could reflect a female matrimonial mobility that is less constrained by linguistic factors than in males. Finally, we apply the island model to mitochondrial and Y-chromosomal data and obtain a female-to-male migration Nnu ratio that was more than double in the northern part of the country. The combined effect of the propensity to inter-populational admixture of females, favored by cultural contacts, and of genetic drift acting on Y-chromosomal diversity could account for the peculiar genetic pattern observed in northern Cameroon.
... However, this estimated expansion time could represent an underestimation and may simply show the expansion of a subset of the diversity within haplogroup R1b1* to west Central Africa through the Bantu expansion, having been shown to be especially frequent in northern Cameroon, near the putative Bantu expansion origin (Cruciani et al. 2002). Surprisingly, no traces of non-African maternal lineages (i.e., mtDNA) have been observed in west Central Africa (Coia et al. 2005;Quintana-Murci et al. 2008), pointing to a putative sexual asymmetrical demographic expansion in Central Africa. Further analyses in an extended group of Central African populations (including Nigeria, Niger, Chad, and Sudan) might be pivotal to shed light on this poorly known demographic event in the region. ...
The expansion of Bantu languages, which started around 5,000 years before present in west/central Africa and spread all throughout sub-Saharan Africa, may represent one of the major and most rapid demographic movements in the history of the human species. Although the genetic footprints of this expansion have been unmasked through the analyses of the maternally inherited mitochondrial DNA lineages, information on the genetic impact of this massive movement and on the genetic composition of pre-Bantu populations is still scarce.
Here, we analyze an extensive collection of Y-chromosome markers—41 single nucleotide polymorphisms and 18 short tandem repeats—in 883 individuals from 22 Bantu-speaking agriculturalist populations and 3 Pygmy hunter-gatherer populations from Gabon and Cameroon. Our data reveal a recent origin for most paternal lineages in west Central African populations most likely resulting from the expansion of Bantu-speaking farmers that erased the more ancient Y-chromosome diversity found in this area. However, some traces of ancient paternal lineages are observed in these populations, mainly among hunter-gatherers. These results are at odds with those obtained from mtDNA analyses, where high frequencies of ancient maternal lineages are observed, and substantial maternal gene flow from hunter-gatherers to Bantu farmers has been suggested. These differences are most likely explained by sociocultural factors such as patrilocality. We also find the intriguing presence of paternal lineages belonging to Eurasian haplogroup R1b1*, which might represent footprints of demographic expansions in central Africa not directly related to the Bantu expansion.
... Niger-Nigeria 132 (Watson et al. 1997) 20 Mauritania 64 (Gonzalez et al. 2006; Rando et al. 1998) 21 Senegal 121 (Rando et al. 1998) 22 Sierra Leone 270 (Jackson et al. 2005) 23 Guinea Bissau 361 (Rosa et al. 2004) 24 Benin 87 (Rowold et al. 2007) 25 Central African Republic 30 (Batini et al. 2007) 26 Popular Republic of Congo 94 (Batini et al. 2007) 27 Sao Tomé e Principe 103 (Trovoada et al. 2004) 28 Chad 448 (Cerny et al. 2007) 29 Cameroon 441 (Coia et al. 2005) 30 Mali 124 (Gonzalez et al. 2006) 31 Angola 44 (Plaza et al. 2004) 32 Rwanda 63 (Rowold et al. 2007) 33 Kenya 100 (Brandstatter et al. 2004) 34 Mozambique 416 (Pereira et al. 2001; Salas et al. 2002) 35 Ethiopia 270 (Kivisild et al. 2004) 36 Sudan 154 (Pereira et al. 2001; Underhill et al. 2000) 37 NEAR EAST Yemen 115 (Kivisild et al. 2004) 38 Saudi Arabia 553 (Abu-Amero et al. 2008) 39 Oman 105 (Rowold et al. 2007) 40 Qatar 90 (Rowold et al. 2007) 41 UAE 131 (Rowold et al. 2007) 42 Iraq 116 (Richards et al. 2000) 43 Israel 117 (Richards et al. 2000) 44 Jordan 146 (Richards et al. 2000) 45 Syria 118 (Richards et al. 2000; Vernesi et al. 2001) 46 Turkey 340 (Di Benedetto et al. 2001; Quintana- Murci et al. 2004; Richards et al. 2000) ...
The mitochondrial DNA variation of 295 Berber-speakers from Morocco (Asni, Bouhria and Figuig) and the Egyptian oasis of Siwa was evaluated by sequencing a portion of the control region (including HVS-I and part of HVS-II) and surveying haplogroup-specific coding region markers. Our findings show that the Berber mitochondrial pool is characterized by an overall high frequency of Western Eurasian haplogroups, a somehow lower frequency of sub-Saharan L lineages, and a significant (but differential) presence of North African haplogroups U6 and M1, thus occupying an intermediate position between European and sub-Saharan populations in PCA analysis. A clear and significant genetic differentiation between the Berbers from Maghreb and Egyptian Berbers was also observed. The first are related to European populations as shown by haplogroup H1 and V frequencies, whereas the latter share more affinities with East African and Nile Valley populations as indicated by the high frequency of M1 and the presence of L0a1, L3i, L4*, and L4b2 lineages. Moreover, haplogroup U6 was not observed in Siwa. We conclude that the origins and maternal diversity of Berber populations are old and complex, and these communities bear genetic characteristics resulting from various events of gene flow with surrounding and migrating populations.
MtDNA comparative African data. The table summarizes previously published mtDNA HVS-I datasets on African populations, here considered for comparative purposes.
Because modern humans originated in Africa and have adapted to diverse environments, African populations have high levels of genetic and phenotypic diversity. Thus, genomic studies of diverse African ethnic groups are essential for understanding human evolutionary history and how this leads to differential disease risk in all humans. Comparative studies of genetic diversity within and between African ethnic groups creates an opportunity to reconstruct some of the earliest events in human population history and are useful for identifying patterns of genetic variation that have been influenced by recent natural selection. Here we describe what is currently known about genetic variation and evolutionary history of diverse African ethnic groups. We also describe examples of recent natural selection in African genomes and how these data are informative for understanding the frequency of many genetic traits, including those that cause disease susceptibility in African populations and populations of recent African descent.
