Mitochondrial DNA Heterogeneity in Tunisian Berbers

Berbers live in groups scattered across North Africa whose origins and genetic relationships with their neighbours are not well established. The first hypervariable segment of the mitochondrial DNA (mtDNA) control region was sequenced in a total of 155 individuals from three Tunisian Berber groups and compared to other North Africans. The mtDNA lineages found belong to a common set of mtDNA haplogroups already described in North Africa. Besides the autochthonous North African U6 haplogroup, a group of L3 lineages characterized by the transition at position 16041 seems to be restricted to North Africans, suggesting that an expansion of this group of lineages took place around 10500 years ago in North Africa, and spread to neighbouring populations. Principal components and the coordinate analyses show that some Berber groups (the Tuareg, the Mozabite, and the Chenini‐Douiret) are outliers within the North African genetic landscape. This outlier position is consistent with an isolation process followed by genetic drift in haplotype frequencies, and with the high heterogeneity displayed by Berbers compared to Arab samples as shown in the AMOVA. Despite this Berber heterogeneity, no significant differences were found between Berber and Arab samples, suggesting that the Arabization was mainly a cultural process rather than a demographic replacement.     

Mitochondrial DNA Variability in Slovaks, with Application to the Roma Origin

To gain insight into the mitochondrial gene pool diversity of European populations, we studied mitochondrial DNA (mtDNA) variability in 207 subjects from western and eastern areas of Slovakia. Sequencing of two hypervariable segments, HVS I and HVS II, in combination with screening of coding region haplogroup-specific RFLP-markers, revealed that the majority of Slovak mtDNAs belong to the common West Eurasian mitochondrial haplogroups (HV, J, T, U, N1, W, and X). However, a few sub-Saharan African (L2a) mtDNAs were detected in a population from eastern part of Slovakia. In addition, about 3% of mtDNAs from eastern Slovakia encompass Roma-specific lineages. By means of complete mtDNA sequencing we demonstrate here that the Roma-specific M-lineages observed in gene pools of different Slavonic populations (Slovaks, Poles and Russians), belong to Indian-specific haplogroups M5a1 and M35. Moreover, we show that haplogroup J lineages found in gene pools of the Roma and some Slavonic populations (Czechs and Slovaks) belong to new subhaplogroup J1a, which is defined by coding region mutation at position 8460.     

Mitochondrial DNA Sequence Diversity in a Sedentary Population from Egypt

The mitochondrial DNA (mtDNA) diversity of 58 individuals from Upper Egypt, more than half (34 individuals) from Gurna, whose population has an ancient cultural history, were studied by sequencing the control‐region and screening diagnostic RFLP markers. This sedentary population presented similarities to the Ethiopian population by the L1 and L2 macrohaplogroup frequency (20.6%), by the West Eurasian component (defined by haplogroups H to K and T to X) and particularly by a high frequency (17.6%) of haplogroup M1. We statistically and phylogenetically analysed and compared the Gurna population with other Egyptian, Near East and sub‐Saharan Africa populations; AMOVA and Minimum Spanning Network analysis showed that the Gurna population was not isolated from neighbouring populations. Our results suggest that the Gurna population has conserved the trace of an ancestral genetic structure from an ancestral East African population, characterized by a high M1 haplogroup frequency. The current structure of the Egyptian population may be the result of further influence of neighbouring populations on this ancestral population.     

MtDNA Profile of West Africa Guineans: Towards a Better Understanding of the Senegambia Region

The matrilineal genetic composition of 372 samples from the Republic of Guiné‐Bissau (West African coast) was studied using RFLPs and partial sequencing of the mtDNA control and coding region. The majority of the mtDNA lineages of Guineans (94%) belong to West African specific sub‐clusters of L0‐L3 haplogroups. A new L3 sub‐cluster (L3h) that is found in both eastern and western Africa is present at moderately low frequencies in Guinean populations. A non‐random distribution of haplogroups U5 in the Fula group, the U6 among the “Brame” linguistic family and M1 in the Balanta‐Djola group, suggests a correlation between the genetic and linguistic affiliation of Guinean populations. The presence of M1 in Balanta populations supports the earlier suggestion of their Sudanese origin. Haplogroups U5 and U6, on the other hand, were found to be restricted to populations that are thought to represent the descendants of a southern expansion of Berbers. Particular haplotypes, found almost exclusively in East‐African populations, were found in some ethnic groups with an oral tradition claiming Sudanese origin.     

