Ancient Substructure in Early mtDNA Lineages of Southern Africa

Among the deepest-rooting clades in the human mitochondrial DNA (mtDNA) phylogeny are the haplogroups defined as L0d and L0k, which are found primarily in southern Africa. These lineages are typically present at high frequency in the so-called Khoisan populations of hunter-gatherers and herders who speak non-Bantu languages, and the early divergence of these lineages led to the hypothesis of ancient genetic substructure in Africa. Here we update the phylogeny of the basal haplogroups L0d and L0k with 500 full mtDNA genome sequences from 45 southern African Khoisan and Bantu-speaking populations. We find previously unreported subhaplogroups and greatly extend the amount of variation and time-depth of most of the known subhaplogroups. Our major finding is the definition of two ancient sublineages of L0k (L0k1b and L0k2) that are present almost exclusively in Bantu-speaking populations from Zambia; the presence of such relic haplogroups in Bantu speakers is most probably due to contact with ancestral pre-Bantu populations that harbored different lineages than those found in extant Khoisan. We suggest that although these populations went extinct after the immigration of the Bantu-speaking populations, some traces of their haplogroup composition survived through incorporation into the gene pool of the immigrants. Our findings thus provide evidence for deep genetic substructure in southern Africa prior to the Bantu expansion that is not represented in extant Khoisan populations.     

Unraveling the complex maternal history of Southern African Khoisan populations

The Khoisan populations of southern Africa are known to harbor some of the deepest‐rooting lineages of human mtDNA; however, their relationships are as yet poorly understood. Here, we report the results of analyses of complete mtDNA genome sequences from nearly 700 individuals representing 26 populations of southern Africa who speak diverse Khoisan and Bantu languages. Our data reveal a multilayered history of the indigenous populations of southern Africa, who are likely to be the result of admixture of different genetic substrates, such as resident forager populations and pre‐Bantu pastoralists from East Africa. We find high levels of genetic differentiation of the Khoisan populations, which can be explained by the effect of drift together with a partial uxorilocal/multilocal residence pattern. Furthermore, there is evidence of extensive contact, not only between geographically proximate groups, but also across wider areas. The results of this contact, which may have played a role in the diffusion of common cultural and linguistic features, are especially evident in the Khoisan populations of the central Kalahari. Am J Phys Anthropol 153:435–448, 2014. © 2013 Wiley Periodicals, Inc.     

Bringing together linguistic and genetic evidence to test the Bantu expansion

The expansion of Bantu languages represents one of the most momentous events in the history of Africa. While it is well accepted that Bantu languages spread from their homeland (Cameroon/Nigeria) approximately 5000 years ago (ya), there is no consensus about the timing and geographical routes underlying this expansion. Two main models of Bantu expansion have been suggested: The 'early-split' model claims that the most recent ancestor of Eastern languages expanded north of the rainforest towards the Great Lakes region approximately 4000 ya, while the 'late-split' model proposes that Eastern languages diversified from Western languages south of the rainforest approximately 2000 ya. Furthermore, it is unclear whether the language dispersal was coupled with the movement of people, raising the question of language shift versus demic diffusion. We use a novel approach taking into account both the spatial and temporal predictions of the two models and formally test these predictions with linguistic and genetic data. Our results show evidence for a demic diffusion in the genetic data, which is confirmed by the correlations between genetic and linguistic distances. While there is little support for the early-split model, the late-split model shows a relatively good fit to the data. Our analyses demonstrate that subsequent contact among languages/populations strongly affected the signal of the initial migration via isolation by distance.     

Bridging near and remote Oceania: mtDNA and NRY variation in the Solomon Islands

Although genetic studies have contributed greatly to our understanding of the colonization of Near and Remote Oceania, important gaps still exist. One such gap is the Solomon Islands, which extend between Bougainville and Vanuatu, thereby bridging Near and Remote Oceania, and include both Austronesian-speaking and Papuan-speaking groups. Here, we describe patterns of mitochondrial DNA (mtDNA) and nonrecombining Y chromosome (NRY) variation in over 700 individuals from 18 populations in the Solomons, including 11 Austronesian-speaking groups, 3 Papuan-speaking groups, and 4 Polynesian Outliers (descended via back migration from Polynesia). We find evidence for ancient (pre-Lapita) colonization of the Solomons in old NRY paragroups as well as from M2-M353, which probably arose in the Solomons ～9,200 years ago and is the most frequent NRY haplogroup there. There are no consistent genetic differences between Austronesian-speaking and Papuan-speaking groups, suggesting extensive genetic contact between them. Santa Cruz, which is located in Remote Oceania, shows unusually low frequencies of mtDNA and NRY haplogroups of recent Asian ancestry. This is in apparent contradiction with expectations based on archaeological and linguistic evidence for an early (～3,200 years ago), direct colonization of Santa Cruz by Lapita people from the Bismarck Archipelago, via a migration that "leapfrogged" over the rest of the Solomons. Polynesian Outliers show dramatic island-specific founder events involving various NRY haplogroups. We also find that NRY, but not mtDNA, genetic distance is correlated with the geographic distance between Solomons groups and that historically attested spheres of cultural interaction are associated with the recent genetic structure of Solomons groups, as revealed by mtDNA HV1 sequence and Y-STR haplotype diversity. Our results fill an important lacuna in human genetic studies of Oceania and aid in understanding the colonization and genetic history of this region.     