This paper situates Martin Bernal's work in context and largely defends it against the sweep ing criticism and allegations brought against it (notab ly in Lefkowitz and MacLean Rogers' 1996 collection Black Athena revisited ; and in Berlinerblau's Heresy in the University , for whom Bernal is 'the academic Elvis' -- i.e. the appropriating White recycling Black ideas) . Even so, serious criticism cannot be avoided, not ably of Bernal's lack of method; his politicised view of hi storical and academic truth; his tendency to confla te culture, language and somatic type; his obsession with origi ns; his literalist approach to myth; his inability to make living socio-cultural history out of reconstruction s of provenance; and his dogged insistence on an un convinc- ing, for non-systematic, Ancient Egyptian etymology of the Greek theonym Athena. Without downright destroying the Black Athena thesis, these various defects could be remedied by the concerted, interdisciplinary collaboration of specialists, to which the argument exhorts the international scholarly community. However, towards the end the argument cannot refrain from more fundamental criticism, chiding Bernal for myopic concentration on the Eastern Mediterranean. Here th e argument goes beyond the Black Athena thesis in the light of state-of-the-art comparative and historica l linguistics, and molecular genetics, which have m ade possible a truly long-range approach to global cult ural history. In passing, we highlight the peculiar Bronze Age Mediterranean presence of Niger-Congo / Bantu linguistic elements (usually associated with sub-Sah aran Africa). Relying on the recently discovered 'Back-i nto-Africa' migration from Central and West Asia fr om the Upper Palaeolithic times onward, and on recent reco nstructions of the Upper Palaeolithic *Borean paren t language, the present argument offers a powerful al ternative for the Black Athena thesis: The Aegean region looks similar to Ancient Egypt, not primarily becau se of diffusion from Egypt in the Late Bronze Age, but because both were the recipients of a demic, lingui stic and cultural movement from West (ultimately Ce ntral) Asia ; and this movement also extended to sub-Saharan Afri ca, producing the same similarities there. Ancient Egypt displays many cultural and religious similari ties with sub-Saharan Africa, not primarily because of diffusion from sub-Saharan Africa to Egypt in Neoli thic times, but the other way around: because the B ack- into-Africa movement, carrying a significant share of Asian genes, as well as cultural, religious and linguistic elements (including *Borean-associated elements tow ards Niger-Congo / Bantu) passed via Egypt on its w ay from Asia to sub-Saharan Africa. However, while thus the argument has rather devasta ting implications for Afrocentrism including the Bernallian variant, it c ould not have been made without Bernal's visionary and path-breaking contribution.
An efficient algorithm is presented in this paper to improve the perturbation efficiency of the adaptive downhill simplex simulated annealing (ASSA) method for magnetotelluric inversion with oblique correlated misfit valleys. The correlated model space is rotated to a less dependent space which is defined by the eigenvectors of the parameter covariance updated progressively by the inversion itself. The downhill simplex step and rotation work together to decorrelate the correlated model space. The application to two synthetic cases and real data indicates that ASSA in the rotated space generally has a better convergence and efficient behaviour than ASSA without rotation. In the rotated space, the high rejection rates, which occurred in the unrotated space, are avoided. At low temperature, the estimated covariance can be used to approximate the global covariance. For all cases, ASSA in the rotated space gives better inversion results.
Controversey surrounds the phylogeography and origin of the R haplotype among Native Americans.
Some researchers have suggested that Europeans spread this haplotype among Native Americans. The purpose
of this study was to determine the origin of the R-M173 y-chromosome among Native Americans . It is the
third most frequent y-chromosome possessed by Native Americans. Native Americans with the highest
frequency of R-M173 haplotypes like the Ojibwa and Seminoles mated frequently with African males. Our
findings indicate that the African male, Native American female pattern of mating in the United States
probably led to the introduction and spread of R-M173 among Native Americans during slavery.
The trans-Atlantic slave trade dramatically changed the demographic makeup of the New World, with varying regions of the African coast exploited differently over roughly a 400 year period. When compared to the discrete mitochondrial haplotype distribution of historically appropriate source populations, the unique distribution within a specific source population can prove insightful in estimating the contribution of each population. Here, we analyzed the first hypervariable region of mitochondrial DNA in a sample from the Caribbean island of Jamaica and compared it to aggregated populations in Africa divided according to historiographically defined segments of the continent's coastline. The results from these admixture procedures were then compared to the wealth of historic knowledge surrounding the disembarkation of Africans on the island.
In line with previous findings, the matriline of Jamaica is almost entirely of West African descent. Results from the admixture analyses suggest modern Jamaicans share a closer affinity with groups from the Gold Coast and Bight of Benin despite high mortality, low fecundity, and waning regional importation. The slaves from the Bight of Biafra and West-central Africa were imported in great numbers; however, the results suggest a deficit in expected maternal contribution from those regions.
When considering the demographic pressures imposed by chattel slavery on Jamaica during the slave era, the results seem incongruous. Ethnolinguistic and ethnographic evidence, however, may explain the apparent non-random levels of genetic perseverance. The application of genetics may prove useful in answering difficult demographic questions left by historically voiceless groups.
We analyzed sequence variation in the mitochondrial DNA (mtDNA) hypervariable segment I (HVS-I) from 201 Black individuals from two Brazilian cities (Rio de Janeiro and Porto Alegre), and compared these data with published information from 21 African populations. A subset of 187 males of the sample was also characterized for 30 Y-chromosome biallelic polymorphisms, and the data were compared with those from 48 African populations. The mtDNA data indicated that respectively 69% and 82% of the matrilineages found in Rio de Janeiro and Porto Alegre originated from West-Central/Southeast Africa. These estimates are in close agreement with historical records which indicated that most of the Brazilian slaves who arrived in Rio de Janeiro were from West-Central Africa. In contrast to mtDNA, Y-chromosome haplogroup analysis did not allow discrimination between places of origin in West or West-Central Africa. Thus, when comparing these two major African regions, there seems to be higher genetic structure with mtDNA than with Y-chromosome data.