Diversity of mtDNA lineages in Portugal: not a genetic edge of European variation

The analysis of the hypervariable regions I and II of mitochondrial DNA in Portugal showed that this Iberian population presents a higher level of diversity than some neighbouring populations. The classification of the different sequences into haplogroups revealed the presence of all the most important European haplogroups, including those that expanded through Europe in the Palaeolithic, and those whose expansion has occurred during the Neolithic. Additionally a rather distinct African influence was detected in this Portuguese survey, as signalled by the distributions of haplogroups U6 and L, present at higher frequencies than those usually reported in Iberian populations. The geographical distributions of both haplogroups were quite different, with U6 being restricted to North Portugal whereas L was widespread all over the country. This seems to point to different population movements as the main contributors for the two haplogroup introductions. We hypothesise that the recent Black African slave trade could have been the mediator of most of the L sequence inputs, while the population movement associated with the Muslim rule of Iberia has predominantly introduced U6 lineages.     

Y-chromosome genetic variation in Rio de Janeiro population.

The present-day Brazilian gene pool is known to be the outcome of an admixture process of populations from different origins, mainly Amerindians, Europeans, and Africans. It is also known that in Brazil, a wide variation in the admixture process occurred in different regions of the country or even in different subpopulations from the same region. In the present study, we aimed to characterize the male lineages present in the Rio de Janeiro population, the second most populated of the 26 Brazilian states. A random sample of 127 unrelated males from Rio de Janeiro was typed for 28 Y-chromosome-specific biallelic markers. In total, 17 different haplogroups were defined within our sample, most of them of European ancestry (88.1%). Those of sub-Saharan African origin (E3a) amounted to 7.9%, while only 2 males carried Amerindian lineages (characterized by the presence of an M3 mutation: haplogroup Q3). Using both Y-STR haplotype and Y-SNP haplogroup information, genetic distances were calculated between the subgroup of Rio de Janeiro males carrying European haplogroups and the Portuguese population. Low, nonsignificant, values were obtained. Thus, in contrast with what is observed in their female counterparts, the vast majority of the present Rio de Janeiro male gene pool is of European extraction, while the original Amerindian lineages are residual and much less frequent than the sub-Saharan component resulting from the slave trade. These observations can be interpreted as the signature of the strong gender asymmetry of the admixture processes in colonial systems.     

Islands inside an island: reproductive isolates on Jerba island.

Jerba Island, located in South Eastern Tunisia, is inhabited by four ethnic groups: Berbers, Arabs, sub-Saharans, and Jews. All live in distinct areas, although the Arabs are also distributed all over the island. The first Arab settlement was founded in the 7th century A.D., so co-existence with Berbers has lasted for more than a millennium. Religious and cultural differences have represented an obstacle to the intermixing of these groups, and among both Arabs and Berbers marriages usually occur between members from the same extended family. Using new mtDNA data and previously described Y-chromosome STR-defined haplotypes, we tested whether this reported inbreeding would be reflected in the differentiation between Berber and Arab communities. Concerning mtDNA, the Berber group presented a greater Eurasian contribution (87%), and, surprisingly, no U6 haplotypes were found; in contrast, the Arabs showed a larger contribution of sub-Saharan lineages (24%) and the U6 haplogroup amounted to 10%. Another source of evidence for the reproductive isolation of the two groups was revealed through the analysis of haplotype matching (both mtDNA and Y-chromosome), showing that matching probabilities between them is of the same order of magnitude of that observed when contrasting samples from different European countries.     

