The origins of the Lemba "Black Jews" of southern Africa: evidence from p12F2 and other Y-chromosome markers.

The Lemba are a southern African Bantu-speaking population claiming Jewish ancestry. Allele frequencies at four different Y-specific polymorphic loci, as well as extended-haplotype frequencies that included data from several loci, were analyzed in an attempt to establish the genetic affinities and origins of the Lemba. The results suggest that > or = 50% of the Lemba Y chromosomes are Semitic in origin, approximately 40% are Negroid, and the ancestry of the remainder cannot be resolved. These Y-specific genetic findings are consistent with Lemba oral tradition, and analysis of the history of Jewish people and their association with Africa indicates that the historical facts are not incompatible with theories concerning the origin of the Lemba.     

High-resolution Y chromosome haplotypes of Israeli and Palestinian Arabs reveal geographic substructure and substantial overlap with haplotypes of Jews

High-resolution Y chromosome haplotype analysis was performed in 143 paternally unrelated Israeli and Palestinian Moslem Arabs (I&P Arabs) by screening for 11 binary polymorphisms and six microsatellite loci. Two frequent haplotypes were found among the 83 detected: the modal haplotype of the I&P Arabs (approximately 14%) was spread throughout the region, while its one-step microsatellite neighbor, the modal haplotype of the Galilee sample (approximately 8%), was mainly restricted to the north. Geographic substructuring within the Arabs was observed in the highlands of Samaria and Judea. Y chromosome variation in the I&P Arabs was compared to that of Ashkenazi and Sephardic Jews, and to that of North Welsh individuals. At the haplogroup level, defined by the binary polymorphisms only, the Y chromosome distribution in Arabs and Jews was similar but not identical. At the haplotype level, determined by both binary and microsatellite markers, a more detailed pattern was observed. Single-step microsatellite networks of Arab and Jewish haplotypes revealed a common pool for a large portion of Y chromosomes, suggesting a relatively recent common ancestry. The two modal haplotypes in the I&P Arabs were closely related to the most frequent haplotype of Jews (the Cohen modal haplotype). However, the I&P Arab clade that includes the two Arab modal haplotypes (and makes up 32% of Arab chromosomes) is found at only very low frequency among Jews, reflecting divergence and/or admixture from other populations.     

Black Jews in the Northern Province: a study of ethnic identity in South Africa

The article examines ways in which the Lemba people of the Northern Province of South Africa have used their oral history and traditional customs associated with distant Semitic origins in Yemen, to claim a modern Jewish identity in racially divided South Africa. While Lemba live in Mozambique and Zimbabwe as well as in South Africa, it is only in the latter that belief in a Jewish origin is found. The article seeks to show that early white missionaries and colonial officials propagated a Semitic identity for the Lemba and in their writings emphasized the differences between the Lemba and their African neighbours through comparisons of Lemba customs with Jewish communities in Europe. Such writings contributed to an ethos of a distinct identity, through which, via the establishment of the Lemba Cultural Association, middle-class Lemba intellectuals sought to promote the Lemba. This was achieved in a situation where the apartheid regime in South Africa pursued a divide and rule policy which allowed the Bantustans to discriminate against ethnic minorities under their control.     

African and Levantine origins of Pakistani YAP+ Y chromosomes.

We surveyed 9 Pakistani subpopulations for variation on the nonrecombining portion of the Y chromosome. The polymorphic systems examined were the Y-chromosome Alu insertion polymorphism (YAP) at DYS287, 5 single nucleotide polymorphisms, and the tetranucleotide microsatellite DYS19. Y chromosomes carrying the YAP element (YAP+) were found in populations from southwestern Pakistan at frequencies ranging from 2% to 8%, whereas northeastern populations appeared to lack YAP+ chromosomes. In contrast to other South Asian populations, several Pakistani subpopulations had a high frequency of the DYS19*B allele, the most frequent allele in West Asian, North African, and European populations. The combination of alleles at all polymorphic sites gave rise to 9 YAP-DYS19 combination haplotypes in Pakistani populations, including YAP+ haplotypes 4-A, 4-B, 5-C, and 5-E. We hypothesize that the geographic distributions of YAP+ haplotypes 4 and 5 trace separate migratory routes to Pakistan: YAP+ haplotype 5 may have entered Pakistan from the Arabian Peninsula by means of migrations across the Gulf of Oman, whereas males possessing YAP+ haplotype 4 may have traveled over land from the Middle East. These inferences are consistent with ethnohistorical data suggesting that Pakistan's ethnic groups have been influenced by migrations from both African and Levantine source populations.     