Há algum tempo dados genéticos vêm sendo utilizados para inferências quanto à natureza do tráfico de escravos ocorrido no período colonial no Atlântico Sul e sobre a origem dos africanos que chegaram ao Brasil. A utilização de marcadores de linhagem mais específicos, como é o caso do DNA mitocondrial (mtDNA) e da região não-recombinante do cromossomo Y (NRY) pode se constituir em poderoso instrumento para o esclarecimento dessas questões. Este trabalho utilizou esses enfoques através do seqüenciamento da HVS-I do mtDNA (highly variable segment I) e de testes em 30 SNPs (single nucleotide polymorphisms) localizados na região não-recombinante do cromossomo Y, em uma amostra de 133 indivíduos classificados como derivados de africanos (preto e pardo) do estado do Rio Grande do Sul (Porto Alegre e região metropolitana), bem como 144 homens classificados do mesmo modo no estado do Rio de Janeiro (Rio de Janeiro e região metropolitana). Os dados do mtDNA indicaram que 89,5% e 78% das matrilinhagens encontradas, respectivamente, no Rio de Janeiro e em Porto Alegre eram de origem africana. Destas, 69% e 82% eram de origem da África Centro-oeste (região típica de povos que falam línguas Bantus), enquanto que a fração complementar teria uma origem no Oeste africano (não-Bantu). Estes resultados estão de acordo com os registros históricos. Os marcadores do cromossomo Y revelaram que 56% (Rio de Janeiro) e 36% (Porto Alegre) destes cromossomos tinham uma origem africana. No entanto, diferentemente do que aconteceu com o mtDNA, as análises não permitiram discriminar os locais de origem dentro do continente africano. Parece, portanto, haver maior estruturação nos dados obtidos com o mtDNA do que com o cromossomo Y, sugerindo uma maior taxa de migração dos homens do que das mulheres dentro do grande tronco lingüístico Niger-Congo. Porto Alegre e Rio de Janeiro quando comparadas em relação ao mtDNA, não apresentam diferenciação significativa, embora pudessem ser observadas algumas diferenças, em destaque a maior presença de linhagens mitocondriais de origem ameríndia em Porto Alegre (16,4%) do que no Rio de Janeiro (8,5%). Já a diferença entre Porto Alegre e o Rio de Janeiro foi significativa quanto aos dados do cromossomo Y. Especialmente notável, é a presença de cromossomos de origem indígena em Porto Alegre: haplogrupos Q* e Q3*, nas freqüências de 3,5% e 1,7%, respectivamente. Analisando somente os indivíduos tipados tanto para o mtDNA quanto para os marcadores do Y, nota-se que ~ 50% deles nas duas amostras apresentam linhagens mitocondriais e do cromossomo Y de origem africana, enquanto de forma complementar, o número de indivíduos com matrilinhagens africanas e cromossomos Y europeus e/ou asiáticos ou ameríndios foi de ~ 41% e ~ 35% para o Rio de Janeiro e Porto Alegre, respectivamente. As amostras estudadas, portanto, caracterizam-se como sendo amplamente mescladas, apenas metade dos genomas considerados sendo de origem completamente africana. Genetic data have been used for some time now for inferences about the nature of the slave trade that occurred in South Atlantic in the Colonial Period, as well as about the origins of the Africans who arrived in Brazil. The use of lineage-specific markers, like mitochondrial DNA (mtDNA) and those of the non-recombining region of the Y chromosome (NRY), can constitute a powerful tool for elucidation of these questions. This work utilized this approach through sequencing of the mtDNA HVS-I (highly variable segment I), as well by testing 30 SNPs (single nucleotide polymorphisms) located in chromosome Y¿s nonrecombining region in a sample of 133 individuals classified as African-derived (black or mulatto) from the state of Rio Grande do Sul (Porto Alegre and metropolitan region), as well as 144 men classified in the same manner in the state of Rio de Janeiro (Rio de Janeiro and metropolitan region). The mtDNA data indicated that 89.5% and 78% of the matrilineages found in Rio de Janeiro and Porto Alegre were of African origin. Of these, respectively, 69% and 82% were of Central-West African origin (region typically of people who speak Bantu languages), while the complementary fraction would have the West African origin (non-Bantu). These results are in accordance with the historical records. The Y chromosome markers revealed that 56% (Rio de Janeiro) and 36% (Porto Alegre) of these chromosomes should have an African origin. But differently of what occurred with the mtDNA results, the analyses did not allow a discrimination of the places of their origin within the African continent. It seems, therefore, that a higher structuration occurs in the mtDNA data as compared to the Y chromosome results, suggesting a higher male in relation to female migration rates within the large Niger-Congo linguistic family. Porto Alegre and Rio de Janeiro do not present significant mtDNA frequency differences, although the Amerindian mtDNA presence is higher in Porto Alegre (16.4%) than Rio de Janeiro (8.5%). On the other hand, Porto Alegre and Rio de Janeiro do show significant differences in the Y chromosome data. Especially notable is the presence of Amerindian chromosomes in Porto Alegre: frequencies of, respectively, 3.5% and 1.7% for haplogroups Q* and Q3*. Considering just the individuals simultaneously typed for mtDNA and the Y chromosome, it is verified that ~50% of then show mtDNA and Y chromosome lineages of African origin, while the number of individuals with African mtDNA but European and/or Asiatic or Amerindian lineages was ~41% for Rio de Janeiro and ~35% for Porto Alegre. The samples studied, therefore, can be characterized as amply admixed, only half of the genomes considered being completely of African origin.
The transition from food collection to food production (FP) modified the nature of selective pressures, and several studies illustrate that genetic adaptation to new lifestyle has occurred in humans since the agricultural revolution. Here we test the hypothesis that high levels of genetic variation at CYP2D6, a locus coding for a detoxifying enzyme of the cytochrome P450 complex, reflect this change.
We compared DNA sequences and predicted the levels of enzyme activity across 10 African, Asian and European populations, six of which currently rely on hunting and gathering (HG) while four on food production (FP).
HG and FP showed similar levels of CYP2D6 diversity, but displayed different substitution patterns at coding DNA sites possibly related to selective differences. Comparison with variation at presumably neutral independent loci confirmed this finding, despite the confounding effects of population history, resulting in higher overall variation in Africans than in Eurasians. The differences between HG and FP populations suggest that new lifestyle and dietary habits acquired in the transition to agriculture affected the variation pattern at CYP2D6, leading to an increase in FP populations of the frequency of alleles that are associated with a slower rate of metabolism. These alleles reached a balanced co-existence with other important and previously selected variants. We suggest that the pronounced substrate-dependent activity of most of these enzymes expanded the spectrum of the metabolic response.
