Y chromosomes traveling south: the cohen modal haplotype and the origins of the Lemba--the "Black Jews of Southern Africa"

The Lemba are a traditionally endogamous group speaking a variety of Bantu languages who live in a number of locations in southern Africa. They claim descent from Jews who came to Africa from "Sena." "Sena" is variously identified by them as Sanaa in Yemen, Judea, Egypt, or Ethiopia. A previous study using Y-chromosome markers suggested both a Bantu and a Semitic contribution to the Lemba gene pool, a suggestion that is not inconsistent with Lemba oral tradition. To provide a more detailed picture of the Lemba paternal genetic heritage, we analyzed 399 Y chromosomes for six microsatellites and six biallelic markers in six populations (Lemba, Bantu, Yemeni-Hadramaut, Yemeni-Sena, Sephardic Jews, and Ashkenazic Jews). The high resolution afforded by the markers shows that Lemba Y chromosomes are clearly divided into Semitic and Bantu clades. Interestingly, one of the Lemba clans carries, at a very high frequency, a particular Y-chromosome type termed the "Cohen modal haplotype," which is known to be characteristic of the paternally inherited Jewish priesthood and is thought, more generally, to be a potential signature haplotype of Judaic origin. The Bantu Y-chromosome samples are predominantly (>80%) YAP+ and include a modal haplotype at high frequency. Assuming a rapid expansion of the eastern Bantu, we used variation in microsatellite alleles in YAP+ sY81-G Bantu Y chromosomes to calculate a rough date, 3,000-5,000 years before the present, for the start of their expansion.     

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.     

The sounds of black resistance in South Africa and America

Frank Marshall Davis, LIVIN’ THE BLUES: MEMORIES OF A BLACK JOURNALIST AND POET, (edited, with an introduction, by John Edgar Tidwell), Madison and London: University of Wisconsin Press, 1993, 373 pp., £22.00.

Veit Erlemann, AFRICAN STARS: STUDIES IN BLACK SOUTH AFRICAN PERFORMANCE, Chicago and London: University of Chicago Press, 1991, 214 pp., npl.     

Density and genetic structure of black bears in coastal South Carolina

The frequency of black bear (Ursus americanus) sightings, vehicle collisions, and nuisance incidents in the coastal region of South Carolina has increased over the past 4 decades. To develop the statewide Black Bear Management and Conservation Strategy, the South Carolina Department of Natural Resources needed reliable information for the coastal population. Because no such data were available, we initiated a study to determine population density and genetic structure of black bears. We selected 2 study areas that were representative of the major habitat types in the study region: Lewis Ocean Bay consisted primarily of Carolina Bays and pocosin habitats, whereas Carvers Bay was representative of extensive pine plantations commonly found in the region. We established hair snares on both study areas to obtain DNA from hair samples during 8 weekly sampling periods in 2008 and again in 2009. We used genotypes to obtain capture histories of sampled bears. We estimated density using spatially explicit capture–recapture (SECR) models and used information-theoretic procedures to fit parameters for capture heterogeneity and behavioral responses and to test if density and model parameters varied by year. Model-averaged density was 0.046 bears/km² (SE = 0.011) for Carvers Bay and 0.339 bears/km² (SE = 0.056) for Lewis Ocean Bay. Next, we sampled habitat covariates for all locations in the SECR sampling grid to derive spatially explicit estimates of density based on habitat characteristics. Addition of habitat covariates had substantial support, and accounted for differences in density between Carvers Bay and Lewis Ocean Bay; black bear density showed a negative association with the area of pine forests (4.5-km² scale) and a marginal, positive association with the area of pocosin habitat (0.3-km² scale). Bear density was not associated with pine forest at a smaller scale (0.3-km²), nor with major road density or an index of largest patch size. Predicted bear densities were low throughout the coastal region and only a few larger areas had high predicted densities, most of which were centered on public lands (e.g., Francis Marion National Forest, Lewis Ocean Bay). We sampled a third bear population in the Green Swamp area of North Carolina for genetic structure analyses and found no evidence of historic fragmentation among the 3 sampled populations. Neither did we find evidence of more recent barriers to gene exchange; with the exception of 1 recent migrant, Bayesian population assignment techniques identified only a single population cluster that incorporated all 3 sampled areas. Bears in the region may best be managed as 1 population. If the goal is to maintain or increase bear densities, demographic connectivity of high-density areas within the low-density landscape matrix is a key consideration and managers would need to mitigate potential impacts of planned highway expansions and anticipated development. Because the distribution of black bears in coastal South Carolina is not fully known, the regional map of potential black bear density can be used to identify focal areas for management and sites that should be surveyed for occupancy or where more intensive studies are needed. © 2012 The Wildlife Society.     

The genetic status of naturally occurring black-nosed impala from northern South Africa

The impala (Aepyceros melampus ssp.) is a widespread antelope species occurring in sub-Saharan Africa. The two recognized subspecies have non-overlapping distribution ranges, with no known natural mixture of these subspecies until human interference. A number of common impala individuals (A. m. melampus) displaying phenotypic characteristics commonly observed in the black-faced impala (A. m. petersi), namely black facial markings, were seen on a farm in the Limpopo Province, South Africa. This farm falls outside the natural distribution range of A. m. petersi. We therefore aimed to identify the taxonomic placement of these individuals (i.e. A. m. melampus or A. m. petersi) through phylogenetic and molecular clock analyses using D-loop and cytochrome subunit b sequence data. Our results showed that these black-nosed impala from Limpopo are in fact A. m. melampus individuals. The existence of the black-nose phenotype in common impala could be more widespread than previously estimated. The occurrence of introgression between the two subspecies in this region could, however, not be fully excluded, and can only be fully assessed through the use of nuclear DNA analysis.     