Y-chromosomal variation in sub-Saharan Africa: insights into the history of Niger-Congo groups

Technological and cultural innovations as well as climate changes are thought to have influenced the diffusion of major language phyla in sub-Saharan Africa. The most widespread and the richest in diversity is the Niger-Congo phylum, thought to have originated in West Africa ～ 10,000 years ago (ya). The expansion of Bantu languages (a family within the Niger-Congo phylum) ～ 5,000 ya represents a major event in the past demography of the continent. Many previous studies on Y chromosomal variation in Africa associated the Bantu expansion with haplogroup E1b1a (and sometimes its sublineage E1b1a7). However, the distribution of these two lineages extends far beyond the area occupied nowadays by Bantu-speaking people, raising questions on the actual genetic structure behind this expansion. To address these issues, we directly genotyped 31 biallelic markers and 12 microsatellites on the Y chromosome in 1,195 individuals of African ancestry focusing on areas that were previously poorly characterized (Botswana, Burkina Faso, Democratic Republic of Congo, and Zambia). With the inclusion of published data, we analyzed 2,736 individuals from 26 groups representing all linguistic phyla and covering a large portion of sub-Saharan Africa. Within the Niger-Congo phylum, we ascertain for the first time differences in haplogroup composition between Bantu and non-Bantu groups via two markers (U174 and U175) on the background of haplogroup E1b1a (and E1b1a7), which were directly genotyped in our samples and for which genotypes were inferred from published data using linear discriminant analysis on short tandem repeat (STR) haplotypes. No reduction in STR diversity levels was found across the Bantu groups, suggesting the absence of serial founder effects. In addition, the homogeneity of haplogroup composition and pattern of haplotype sharing between Western and Eastern Bantu groups suggests that their expansion throughout sub-Saharan Africa reflects a rapid spread followed by backward and forward migrations. Overall, we found that linguistic affiliations played a notable role in shaping sub-Saharan African Y chromosomal diversity, although the impact of geography is clearly discernible.     

Different genetic components in the Ethiopian population,identified by mtDNA and Y-chromosome polymorphisms.

Seventy-seven Ethiopians were investigated for mtDNA and Y chromosome-specific variations, in order to (1) define the different maternal and paternal components of the Ethiopian gene pool, (2) infer the origins of these maternal and paternal lineages and estimate their relative contributions, and (3) obtain information about ancient populations living in Ethiopia. The mtDNA was studied for the RFLPs relative to the six classical enzymes (HpaI, BamHI, HaeII, MspI, AvaII, and HincII) that identify the African haplogroup L and the Caucasoid haplogroups I and T. The sample was also examined at restriction sites that define the other Caucasoid haplogroups (H, U, V, W, X, J, and K) and for the simultaneous presence of the DdeI10394 and AluI10397 sites, which defines the Asian haplogroup M. Four polymorphic systems were examined on the Y chromosome: the TaqI/12f2 and the 49a,f RFLPs, the Y Alu polymorphic element (DYS287), and the sY81-A/G (DYS271) polymorphism. For comparison, the last two Y polymorphisms were also examined in 87 Senegalese previously classified for the two TaqI RFLPs. Results from these markers led to the hypothesis that the Ethiopian population (1) experienced Caucasoid gene flow mainly through males, (2) contains African components ascribable to Bantu migrations and to an in situ differentiation process from an ancestral African gene pool, and (3) exhibits some Y-chromosome affinities with the Tsumkwe San (a very ancient African group). Our finding of a high (20%) frequency of the "Asian" DdeI10394AluI10397 (++) mtDNA haplotype in Ethiopia is discussed in terms of the "out of Africa" model.     

Haplotypes of two diallelic Y chromosome loci in the indigenous and migrant populations of Siberia

Two diallelic Y-chromosome markers, the Y Alu polymorphism (YAP) and the T-C transition (Tat), were analyzed in the indigenous (Tuvinian, Buryat, Northern Altaic, and Tatar) and migrant (Slavic) populations of Siberia. A high frequency of the allele C was revealed in several indigenous populations (25-55%) and in Russians (20.8%). The YAP+ allele occurred at a surprisingly high frequency (31.4%) and was completely linked with the C allele in Buryats. The YAP+ chromosome was also found in the Tuvinian population (1.5%). The two diallelic loci showed a marked linkage disequilibrium (D = 92.4%) in the total sample. The YAP-/T and YAP-/C haplotypes prevailed in both indigenous and migrant populations: their respective frequencies were 80.4 and 19.6% in the Slavic population and 71.8 and 19.9%, respectively, in the indigenous one. The YAP+/C (7.8%) and YAP+/T (0.5%) haplotypes were found only in the indigenous population. An appreciable heterogeneity in haplotype frequency distribution between regional subpopulations was revealed in Russians, Tuvinians, and Buryats. The origin and evolution of Y-chromosome lines in Northern Asia are considered.     