Notre patrimoine génétique dévoile, de plus en plus, les passerelles démogénétiques d’une susceptibilité plus accrue de certains individus à des maladies infectieuses complexes. En vue d’une caractérisation de la variabilité génétique des populations ouest-africaines, nous avons analysé 659 chromosomes X au locus dys44 qui comprend, 35 SNPs et un microsatellite distribués sur 2853 pb en amont et 5034 pb en aval de l’exon 44 du gène de la dystrophine en Xp21.3. Les génotypes obtenus, par ASO dynamique et électrophorèse sur gel d’acrylamide, ont servi à la détermination des haplotypes. Des paramètres comme la diversité haplotypique (G) et l'indice de fixation (Fst) ont été calculés. Des analyses en composantes principales ainsi que multidimensionnelles ont été réalisées. Sur 68 haplotypes détectés, 26 sont nouveaux, et cette région, avec une diversité haplotypique moyenne (Gmoy) de 0,91 ± 0,03, se révèle beaucoup plus hétérogène que le reste du continent (Gmoy = 0,85 ± 0,04). Toutefois, malgré l’existence de disparités sous régionales dans la distribution des variants du marqueur dys44, l’AMOVA montre d’une manière générale, une faible érosion de l’éloignement génétique entre les populations subsahariennes (Fst = 1,5% ; p<10-5). Certains variants tel que l’haplotype eurasien B006 paraissent indiquer des flux transsahariens de gènes entre les populations nord-africaines et celles subsahariennes, comme l’exemplifie le pool génétique de l’une des populations ubiquitaires de la famille linguistique Nigéro-congolaise : Les Fulani. Nos résultats vont aussi dans le sens d’un héritage phylétique commun entre les Biaka, les Afro-américains et les populations de la sous-famille de langues Volta-Congo. The unravelling of our genetic heritage has revealed a demogenetic segueway leading to an increased susceptibility of certain individuals to complex infectious diseases. In order to characterize genetic variability among the West African populations, we analyzed 659 X chromosomes at the dys44 locus which comprises 35 SNPs and a microsatellite spanning a region 2853 bp upstream and 5034 bp downstream of exon 44 of the dystrophine gene in Xp21.3. The resulting genotypes, obtained by dynamic allele specific oligonucleotide hybridization and acrylamide gel electrophoresis, were used for haplotype construction. Gene diversity parameters such as the haplotypic diversity (G) and fixation indexes (Fst) were estimated. Multidimensional analysis of the data, including principal component analysis was also performed. Of the 68 distinct haplotypes detected in our data set, 26 were novel. The mean haplotypic diversity (Gmoy) was 0.91 ± 0.03 for this West African region which was shown to be more heterogeneous than the rest of the continent (Gmoy = 0.85 ± 0.04). However, despite certain sub-regional differences in the distribution of dys44 variants, the analysis of molecular variance showed an overall decline in the genetic distance between Sub-Saharan populations (Fst = 1.5% ; p<10-5). Certain variants, such as the Eurasian-specific haplotype B006, appear to suggest a Trans-Saharan gene flux between North African and Sub-Saharan populations as exemplified by the observed genetic pool of one of the ubiquitous populations of the Nigerian-Congolese linguistic family: The Fulani. Our results are also in agreement with a phyletic heritage between the Biaka, the Afro-Americans and the populations of the Volta-Congo language subfamilies.
The Malagasy have been shown to be a genetically admixed population combining parental lineages with African and South East Asian ancestry. In the present paper, we fit the Malagasy admixture history in a highly resolved phylogeographic framework by typing a large set of mitochondrial DNA and Y DNA markers in unrelated individuals from inland (Merina) and coastal (Antandroy, Antanosy, and Antaisaka) ethnic groups. This allowed performance of a multilevel analysis in which the diversity among main ethnic divisions, lineage ancestries, and modes of inheritance could be concurrently evaluated. Admixture was confirmed to result from the encounter of African and Southeast Asian people with minor recent male contributions from Europe. However, new scenarios are depicted about Malagasy admixture history. The distribution of ancestral components was ethnic and sex biased, with the Asian ancestry appearing more conserved in the female than in the male gene pool and in inland than in coastal groups. A statistic based on haplotype sharing (D(HS)), showing low sampling error and time linearity over the last 200 generations, was introduced here for the first time and helped to integrate our results with linguistic and archeological data. The focus about the origin of Malagasy lineages was enlarged in space and pushed back in time. Homelands could not be pinpointed but appeared to comprise two vast areas containing different populations from sub-Saharan Africa and South East Asia. The pattern of diffusion of uniparental lineages was compatible with at least two events: a primary admixture of proto-Malay people with Bantu speakers bearing a western-like pool of haplotypes, followed by a secondary flow of Southeastern Bantu speakers unpaired for gender (mainly male driven) and geography (mainly coastal).
Three sets of genetic markers (blood group plus protein polymorphisms, mitochondrial DNA, and Y-chromosome) were compared in four French Guiana and one Brazilian Amerindian populations. Spearman's rank correlation coefficient between five gene diversity statistics and historical or present-day population sizes showed significant values, indicating loss of diversity due to population bottlenecks. The three sets of markers furnished distinct admixture estimates, and the blood group plus protein polymorphisms could have overestimated the European contribution to their gene pool. Correspondence analysis distinguished the coastal from the interior populations, possibly reflecting past migration events.
To investigate associations between genetic, linguistic, and geographic variation in Africa, we type 50 Y chromosome SNPs in 1122 individuals from 40 populations representing African geographic and linguistic diversity. We compare these patterns of variation with those that emerge from a similar analysis of published mtDNA HVS1 sequences from 1918 individuals from 39 African populations. For the Y chromosome, Mantel tests reveal a strong partial correlation between genetic and linguistic distances (r=0.33, P=0.001) and no correlation between genetic and geographic distances (r=-0.08, P>0.10). In contrast, mtDNA variation is weakly correlated with both language (r=0.16, P=0.046) and geography (r=0.17, P=0.035). AMOVA indicates that the amount of paternal among-group variation is much higher when populations are grouped by linguistics (Phi(CT)=0.21) than by geography (Phi(CT)=0.06). Levels of maternal genetic among-group variation are low for both linguistics and geography (Phi(CT)=0.03 and 0.04, respectively). When Bantu speakers are removed from these analyses, the correlation with linguistic variation disappears for the Y chromosome and strengthens for mtDNA. These data suggest that patterns of differentiation and gene flow in Africa have differed for men and women in the recent evolutionary past. We infer that sex-biased rates of admixture and/or language borrowing between expanding Bantu farmers and local hunter-gatherers played an important role in influencing patterns of genetic variation during the spread of African agriculture in the last 4000 years.