Joining the Pillars of Hercules: mtDNA Sequences Show Multidirectional Gene Flow in the Western Mediterranean

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 characterisation of two Spanish populations from the Vera and Bejar valleys (Central Spain)

This survey reports the mitochondrial data of two Spanish populations living in the Vera and Bejar valleys, on the opposite slopes of the Sierra de Gredos (Central Spain), which crosses Spain east to west. The aim of the study was to characterise the mitochondrial genetic pool of the Vera and Bejar populations to investigate a putative mitogenetic differentiation between them, evidence that would support the role of the Sierra de Gredos as a genetic barrier in their micro-evolutionary histories. Blood samples of 137 people (66 from Vera and 71 from Bejar) were collected and mtDNA hypervariable regions I and II (HVR-I and HVR-II) were dissected along with several mtDNA-coding region SNPs. The main European mitochondrial lineages have been found both in Vera and in Bejar, together with the typical African haplogroups L (in Vera) and U6 (in Bejar). F_ST value and the 95% credible regions calculated for haplogroup frequencies do not reveal genetic differentiation among the populations. Vera and Bejar contain an expected mitochondrial variability within them, but they do not seem to be genetically different from each other, leading us to conclude that the Sierra de Gredos is not a significant genetic barrier in their maternal genetic history.     

Alu polymorphisms in Jerba Island population (Tunisia): comparative study in Arab and Berber groups

Jerba Island represents an interesting area because four distinct ethnic groups have been cohabiting there until now: Arabs, Berbers, dark-skinned people of sub-Saharan origin and Jews. Religious and cultural differences seem to have constituted an obstacle to their intermixing. Our aim is to provide further information on the genetic structure of the Arab and Berber groups for whom previous data based on haploid markers confirmed their reproductive isolation. Five polymorphic Alu markers (HS 4.69, Sb 19.3, TPA-25, ACE and APO-A1) were analysed in a sample of 43 Arabs and 48 Berbers of Jerba. The genetic relationships among these groups and several populations from North Africa, sub-Saharan Africa and Europe were analysed using genetic distances based on allele frequencies. The results showed a homogeneous distribution of Alu insertions in the two geographically close groups, reflecting ancient relationships between them. This study also revealed that Arabs from Jerba present close genetic distances to other North African populations, whilst Berbers of Jerba occupy an intermediate position among Mediterranean populations.     

A recent genetic link between Sami and the Volga-Ural region of Russia

The genetic origin of the Sami is enigmatic and contributions from Continental Europe, Eastern Europe and Asia have been proposed. To address the evolutionary history of northern and southern Swedish Sami, we have studied their mtDNA haplogroup frequencies and complete mtDNA genome sequences. While the majority of mtDNA diversity in the northern Swedish, Norwegian and Finnish Sami is accounted for by haplogroups V and U5b1b1, the southern Swedish Sami have other haplogroups and a frequency distribution similar to that of the Continental European population. Stratification of the southern Sami on the basis of occupation indicates that this is the result of recent admixture with the Swedish population. The divergence time for the Sami haplogroup V sequences is 7600 YBP (years before present), and for U5b1b1, 5500 YBP amongst Sami and 6600 YBP amongst Sami and Finns. This suggests an arrival in the region soon after the retreat of the glacial ice, either by way of Continental Europe and/or the Volga-Ural region. Haplogroup Z is found at low frequency in the Sami and Northern Asian populations but is virtually absent in Europe. Several conserved substitutions group the Sami Z lineages strongly with those from Finland and the Volga-Ural region of Russia, but distinguish them from Northeast Asian representatives. This suggests that some Sami lineages shared a common ancestor with lineages from the Volga-Ural region as recently as 2700 years ago, indicative of a more recent contribution of people from the Volga-Ural region to the Sami population.     

Mitochondrial DNA characterisation of European isolates: the Maragatos from Spain

Mitochondrial DNA analysis confirms that Maragatos from Spain are a genetically isolated human group. Genetic distances between Maragatos and the comparison samples are significantly different even with the León sample (P<0.001) which shares the same geographic area as the Maragatos. Although the north-African haplogroup U6 is present in them, their attributed Berber origin is weakened, as this haplogroup is also detected in surrounding populations with which, in addition, Maragatos have the smaller genetic distances. These U6 haplotypes are ascribed to a pre-historic African colonisation that influenced all the Iberian Peninsula. The presence of Neolithic haplogroups in this sample suggests that their isolation culture was not absolute until recent times.     