Genetic variation of the Y chromosome in Chibcha-speaking Amerindians of Costa Rica and Panama

Genetic variation of the Y chromosome in five Chibchan tribes (Bribri, Cabecar, Guaymi, Huetar, and Teribe) of Costa Rica and Panama was analyzed using six microsatellite loci (DYS19, DYS389A, DYS389B, DYS390, DYS391, and DYS393), the Y-chromosome-specific alphoid system (alphah), the Y-chromosome Alu polymorphism (YAP), and a specific pre-Columbian transition (C-->T) (M3 marker) in the DYS 199 locus that defines the Q-M3 haplogroup. Thirty-nine haplotypes were found, resulting in a haplotype diversity of 0.937. The Huetar were the most diverse tribe, probably because of their high levels of interethnic admixture. A candidate founder Y-chromosome haplotype was identified (15.1% of Chibchan chromosomes), with the following constitution: YAP-, DYS199*T, alphah-II, DYS19*13, DYS389A*17, DYS389B*10, DYS390*24, DYS391*10, and DYS393*13. This haplotype is the same as the one described previously as one of the most frequent founder paternal lineages in native American populations. Analysis of molecular variance indicated that the between-population variation was smaller than the within-population variation, and the comparison with mtDNA restriction data showed no evidence of differential structuring between maternally and paternally inherited genes in the Chibchan populations. The mismatch-distribution approach indicated estimated coalescence times of the Y chromosomes of the Q-M3 haplogroup of 3,113 and 13,243 years before present; for the mtDNA-restriction haplotypes the estimated coalescence time was between 7,452 and 9,834 years before present. These results are compatible with the suggested time for the origin of the Chibchan group based on archeological, linguistic, and genetic evidence.     

The genetic legacy of western Bantu migrations

There is little knowledge on the demographic impact of the western wave of the Bantu expansion. Only some predictions could be made based mainly on indirect archaeological, linguistic, and genetic evidences. Apart from the very limited available data on the mitochondrial DNA (mtDNA) side, there are not, however, Y-chromosome studies revealing–if any–the male contribution of western Bantu-farmers. To elucidate the still poorly characterized western Bantu expansion, we analyzed Y-chromosome (25 biallelic polymorphisms and 15 microsatellite markers) and mtDNA (hypervariable control regions I and II and selected coding region RFLPs) variation in a population of 110 individuals from southwest Africa, and compared it with a database of 2,708 Y-chromosome profiles and of 2,565 mtDNAs from all other regions of Africa. This study reveals (1) a dramatic displacement of male and female Khoisan-speaking groups in the southwest, since both the maternal and the paternal genetic pools were composed exclusively by types carried by Bantu-speakers; (2) a clear bias in the admixture process towards the mating of male Europeans with female Sub-Saharan Africans; (3) the assimilation of east African lineages by the southwest (mainly mtDNA-L3f and Y-chromosome-B2a lineages); and (4) signatures of recent male and female gene flow from the southeast into the southwest. The data also indicate that the western stream of the Bantu expansion was a more gradual process than the eastern counterpart, which likely involved multiple short dispersals.Electronic Supplementary Material Supplementary material is available for this article at     

Haplotype of Y-chromosomes in the Central Asia population

The distribution of alleles and haplotypes of three diallellic Y-specific loci (YAP, DYF155S2, and Tat) in the populations of Kyrgyz, Uzbeks and Tajiks was analyzed. In Kyrgyzes and Uzbeks, a relatively high frequency of the DYF155S2 deletion (20 and 12.5%, respectively) and the C allele at the Tat locus (11.2 and 8.3%, respectively) were revealed. In the populations of southern Kyrgyzes and Uzbeks, two chromosomes carrying the YAP+ allele were detected. In both cases the YAP+ allele was found within the YAP+/DYF155S2+/TatT haplotype. The Tajik population was monomorphic in respect to the polymorphisms studied. The Tajiks demonstrated the presence of only the YAP-/DYF155S2+/TatT haplotype. This haplotype appeared to be most frequent in Kyrgyz (78.8%) and Uzbeks (83.3%). The question on the origin and the distribution of Y-chromosome variants in Eurasia are discussed.     