Founder analysis is a method for analysis of nonrecombining DNA sequence data, with the aim of identification and dating of migrations into new territory. The method picks out founder sequence types in potential source populations and dates lineage clusters deriving from them in the settlement zone of interest. Here, using mtDNA, we apply the approach to the colonization of Europe, to estimate the proportion of modern lineages whose ancestors arrived during each major phase of settlement. To estimate the Palaeolithic and Neolithic contributions to European mtDNA diversity more accurately than was previously achievable, we have now extended the Near Eastern, European, and northern-Caucasus databases to 1,234, 2, 804, and 208 samples, respectively. Both back-migration into the source population and recurrent mutation in the source and derived populations represent major obstacles to this approach. We have developed phylogenetic criteria to take account of both these factors, and we suggest a way to account for multiple dispersals of common sequence types. We conclude that (i) there has been substantial back-migration into the Near East, (ii) the majority of extant mtDNA lineages entered Europe in several waves during the Upper Palaeolithic, (iii) there was a founder effect or bottleneck associated with the Last Glacial Maximum, 20,000 years ago, from which derives the largest fraction of surviving lineages, and (iv) the immigrant Neolithic component is likely to comprise less than one-quarter of the mtDNA pool of modern Europeans.
The complete sequence of the 16,569-base pair human mitochondrial genome is presented. The genes for the 12S and 16S rRNAs, 22 tRNAs, cytochrome c oxidase subunits I, II and III, ATPase subunit 6, cytochrome b and eight other predicted protein coding genes have been located. The sequence shows extreme economy in that the genes have none or only a few noncoding bases between them, and in many cases the termination codons are not coded in the DNA but are created post-transcriptionally by polyadenylation of the mRNAs.
The nonrecombining portion of the human Y chromosome has proven to be a valuable tool for the study of population history. The maintenance of extended haplotypes characteristic of particular geographic regions, despite extensive admixture, allows complex demographic events to be deconstructed. In this study we report the frequencies of 23 Y-chromosome biallelic polymorphism haplotypes in 1,935 men from 49 Eurasian populations, with a particular focus on Central Asia. These haplotypes reveal traces of historical migrations, and provide an insight into the earliest patterns of settlement of anatomically modern humans on the Eurasian continent. Central Asia is revealed to be an important reservoir of genetic diversity, and the source of at least three major waves of migration leading into Europe, the Americas, and India. The genetic results are interpreted in the context of Eurasian linguistic patterns.
Hypervariable parts of mitochondrial DNA (mtDNA) were amplified enzymatically and sequenced directly by using genomic DNA from single plucked human hairs. This method has been applied to study mtDNA sequence variation among 15 members of the !Kung population. A genealogical tree relating these aboriginal, Khoisan-speaking southern Africans to 68 other humans and to one chimpanzee has the deepest branches occurring amongst the !Kung, a result consistent with an African origin of human mtDNA. Fifteen cases of unrelated individuals having identical sequences in the most variable parts of the mtDNA control region were found within populations of !Kung, Western Pygmies, and Eastern Pygmies, but no cases of identity were evident among these populations. This and other evidence of geographic structuring of the mitochondrial diversity in Africa, together with knowledge of the rate of accumulation of base changes in human mtDNA, implies that the average rate at which female lineages have moved their home bases during hunter-gatherer times could be as low as 13 meters per year. The technique of enzymatic amplification and direct sequencing applied to readily collected, highly stable biological materials such as hairs makes it possible to examine with high resolution many representatives of virtually any population.
Many highly polymorphic minisatellite loci can be detected simultaneously in the human genome by hybridization to probes consisting of tandem repeats of the 'core' sequence. The resulting DNA fingerprints produced by Southern blot hybridization are comprised of multiple hypervariable DNA fragments, show somatic and germline stability and are completely specific to an individual. We now show that this technique can be used for forensic purposes; DNA of high relative molecular mass (Mr) can be isolated from 4-yr-old bloodstains and semen stains made on cotton cloth and digested to produce DNA fingerprints suitable for individual identification. Further, sperm nuclei can be separated from vaginal cellular debris, obtained from semen-contaminated vaginal swabs, enabling positive identification of the male donor/suspect. It is envisaged that DNA fingerprinting will revolutionize forensic biology particularly with regard to the identification of rape suspects.
Although the Canary Islands were settled by humans, possibly of Berber origin, as late as 2500 years ago, the precise course and numbers of early migrations to the archipelago remain controversial. We have therefore analysed mtDNA variation (HVS-I as well as selected RFLP sites) in 300 individuals from the seven Canary Islands. The distribution and variation across the islands in a specific mtDNA clade of Northwest African ancestry suggest that there was one dominant initial settlement process that affected all the islands, from east to west. This indicates that a certain genetic affinity of present-day Canary Islanders to Northwest African Berbers mainly stems from the autochthonous population rather than slaves captured on the neighbouring African coast. The slave trade after the European conquest left measurable, though minor, traces in the mtDNA pool of the Canary Islands, which in its majority testifies to the European immigration.
A genetic perspective of human history in Europe was derived from 22 binary markers of the nonrecombining Y chromosome (NRY). Ten lineages account for >95% of the 1007 European Y chromosomes studied. Geographic distribution and age estimates of alleles are compatible with two Paleolithic and one Neolithic migratory episode that have contributed to the modern European gene pool. A significant correlation between the NRY haplotype data and principal components based on 95 protein markers was observed, indicating the effectiveness of NRY binary polymorphisms in the characterization of human population composition and history.
Although molecular genetic evidence continues to accumulate that is consistent with a recent common African ancestry of modern humans, its ability to illuminate regional histories remains incomplete. A set of unique event polymorphisms associated with the non-recombining portion of the Y-chromosome (NRY) addresses this issue by providing evidence concerning successful migrations originating from Africa, which can be interpreted as subsequent colonizations, differentiations and migrations overlaid upon previous population ranges. A total of 205 markers identified by denaturing high performance liquid chromatography (DHPLC), together with 13 taken from the literature, were used to construct a parsimonious genealogy. Ancestral allelic states were deduced from orthologous great ape sequences. A total of 131 unique haplotypes were defined which trace the microevolutionary trajectory of global modern human genetic diversification. The genealogy provides a detailed phylogeographic portrait of contemporary global population structure that is emblematic of human origins, divergence and population history that is consistent with climatic, paleoanthropological and other genetic knowledge.
We determine the phylogenetic backbone of the East Asian mtDNA tree by using published complete mtDNA sequences and assessing
both coding and control region variation in 69 Han individuals from southern China. This approach assists in the interpretation
of published mtDNA data on East Asians based on either control region sequencing or restriction fragment length polymorphism
(RFLP) typing. Our results confirm that the East Asian mtDNA pool is locally region-specific and completely covered by the
two superhaplogroups M and N. The phylogenetic partitioning based on complete mtDNA sequences corroborates existing RFLP-based
classification of Asian mtDNA types and supports the distinction between northern and southern populations. We describe new
haplogroups M7, M8, M9, N9, and R9 and demonstrate by way of example that hierarchically subdividing the major branches of
the mtDNA tree aids in recognizing the settlement processes of any particular region in appropriate time scale. This is illustrated
by the characteristically southern distribution of haplogroup M7 in East Asia, whereas its daughter-groups, M7a and M7b2,
specific for Japanese and Korean populations, testify to a presumably (pre-)Jomon contribution to the modern mtDNA pool of
Japan.