Investigating the effects of prehistoric migrations in Siberia: genetic variation and the origins of Yakuts

The Yakuts (also known as Sakha), Turkic-speaking cattle- and horse-breeders, inhabit a vast territory in Central and northeastern Siberia. On the basis of the archaeological, ethnographic and linguistic evidence, they are assumed to have migrated north from their original area of settlement in the vicinity of Lake Baykal in South Siberia under the pressure of the Mongol expansion during the thirteenth to fifteenth century AD: . During their initial migration and subsequent expansion, the ancestors of the Yakuts settled in the territory originally occupied by Tungusic- and Uralic-speaking reindeer-herders and hunters. In this paper we use mtDNA and Y-chromosomal analyses to elucidate whether the Yakut immigration and expansion was accompanied by admixture with the indigenous populations of their new area of settlement or whether the Yakuts displaced the original inhabitants without intermarriage. The mtDNA results show a very close affinity of the Yakuts with Central Asian and South Siberian groups, which confirms their southern origin. There is no conclusive evidence for admixture with indigenous populations, though a small amount cannot be excluded on the basis of the mtDNA data alone. The Y-chromosomal results confirm previous findings of a very strong bottleneck in the Yakuts, the age of which is in good accordance with the hypothesis that the Yakuts migrated north under Mongol pressure. Furthermore, the genetic results show that the Yakuts are a very homogenous population, notwithstanding their current spread over a very large territory. This confirms the historical accounts that they spread over their current area of settlement fairly recently.     

Mitochondrial DNA evidence for admixed origins of central Siberian populations

The Yakuts of northeastern Siberia are a Turkic-speaking population of horse- and cattle-breeders surrounded by Tungusic-speaking reindeer-herders and hunter-gatherers. Archaeological and ethnohistorical data suggest that Yakuts stem from a common ancestral population with the Buryats living near Lake Baikal. To address this hypothesis, we obtained sequences of the first hypervariable segment (HV1) of the mitochondrial DNA control region from Yakuts and Buryats and compared these with sequences from other Eurasian populations. The mtDNA results show that the Buryats have close affinities with both Central Asian Turkic groups and Mongols, while the Yakuts have close affinities with northeastern Siberian, Tungusic-speaking Evenks and south Siberian, Turkic-speaking Tuvans. This different ancestry of the Yakuts and the Tuvans (compared with other Turkic-speaking groups) most likely reflects extensive admixture that occurred between Turkic-speaking steppe groups and Evenks as the former migrated into Siberia. Moreover, the Yakuts are unique among Siberian populations in having a high number of haplotypes shared exclusively with Europeans, suggesting, contrary to the historical record, that occasionally Yakut men took Russian women as wives.     

Distribution of the ABO blood groups and the HP,TF, GC,PI and C3 serum proteins in Yakuts

In Yakut populations examined, polymorphisms of immunological and serum protein markers, including AB0 and Rhesus blood groups, HP, TF, GC, PI and C3, were revealed. Gene frequencies for the systems studied fell into the following ranges: AB0 system: r, 0.514 to 0.663; p, 0.136 to 0.306; q, 0.110 to 0.337; haptoglobin HP*1: 0.214 to 0.431; transferrin TF*C: 0.700 to 1.0; group specific component GC*1: 0.821 to 0.978; PI*M1 proteinase inhibitor (or alpha 1-antitrypsin) PIM1: 0.860 to 0.946; and third component of the complement C3*F: 0.031 to 0.143.     

Genetic polymorphism of erythrocytic enzymes in Yakut populations

Polymorphism of the erythrocytic enzymes PGM1, ACP1, ESD, and GLO1 was found in Yakut populations. The allelic frequencies of the polymorphic systems studied varied within the following ranges: PGM1*1+, 0.5833-0.7791; PGM1*1-, 0.0345-0.1176; PGM1*2+, 0.1250-0.2813; ACP1*A, 0.1429-0.3382; ACP1*B, 0.6548-0.8571; ESD*2, 0.1250-0.4643; and GLO1*1, 0.0116-0.2845.     

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.