Alu polymorphisms in Jerba Island population (Tunisia): Comparative study in Arab and Berber groups

Jerba Island represents an interesting area because four distinct ethnic groups have been cohabiting there until now: Arabs, Berbers, dark-skinned people of sub-Saharan origin and Jews. Religious and cultural differences seem to have constituted an obstacle to their intermixing. Our aim is to provide further information on the genetic structure of the Arab and Berber groups for whom previous data based on haploid markers confirmed their reproductive isolation. Five polymorphic Alu markers (HS 4.69, Sb 19.3, TPA-25, ACE and APO-A1) were analysed in a sample of 43 Arabs and 48 Berbers of Jerba. The genetic relationships among these groups and several populations from North Africa, sub-Saharan Africa and Europe were analysed using genetic distances based on allele frequencies. The results showed a homogeneous distribution of Alu insertions in the two geographically close groups, reflecting ancient relationships between them. This study also revealed that Arabs from Jerba present close genetic distances to other North African populations, whilst Berbers of Jerba occupy an intermediate position among Mediterranean populations.     

Mitochondrial DNA variation in Jordanians and their genetic relationship to other Middle East populations

Background: The Levant is a crucial region in understanding human migrations between Africa and Eurasia. Although some mitochondrial DNA (mtDNA) studies have been carried out in this region, they have not included the Jordan area. This paper deals with the mtDNA composition of two Jordan populations.

Aim: The main objectives of this article are: first, to report mtDNA sequences of an urban and an isolate sample from Jordan and, second, to compare them with each other and with other nearby populations.

Subjects and methods: The analyses are based on HVSI and HVSII mtDNA sequences and diagnostic RFLPs to unequivocally classify into haplogroups 101 Amman and 44 Dead Sea unrelated individuals from Jordan.

Results: Statistical analysis revealed that, whereas the sample from Amman did not significantly differ from their Levantine neighbours, the Dead Sea sample clearly behaved as a genetic outlier in the region. Its outstanding Eurasian haplogroup U3 frequency (39%) and its south-Saharan Africa lineages (19%) are the highest in the Middle East. On the contrary, the lack ((preHV)1) or comparatively low frequency (J and T) of Neolithic lineages is also striking. Although strong drift by geographic isolation could explain the anomalous mtDNA pool of the Dead Sea sample, the fact that its mtDNA lineage composition mirrors, in geographic origin and haplogroup frequencies, its Y-chromosome pool, points to founder effect as the main cause. Ancestral M1 lineages detected in Jordan that have affinities with those recently found in Northwest but not East Africa question the African origin of the M1 haplogroup.

Conclusion: Results are in agreement with an old human settlement in the Jordan region. However, in spite of the attested migratory spreads, genetically divergent populations, such as that of the Dead Sea, still exist in the area.     

Reconstructing the phylogeny of African mitochondrial DNA lineages in Slavs

To elucidate the origin of African-specific mtDNA lineages, revealed previously in Slavonic populations (at frequency of about 0.4%), we completely sequenced eight African genomes belonging to haplogroups L1b, L2a, L3b, L3d and M1 gathered from Russians, Czechs, Slovaks and Poles. Results of phylogeographic analysis suggest that at least part of the African mtDNA lineages found in Slavs (such as L1b, L3b1, L3d) appears to be of West African origin, testifying to an opportunity of their occurrence as a result of migrations to Eastern Europe through Iberia. However, a prehistoric introgression of African mtDNA lineages into Eastern Europe (approximately 10 000 years ago) seems to be probable only for European-specific subclade L2a1a, defined by coding region mutations at positions 6722 and 12903 and detected in Czechs and Slovaks. Further studies of the nature of African admixture in gene pools of Europeans require the essential enlargement of databases of African complete mitochondrial genomes.European Journal of Human Genetics (2008) 16, 1091-1096; doi:10.1038/ejhg.2008.70; published online 9 April 2008.     