High-resolution analysis of human Y-chromosome variation shows a sharp discontinuity and limited gene flow between northwestern Africa and the Iberian Peninsula

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.     

Yearning for the long lost home: the Lemba and Jewish narrative of genetic return

This commentary examines the relationship between genetics and Jewish identity. It focuses especially on the use of Y-chromosome testing to map the genealogies of the Lemba in southern Africa.     

Constructing black Jews: genetic tests and the Lemba--the 'black Jews' of South Africa

This commentary examines the use of Y-chromosome testing to reconstruct a genetic ancestry for the Lemba, a group in southern Africa that has long considered itself Jewish. The commentary looks especially at the reasons why this project drew such attention from the mainstream media.     

Ethiopians and Khoisan Share the Deepest Clades of the Human Y-Chromosome Phylogeny

The genetic structure of 126 Ethiopian and 139 Senegalese Y chromosomes was investigated by a hierarchical analysis of 30 diagnostic biallelic markers selected from the worldwide Y-chromosome genealogy. The present study reveals that (1) only the Ethiopians share with the Khoisan the deepest human Y-chromosome clades (the African-specific Groups I and II) but with a repertoire of very different haplotypes; (2) most of the Ethiopians and virtually all the Senegalese belong to Group III, whose precursor is believed to be involved in the first migration out of Africa; and (3) the Ethiopian Y chromosomes that fall into Groups VI, VIII, and IX may be explained by back migrations from Asia. The first observation confirms the ancestral affinity between the Ethiopians and the Khoisan, which has previously been suggested by both archaeological and genetic findings.     

Combined use of biallelic and microsatellite Y-chromosome polymorphisms to infer affinities among African populations.

To define Y-chromosome haplotypes, we studied seven biallelic polymorphic sites. We combined data with those from four dinucleotide-repeat polymorphisms, to establish Y-chromosome compound superhaplotypes. Eight biallelic haplotypes that matched the dendrogram proposed by other investigators were identified in 762 Y chromosomes from 25 African populations. For each biallelic site, coalescence time of lineages carrying the derived allele was estimated and compared with previous estimates. The "ancestral" haplotype (haplotype 1A) was observed among Ethiopians, "Khoisan" (!Kung and Khwe), and populations from northern Cameroon. Microsatellite distributions within this haplotype showed that the Khoisan haplotypes 1A are widely divergent from those of the other two groups. Populations from northern Africa and northern Cameroon share a haplotype (i.e., 1C), which is not observed in other African populations but represents a major Eurasian cluster. Haplotypes 1C of northern Cameroon are clearly distinct from those of Europe, whereas haplotypes 1C of northern African are well intermingled with those of the other two groups. Apportionment of diversity for the Y-chromosomal biallelic haplotypes was calculated after populations were clustered into different configurations. Despite some correspondence between language affiliation and genetic similarity, geographic proximity seems to be a better predictor of genetic affinity.     

The origin of sickle cell alleles in Israel

Summary Molecular genetic studies were undertaken to determine the source of chromosomes carrying the sickle cell allele in Israeli patients. Analysis of restriction fragment length polymorphism (RFLP) patterns (haplotypes) along the -globin gene cluster was performed on 31 sickle chromosomes obtained from 10 unrelated families living in Israel. One is a Caucasian Jewish family, recently found to be carrying the sickle allele, and the other 9 are Arab families of various communities. The Jewish family, previously noted not to carry African red blood cell markers, was discovered to have the most common African haplotype of the -globin gene cluster, Benin. Similarly, 8 of the Arab families were also found to carry the Benin haplotype, whereas the ninth has the CAR (Central African Republic or Bantu) haplotype. The results suggest that sickle alleles in Israel originated in Africa, probably in two different regions, and migrated north into Arab and Jewish populations.     

On the edge of Bantu expansions: mtDNA, Y chromosome and lactase persistence genetic variation in southwestern Angola

Background  

Current information about the expansion of Bantu-speaking peoples is hampered by the scarcity of genetic data from well identified populations from southern Africa. Here, we fill an important gap in the analysis of the western edge of the Bantu migrations by studying for the first time the patterns of Y-chromosome, mtDNA and lactase persistence genetic variation in four representative groups living around the Namib Desert in southwestern Angola (Ovimbundu, Ganguela, Nyaneka-Nkumbi and Kuvale). We assessed the differentiation between these populations and their levels of admixture with Khoe-San groups, and examined their relationship with other sub-Saharan populations. We further combined our dataset with previously published data on Y-chromosome and mtDNA variation to explore a general isolation with migration model and infer the demographic parameters underlying current genetic diversity in Bantu populations.     