Until recently, the Y chromosome seemed to fulfil the role of juvenile delinquent among human chromosomes--rich in junk, poor in useful attributes, reluctant to socialize with its neighbours and with an inescapable tendency to degenerate. The availability of the near-complete chromosome sequence, plus many new polymorphisms, a highly resolved phylogeny and insights into its mutation processes, now provide new avenues for investigating human evolution. Y-chromosome research is growing up.
Analysis of 89 biallelic polymorphisms in 523 Turkish Y chromosomes revealed 52 distinct haplotypes with considerable haplogroup substructure, as exemplified by their respective levels of accumulated diversity at ten short tandem repeat (STR) loci. The major components (haplogroups E3b, G, J, I, L, N, K2, and R1; 94.1%) are shared with European and neighboring Near Eastern populations and contrast with only a minor share of haplogroups related to Central Asian (C, Q and O; 3.4%), Indian (H, R2; 1.5%) and African (A, E3*, E3a; 1%) affinity. The expansion times for 20 haplogroup assemblages was estimated from associated STR diversity. This comprehensive characterization of Y-chromosome heritage addresses many multifaceted aspects of Anatolian prehistory, including: (1) the most frequent haplogroup, J, splits into two sub-clades, one of which (J2) shows decreasing variances with increasing latitude, compatible with a northward expansion; (2) haplogroups G1 and L show affinities with south Caucasus populations in their geographic distribution as well as STR motifs; (3) frequency of haplogroup I, which originated in Europe, declines with increasing longitude, indicating gene flow arriving from Europe; (4) conversely, haplogroup G2 radiates towards Europe; (5) haplogroup E3b3 displays a latitudinal correlation with decreasing frequency northward; (6) haplogroup R1b3 emanates from Turkey towards Southeast Europe and Caucasia and; (7) high resolution SNP analysis provides evidence of a detectable yet weak signal (<9%) of recent paternal gene flow from Central Asia. The variety of Turkish haplotypes is witness to Turkey being both an important source and recipient of gene flow.
The Y chromosome contains the largest nonrecombining block in the human genome. By virtue of its many polymorphisms, it is now the most informative haplotyping system, with applications in evolutionary studies, forensics, medical genetics, and genealogical reconstruction. However, the emergence of several unrelated and nonsystematic nomenclatures for Y-chromosomal binary haplogroups is an increasing source of confusion. To resolve this issue, 245 markers were genotyped in a globally representative set of samples, 74 of which were males from the Y Chromosome Consortium cell line repository. A single most parsimonious phylogeny was constructed for the 153 binary haplogroups observed. A simple set of rules was developed to unambiguously label the different clades nested within this tree. This hierarchical nomenclature system supersedes and unifies past nomenclatures and allows the inclusion of additional mutations and haplogroups yet to be discovered.
[Supplementary Table 1, available as an online supplement at www.genome.org , lists all published markers included in this survey and primer information.]
mtDNA studies support an African origin for modern Eurasians, but expansion events within Africa have not previously been investigated. We have therefore analyzed 407 mtDNA control-region sequences from 13 African ethnic groups. A number of sequences (13%) were highly divergent and coalesced on the "mitochondrial Eve" in Africans. The remaining sequences also ultimately coalesced on this sequence but fell into four major clusters whose starlike phylogenies testify to demographic expansions. The oldest of these African expansions dates to approximately 60,000-80,000 years ago. Eurasian sequences are derived from essentially one sequence within this ancient cluster, even though a diverse mitochondrial pool was present in Africa at the time.
Variation in the human mitochondrial genome (mtDNA) is now routinely described and used to infer the histories of peoples, by means of one of two procedures, namely, the assaying of RFLPs throughout the genome and the sequencing of parts of the control region (CR). Using 95 samples from the Near East and northwest Caucasus, we present an analysis based on both systems, demonstrate their concordance, and, using additional available information, present the most refined phylogeny to date of west Eurasian mtDNA. We describe and apply a nomenclature for mtDNA clusters. Hypervariable nucleotides are identified, and the relative mutation rates of the two systems are evaluated. We point out where ambiguities remain. The identification of signature mutations for each cluster leads us to apply a hierarchical scheme for determining the cluster composition of a sample of Berber speakers, previously analyzed only for CR variation. We show that the main indigenous North African cluster is a sister group to the most ancient cluster of European mtDNAs, from which it diverged approximately 50,000 years ago.
Genetic studies have emphasized the contrast between North African and sub-Saharan populations, but the particular affinities of the North African mtDNA pool to that of Europe, the Near East, and sub-Saharan Africa have not previously been investigated. We have analysed 268 mtDNA control-region sequences from various Northwest African populations including several Senegalese groups and compared these with the mtDNA database. We have identified a few mitochondrial motifs that are geographically specific and likely predate the distribution and diversification of modern language families in North and West Africa. A certain mtDNA motif (16172C, 16219G), previously found in Algerian Berbers at high frequency, is apparently omnipresent in Northwest Africa and may reflect regional continuity of more than 20,000 years. The majority of the maternal ancestors of the Berbers must have come from Europe and the Near East since the Neolithic. The Mauritanians and West-Saharans, in contrast, bear substantial though not dominant mtDNA affinity with sub-Saharans.
This study analyzes the distribution of ten protein genetic polymorphisms in eighteen populations from the most densely inhabited areas of Cameroon. The languages spoken belong to three different linguistic families [Afro-Asiatic (AA), Nilo-Saharan (NS) and Niger-Kordofanian (NK)]. The analysis of variation of allele frequencies indicates that the level of genetic interpopulation differentiation is rather low (F(st) = 0.011 +/- 0.006) but statistically significant (p < 0.001). This result is not unexpected because of the relatively small geographic area covered by our survey. This value is also significantly lower than the one estimated for other groups of African populations. Among the factors responsible for this, we discuss the possible role of gene flow. There is a considerable genetic differentiation among the AA populations of north Cameroon as is to be expected because they all originated from the first agriculturists of the farming "savanna complex." The Podowko and Uldeme are considerably different from all the other AA groups, probably due to the combined effect of genetic drift and isolation. In the case of the Wandala and Massa, our analyses suggest that genetic admixture with allogeneous groups (especially with the Kanuri) played an important role in determining their genetic differentiation from other AA speaking groups. The Bantu speaking populations (Bakaka, Bamileke Bassa and Ewondo, NK family, Benué Congo subfamily) settled in western and southern Cameroon are more tightly clustered than AA speaking groups. This result shows that the linguistic affinity among these four populations coincides with a substantial genetic similarity despite their different origin. Finally, the Fulbe are genetically distinct from all the populations that belong to their same linguistic phylum (NK), and closer to the neighboring Fali and Tupuri, eastern Adamawa speaking groups of north Cameroon.