Mitochondrial DNA Variability in Bosnians and Slovenians

Mitochondrial DNA variability in two Slavonic‐speaking populations of the northwestern Balkan peninsula, Bosnians (N = 144) and Slovenians (N = 104), was studied by hypervariable segments I and II (HVS I and II) sequencing and restriction fragment‐length polymorphism (RFLP) analysis of the mtDNA coding region. The majority of the mtDNA detected in Southern Slavonic populations falls into the common West Eurasian mitochondrial haplogroups (e.g., H, pre‐V, J, T, U, K, I, W, and X). About 2% of the Bosnian mtDNAs encompass East Eurasian and African lineages (e.g., M and L1b, respectively). The distribution of mtDNA subclusters in Bosnians, Slovenians and the neighbouring European populations reveals that the common genetic substratum characteristic for Central and Eastern European populations (such as Germans, Poles, Russians and Finns) penetrates also South European territories as far as the Western Balkans. However, the observed differentiation between Bosnian and Slovenian mtDNAs suggests that at least two different migration waves of the Slavs may have reached the Balkans in the early Middle Ages.     

Y-chromosome Lineages from Portugal, Madeira and Açores Record Elements of Sephardim and Berber Ancestry

A total of 553 Y‐chromosomes were analyzed from mainland Portugal and the North Atlantic Archipelagos of Açores and Madeira, in order to characterize the genetic composition of their male gene pool. A large majority (78–83% of each population) of the male lineages could be classified as belonging to three basic Y chromosomal haplogroups, R1b, J, and E3b. While R1b, accounting for more than half of the lineages in any of the Portuguese sub‐populations, is a characteristic marker of many different West European populations, haplogroups J and E3b consist of lineages that are typical of the circum‐Mediterranean region or even East Africa. The highly diverse haplogroup E3b in Portuguese likely combines sub‐clades of distinct origins. The present composition of the Y chromosomes in Portugal in this haplogroup likely reflects a pre‐Arab component shared with North African populations or testifies, at least in part, to the influence of Sephardic Jews. In contrast to the marginally low sub‐Saharan African Y chromosome component in Portuguese, such lineages have been detected at a moderately high frequency in our previous survey of mtDNA from the same samples, indicating the presence of sex‐related gene flow, most likely mediated by the Atlantic slave trade.     

Mitochondrial DNA Diversity in the Polish Roma

Mitochondrial DNA variability in the Polish Roma population has been studied by means of hypervariable segment I and II (HVS I and II) sequencing and restriction fragment‐length polymorphism analysis of the mtDNA coding region. The mtDNA haplotypes detected in the Polish Roma fall into the common Eurasian mitochondrial haplogroups (H, U3, K, J1, X, I, W, and M*). The results of complete mtDNA sequencing clearly indicate that the Romani M*‐lineage belongs to the Indian‐specific haplogroup M5, which is characterized by three transitions in the coding region, at sites 12477, 3921 and 709. Molecular variance analysis inferred from mtDNA data reveals that genetic distances between the Roma groups are considerably larger than those between the surrounding European populations. Also, there are significant differences between the Bulgarian Roma (Balkan and Vlax groups) and West European Roma (Polish, Lithuanian and Spanish groups). Comparative analysis of mtDNA haplotypes in the Roma populations shows that different haplotypes appear to demonstrate impressive founder effects: M5 and H (16261–16304) in all Romani groups; U3, I and J1 in some Romani groups. Interestingly, haplogroup K (with HVS I motif 16224‐16234‐16311) found in the Polish Roma sample seems to be specific for Ashkenazi Jewish populations.     

Genetic relationship between the Canary Islanders and their African and Spanish ancestors inferred from mitochondrial DNA sequences

Nucleotide sequences of the hypervariable segment I of the control region of the mtDNA were determined in 101 individuals: 54 Canary Islanders, 18 North African Berbers, 18 Spanish mainlanders and 11 sub-Saharan Guineans. In spite of the fact that only members of the Fang tribe were analysed, nucleotide diversity in Guineans (θ× 100 = 2·33)is one of the highest found in African populations.
Estimates of genetic contribution to the Canarians from their putative parental populations based on mtDNA (43·25 ± 1·38% Berbers, 35·54 ± 0·55% Spanish, 21·21 ± 1·92% Guineans) showed an important North African substrate. These mtDNA results, when compared with data based on nuclear markers, point to a strong male-female asymmetry, 75% of the Spanish nuclear contribution was due to males and practically all the Berber and Guinean was due to females. These results are in agreement with the way that the Canary Islands were conquered.
Pairwise difference distributions in Guineans and Berbers are compatible with the model of populations in expansion. Departures from a Poisson distribution for the Canarians and Spanish can be explained by admixture and the way of sampling respectively.