Increased resolution of Y chromosome haplogroup T defines relationships among populations of the Near East, Europe, and Africa

Increasing phylogenetic resolution of the Y chromosome haplogroup tree has led to finer temporal and spatial resolution for studies of human migration. Haplogroup T, initially known as K2 and defined by mutation M70, is found at variable frequencies across West Asia, Africa, and Europe. While several SNPs were recently discovered that extended the length of the branch leading to haplogroup T, only two SNPs are known to mark internal branches of haplogroup T. This low level of phylogenetic resolution has hindered studies of the origin and dispersal of this interesting haplogroup, which is found in Near Eastern non-Jewish populations, Jewish populations from several communities, and in the patrilineage of President Thomas Jefferson. Here we map 10 new SNPs that, together with the previously known SNPs, mark 11 lineages and two large subclades (T1a and T1b) of haplogroup T. We also report a new SNP that links haplogroups T and L within the major framework of Y chromosome evolution. Estimates of the timing of the branching events within haplogroup T, along with a comprehensive geographic survey of the major T subclades, suggest that this haplogroup began to diversify in the Near East -25 kya. Our survey also points to a complex history of dispersal of this rare and informative haplogroup within the Near East and from the Near East to Europe and sub-Saharan Africa. The presence of T1a2 chromosomes in Near Eastern Jewish and non-Jewish populations may reflect early exiles between the ancient lands of Israel and Babylon. The presence of different subclades of T chromosomes in Europe may be explained by both the spread of Neolithic farmers and the later dispersal of Jews from the Near East. Finally, the moderately high frequency (-18%) of T1b* chromosomes in the Lemba of southern Africa supports the hypothesis of a Near Eastern, but not necessarily a Jewish, origin for their paternal line.     

Microsatellite variation and evolutionary history of PCDHX/Y gene pair within the Xq21.3/Yp11.2 hominid-specific homology block

To better understand the evolutionary dynamics of repetitive sequences in human sex chromosomes, we have analyzed seven new X/Y homologous microsatellites located within PCDHX/Y, one of the two recently described gene pairs in the Xq21.3/Yp11.2 hominid-specific homology block, in samples from Portugal and Mozambique. Sharp differences were observed on X/Y allele distributions, concerning both the presence of private alleles and a different modal repeat length for X-linked and Y-linked markers, and this difference was statistically significant. Higher diversity was found in X-linked microsatellites than in their Y chromosome counterparts; when comparing populations, Mozambicans showed more allele diversity for the X chromosome, but the contrary was true for the Y chromosome microsatellites. Evolutionary patterns, relying on intragenic PCDHX/Y SNPs, also revealed distinct scenarios for X and Y chromosomes. Greater microsatellite diversity was displayed by African X chromosomes within the most common haplotypes shared by both populations, whereas higher microsatellite diversity was found in Portugal for the ancestral Y chromosome haplotype. The most frequent PCDHY haplotype in Portuguese was the derived one, and it was not found in Mozambicans. TMRCA estimated by the rho parameter resulted in 13,700 years (7,500-20,000 years), which is consistent with a recent, post-Out-of-Africa origin for this haplotype. In conclusion, the newly described microsatellite loci generally displayed greater X-linked to Y-linked diversity and this pattern was also detected with slower evolving markers, with a remarkable differentiation between populations observed for Y chromosome haplotypes and, thus, greater divergence among Y chromosomes in human populations.     

A Y-chromosome signature of hegemony in Gaelic Ireland

Seventeen-marker simple tandem repeat genetic analysis of Irish Y chromosomes reveals a previously unnoted modal haplotype that peaks in frequency in the northwestern part of the island. It shows a significant association with surnames purported to have descended from the most important and enduring dynasty of early medieval Ireland, the Ui Neill. This suggests that such phylogenetic predominance is a biological record of past hegemony and supports the veracity of semimythological early genealogies. The fact that about one in five males sampled in northwestern Ireland is likely a patrilineal descendent of a single early medieval ancestor is a powerful illustration of the potential link between prolificacy and power and of how Y-chromosome phylogeography can be influenced by social selection.