In the present study we have analyzed 44 Y-chromosome biallelic polymorphisms in population samples from northwestern (NW) Africa and the Iberian Peninsula, which allowed us to place each chromosome unequivocally in a phylogenetic tree based on >150 polymorphisms. The most striking results are that contemporary NW African and Iberian populations were found to have originated from distinctly different patrilineages and that the Strait of Gibraltar seems to have acted as a strong (although not complete) barrier to gene flow. In NW African populations, an Upper Paleolithic colonization that probably had its origin in eastern Africa contributed 75% of the current gene pool. In comparison, approximately 78% of contemporary Iberian Y chromosomes originated in an Upper Paleolithic expansion from western Asia, along the northern rim of the Mediterranean basin. Smaller contributions to these gene pools (constituting 13% of Y chromosomes in NW Africa and 10% of Y chromosomes in Iberia) came from the Middle East during the Neolithic and, during subsequent gene flow, from Sub-Saharan to NW Africa. Finally, bidirectional gene flow across the Strait of Gibraltar has been detected: the genetic contribution of European Y chromosomes to the NW African gene pool is estimated at 4%, and NW African populations may have contributed 7% of Iberian Y chromosomes. The Islamic rule of Spain, which began in a.d. 711 and lasted almost 8 centuries, left only a minor contribution to the current Iberian Y-chromosome pool. The high-resolution analysis of the Y chromosome allows us to separate successive migratory components and to precisely quantify each historical layer.
Various populations have contributed to the present-day gene pool of Morocco, including the autochthonous Berber population, Phoenicians, Sephardic Jews, Bedouin Arabs and sub-Saharan Africans.
The primary objective of the study was to complete a genetic description of the Berber-speaking population in the Souss region of southern Morocco, based on mitochondrial DNA (mtDNA) sequence analysis.
The first hypervariable segment of the mtDNA control region was sequenced in a sample of 50 individuals from the Souss Valley, and the results compared with the extensive body of data available on mtDNA sequence variation in Europe and sub-Saharan Africa.
Thirty-four different sequences were found: an estimated 68% of the sequences occurred throughout Europe, West Asia and North Africa, 26% originated in sub-Saharan Africa, and 6% belonged to the North African specific haplogroup U6. The Souss Valley mtDNA sequences indicated the presence of two populations which expanded at different times: the West Eurasian sequences in the Souss sample had a smaller average number of pairwise differences than pairs of sub-Saharan sequences.
Detailed knowledge of the possible geographic origin of each sequence facilitated an interpretation of both internal diversity parameters and between-population relationships. The sub-Saharan admixture in the Souss Valley matched the south-north cline of sub-Saharan influence in North Africa, also evident in the genetic distances of North African populations to Europeans and sub-Saharan Africans.
The variation of 77 biallelic sites located in the nonrecombining portion of the Y chromosome was examined in 608 male subjects from 22 African populations. This survey revealed a total of 37 binary haplotypes, which were combined with microsatellite polymorphism data to evaluate internal diversities and to estimate coalescence ages of the binary haplotypes. The majority of binary haplotypes showed a nonuniform distribution across the continent. Analysis of molecular variance detected a high level of interpopulation diversity (PhiST=0.342), which appears to be partially related to the geography (PhiCT=0.230). In sub-Saharan Africa, the recent spread of a set of haplotypes partially erased pre-existing diversity, but a high level of population (PhiST=0.332) and geographic (PhiCT=0.179) structuring persists. Correspondence analysis shows that three main clusters of populations can be identified: northern, eastern, and sub-Saharan Africans. Among the latter, the Khoisan, the Pygmies, and the northern Cameroonians are clearly distinct from a tight cluster formed by the Niger-Congo-speaking populations from western, central western, and southern Africa. Phylogeographic analyses suggest that a large component of the present Khoisan gene pool is eastern African in origin and that Asia was the source of a back migration to sub-Saharan Africa. Haplogroup IX Y chromosomes appear to have been involved in such a migration, the traces of which can now be observed mostly in northern Cameroon.
Africa presents the most complex genetic picture of any continent, with a time depth for mitochondrial DNA (mtDNA) lineages >100,000 years. The most recent widespread demographic shift within the continent was most probably the Bantu dispersals, which archaeological and linguistic evidence suggest originated in West Africa 3,000-4,000 years ago, spreading both east and south. Here, we have carried out a thorough phylogeographic analysis of mtDNA variation in a total of 2,847 samples from throughout the continent, including 307 new sequences from southeast African Bantu speakers. The results suggest that the southeast Bantu speakers have a composite origin on the maternal line of descent, with approximately 44% of lineages deriving from West Africa, approximately 21% from either West or Central Africa, approximately 30% from East Africa, and approximately 5% from southern African Khoisan-speaking groups. The ages of the major founder types of both West and East African origin are consistent with the likely timing of Bantu dispersals, with those from the west somewhat predating those from the east. Despite this composite picture, the southeastern African Bantu groups are indistinguishable from each other with respect to their mtDNA, suggesting that they either had a common origin at the point of entry into southeastern Africa or have undergone very extensive gene flow since.
We have analyzed and compared mitochondrial DNA variation of populations from the Near East and Africa and found a very high frequency of African lineages present in the Yemen Hadramawt: more than a third were of clear sub-Saharan origin. Other Arab populations carried approximately 10% lineages of sub-Saharan origin, whereas non-Arab Near Eastern populations, by contrast, carried few or no such lineages, suggesting that gene flow has been preferentially into Arab populations. Several lines of evidence suggest that most of this gene flow probably occurred within the past approximately 2,500 years. In contrast, there is little evidence for male-mediated gene flow from sub-Saharan Africa in Y-chromosome haplotypes in Arab populations, including the Hadramawt. Taken together, these results are consistent with substantial migration from eastern Africa into Arabia, at least in part as a result of the Arab slave trade, and mainly female assimilation into the Arabian population as a result of miscegenation and manumission.