Ethnic communities in Israel: The genetic blood markers of the Moroccan Jews

One hundred and ninety-six Moroccan Jews now settled in Israel were typed for 7 blood groups, 12 red cell enzymes and 2 plasma protein systems. Their blood group picture is in agreement with results previously obtained on different samples of Moroccan Jews: rather high B in ABO, somewhat elevated frequencies of cDE and cDe in Rh and K in Kell. Differences in various blood markers exist between them and other North African Jewish communities. This fact, together with data on disease distribution and HLA frequencies, supports our assumption that Jews in the North African diaspora lived as small secluded isolates even within the same geographical zones. Comparisons with meager data on the neighboring non-Jewish populations do not disclose any resemblance to either Arab or Berber inhabitants of Morocco.     

The genetic history of Cochin Jews from India

Cochin Jews form a small and unique community on the Malabar coast in southwest India. While the arrival time of any putative Jewish ancestors of the community has been speculated to have taken place as far back as biblical times (King Solomon’s era), a Jewish community in the Malabar coast has been documented only since the 9th century CE. Here, we explore the genetic history of Cochin Jews by collecting and genotyping 21 community members and combining the data with that of 707 individuals from 72 other Indian, Jewish, and Pakistani populations, together with additional individuals from worldwide populations. We applied comprehensive genome-wide analyses based on principal component analysis, F _ST, ADMIXTURE, identity-by-descent sharing, admixture linkage disequilibrium decay, haplotype sharing, allele sharing autocorrelation decay and contrasting the X chromosome with the autosomes. We find that, as reported by several previous studies, the genetics of Cochin Jews resembles that of local Indian populations. However, we also identify considerable Jewish genetic ancestry that is not present in any other Indian or Pakistani populations (with the exception of the Jewish Bene Israel, which we characterized previously). Combined, Cochin Jews have both Jewish and Indian ancestry. Specifically, we detect a significant recent Jewish gene flow into this community 13–22 generations (~470–730 years) ago, with contributions from Yemenite, Sephardi, and Middle-Eastern Jews, in accordance with historical records. Genetic analyses also point to high endogamy and a recent population bottleneck in this population, which might explain the increased prevalence of some recessive diseases in Cochin Jews.     

Ethnic communities in Israel: The genetic blood markers of the Babylonian Jews

One hundred eighty-eight Jewish individuals who either they or whose both parents were born in Iraq were typed for 7 blood groups (ABO, MNS, Rh, Kell, Duffy, P and Kidd), 12 red cell enzyme systems and 2 serum proteins. Iraqi Jews are characterized by a high frequency of A (in ABO), N (in MNS), low cde (Rh) and low Hp-1. Several rare electrophoretic variants were encountered: PGM₁ 6-1, PHI 3-1 and PHI 2-1, and an unidentified AK phenotype. No evidence of Negroid admixture was found in their gene pool. Comparisons with results previously obtained in Iraqi Jews show general similarities in frequencies while comparisons with neighboring non-Jewish populations suggest divergence in most systems investigated. The difficulties of assessing relationships on the basis of a few selected differences and the need for careful interpretations of similarities are emphasized.     

Microsatellite based analysis of genetic diversity of popular black pepper genotypes in South India

The genotypes of black pepper are morphologically and genotypically highly diverse and carry all the cumulative variations inherited and maintained through generations. The present study describes the Simple Sequence Repeat (SSR) or microsatellite based assessment of genetic diversity among forty popular genotypes and four different species of black pepper in Southern region of India. For isolation of SSR primers, our earlier attempts with enrichment strategies like ‘Triplex affinity capture’ did not extract a single SSR primer due to close proximity of restriction sites to the SSR motif. Hence we developed a ‘Sequential Reverse Genome Walking (SRGW)’ strategy with better enrichment efficiency of 72% that generated seven new SSR primers. Genotyping precisely discriminated majority of genotypes which indicated that the SSR primers are very informative. A total of 62 alleles with an average of 15.5 alleles over 4 loci were identified. All the SSR primers showed an average Polymorphism Information Content (PIC) value of 0.85. The estimated average Shared Allele Frequency ranged between 1.57 and 20.12%. The PCA plot revealed four closely related individual groups and identified Karimunda, Wild pepper and a local landrace ‘local b’ as the most divergent genotypes. Cluster analysis exposed the genetic relatedness between hybrids and selections with other known cultivars. The introduction of black pepper from South India to Malaysia was emphasized from the observation of genetic similarity of Malaysian cultivar ‘Kuching’ with other indigenous popular cultivars. The study was first to portray the precise genetic relatedness among the major indigenous genotypes of black pepper.     

The genetic bases for syndromic and nonsyndromic deafness among Jews

There are hundreds of different mutated genes associated with hearing loss. However, recent findings indicate that a large proportion of both syndromic and nonsyndromic forms of deafness in some Jewish populations is caused by a small number of founder mutations. This review is focused on genetic disorders such as nonsyndromic deafness, Usher syndrome and Alport syndrome, in which hearing loss is a major part of the phenotype and in which the underlying prevalent founder mutations have been recently identified in different Jewish populations. These and other examples of common mutations within a distinct population allow for sensitive and specific use of genetic testing for carrier screening and diagnosis, and are an impetus for development of therapeutic strategies.