Phylogenetic analysis of mitochondrial DNA (mtDNA) performed in Western Mediterranean populations has shown that both shores share a common set of mtDNA haplogroups already found in Europe and the Middle East. Principal co-ordinates of genetic distances and principal components analyses based on the haplotype frequencies show that the main genetic difference is attributed to the higher frequency of sub-Saharan L haplogroups in NW Africa, showing some gene flow across the Sahara desert, with a major impact in the southern populations of NW Africa. The AMOVA demonstrates that SW European populations are highly homogeneous whereas NW African populations display a more heterogeneous genetic pattern, due to an east-west differentiation as a result of gene flow coming from the East. Despite the shared haplogroups found in both areas, the European V and the NW African U6 haplogroups reveal the traces of the Mediterranean Sea permeability to female migrations, and allowed for determination and quantification of the genetic contribution of both shores to the genetic landscape of the geographic area.
Comparison of mtDNA data with autosomal markers and Y-chromosome lineages, analysed in the same populations, shows a congruent pattern, although female-mediated gene flow seems to have been more intense than male-mediated gene flow.
Mitochondrial DNA (mtDNA) lineages of 232 individuals from 12 Central Asian populations were sequenced for both control region hypervariable segments, and additional informative sites in the coding region were also determined. Most of the mtDNA lineages belong to branches of the haplogroups with an eastern Eurasian (A, B, C, D, F, G, Y, and M haplogroups) or a western Eurasian (HV, JT, UK, I, W, and N haplogroups) origin, with a small fraction of Indian M lineages. This suggests that the extant genetic variation found in Central Asia is the result of admixture of already differentiated populations from eastern and western Eurasia. Nonetheless, two groups of lineages, D4c and G2a, seem to have expanded from Central Asia and might have their Y-chromosome counterpart in lineages belonging to haplotype P(xR1a). The present results suggest that the mtDNA found out of Africa might be the result of a maturation phase, presumably in the Middle East or eastern Africa, that led to haplogroups M and N, and subsequently expanded into Eurasia, yielding a geographically structured group of external branches of these two haplogroups in western and eastern Eurasia, Central Asia being a contact zone between two differentiated groups of peoples.
The Eastern Pygmies from Zaire and Western Pygmies from Cameroon, Congo, and the Central African Republic represent the two principal groups of African Pygmies. In the "recent divergence" hypothesis in which Western Pygmies are thought to be the result of hybridization between the ancestors of Eastern Pygmies and Bantu farmers who penetrated the equatorial belt and came into contact with Pygmies around 2-3 kiloyears ago. On the basis of recent archaeological research in the tropical rain forest, we propose a "pre-Bantu divergence" hypothesis, which posits the separation between the ancestors of Eastern and Western Pygmies earlier than 18 kiloyears ago. In order to test the two hypotheses, we analyzed the variation of the hypervariable region 1 of the mitochondrial DNA in the Mbenzele, Western Pygmies of the Central African Republic, and compared our results with those of previous mtDNA and Y chromosome studies. Distribution, sequence variation, and age of haplogroups along with genetic distances among populations, estimates of divergence times, and simulations based on the coalescent approach were found to be congruent with the pre-Bantu divergence but failed to support the recent divergence hypothesis.
Paleoanthropological evidence indicates that both the Levantine corridor and the Horn of Africa served, repeatedly, as migratory corridors between Africa and Eurasia. We have begun investigating the roles of these passageways in bidirectional migrations of anatomically modern humans, by analyzing 45 informative biallelic markers as well as 10 microsatellite loci on the nonrecombining region of the Y chromosome (NRY) in 121 and 147 extant males from Oman and northern Egypt, respectively. The present study uncovers three important points concerning these demic movements: (1) The E3b1-M78 and E3b3-M123 lineages, as well as the R1*-M173 lineages, mark gene flow between Egypt and the Levant during the Upper Paleolithic and Mesolithic. (2) In contrast, the Horn of Africa appears to be of minor importance in the human migratory movements between Africa and Eurasia represented by these chromosomes, an observation based on the frequency distributions of E3b*-M35 (no known downstream mutations) and M173. (3) The areal diffusion patterns of G-M201, J-12f2, the derivative M173 haplogroups, and M2 suggest more recent genetic associations between the Middle East and Africa, involving the Levantine corridor and/or Arab slave routes. Affinities to African groups were also evaluated by determining the NRY haplogroup composition in 434 samples from seven sub-Saharan African populations. Oman and Egypt's NRY frequency distributions appear to be much more similar to those of the Middle East than to any sub-Saharan African population, suggesting a much larger Eurasian genetic component. Finally, the overall phylogeographic profile reveals several clinal patterns and genetic partitions that may indicate source, direction, and relative timing of different waves of dispersals and expansions involving these nine populations.
We have typed 275 men from five populations in Algeria, Tunisia, and Egypt with a set of 119 binary markers and 15 microsatellites from the Y chromosome, and we have analyzed the results together with published data from Moroccan populations. North African Y-chromosomal diversity is geographically structured and fits the pattern expected under an isolation-by-distance model. Autocorrelation analyses reveal an east-west cline of genetic variation that extends into the Middle East and is compatible with a hypothesis of demic expansion. This expansion must have involved relatively small numbers of Y chromosomes to account for the reduction in gene diversity towards the West that accompanied the frequency increase of Y haplogroup E3b2, but gene flow must have been maintained to explain the observed pattern of isolation-by-distance. Since the estimates of the times to the most recent common ancestor (TMRCAs) of the most common haplogroups are quite recent, we suggest that the North African pattern of Y-chromosomal variation is largely of Neolithic origin. Thus, we propose that the Neolithic transition in this part of the world was accompanied by demic diffusion of Afro-Asiatic-speaking pastoralists from the Middle East.
M173 and the low frequency of U6 found in North Cameroon contrast sharply with the low frequency of R1*-M173 and the high frequency of U6 in North Africa
- Bosch
nally, it is important to note that the high frequency of R1*-M173 and the low frequency of U6 found in North Cameroon contrast sharply with the low frequency of R1*-M173 and the high frequency of U6 in North Africa (Bosch et al., 2001; Cruciani et al., 2002; Cinnioglu et al., 2004; Luis et al., 2004; Arredi et al., 2004; Salas et al., 2002).
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evolutionary marker comes of age. Nat Rev Genet 4:598 – 612.