Genetic variation reveals large-scale population expansion and migration during the expansion of Bantu-speaking peoples

The majority of sub-Saharan Africans today speak a number of closely related languages collectively referred to as ‘Bantu’ languages. The current distribution of Bantu-speaking populations has been found to largely be a consequence of the movement of people rather than a diffusion of language alone. Linguistic and single marker genetic studies have generated various hypotheses regarding the timing and the routes of the Bantu expansion, but these hypotheses have not been thoroughly investigated. In this study, we re-analysed microsatellite markers typed for large number of African populations that—owing to their fast mutation rates—capture signatures of recent population history. We confirm the spread of west African people across most of sub-Saharan Africa and estimated the expansion of Bantu-speaking groups, using a Bayesian approach, to around 5600 years ago. We tested four different divergence models for Bantu-speaking populations with a distribution comprising three geographical regions in Africa. We found that the most likely model for the movement of the eastern branch of Bantu-speakers involves migration of Bantu-speaking groups to the east followed by migration to the south. This model, however, is only marginally more likely than other models, which might indicate direct movement from the west and/or significant gene flow with the western Branch of Bantu-speakers. Our study use multi-loci genetic data to explicitly investigate the timing and mode of the Bantu expansion and it demonstrates that west African groups rapidly expanded both in numbers and over a large geographical area, affirming the fact that the Bantu expansion was one of the most dramatic demographic events in human history

Genetic variation in Khoisan-speaking populations from southern Africa

PhD, Faculty of Health Sciences, University of the WitwatersrandThe San and Khoe people currently represent remnant groups of a much larger and widely distributed population of hunter gatherers and cattle herders, respectively, who had exclusive occupation of southern Africa before the arrival of Bantu-speaking groups in the past 1,200 years and sea-borne immigrants within the last 350 years. This project made use of mitochondrial DNA (mtDNA), Y-chromosome DNA and autosomal DNA markers to examine the population structure of various San and Khoe groups and to reconstruct their prehistory. The groups included in the study consists of six different Khoe-San groups (‡Khomani, Nama, Khwe, !Xun, /Gui + //Gana + Kgalagari and Ju\’hoansi), four different Coloured groups and five other population groups that were included in the comparative analysis. For the mtDNA study a minisequencing technique was successfully developed which allowed the assignment of mtDNA lineages into the 10 global mtDNA macro-haplogroups. Haplogroups were further resolved using control region sequence data obtained from both hypervariable regions (HVR I and HVR II). Using this approach 538 individuals (both males and females) were screened and their mtDNA types were resolved into 18 haplogroups encompassing 245 unique haplotypes. In addition, 353 males were examined for Ychromosome DNA variation using 46 bi-allelic Y-chromosome markers and 12 Y-STR markers. The Y-chromosomes in the sample were assigned into 29 haplogroups (using biallelic variation) following the nomenclature initially recommended by the Y-chromosome Consortium and resolved into 268 unique haplotypes (Y-STR variation). To assess the level of autosomal variation, 220 genome wide autosomal SNPs were typed in 352 individuals. These SNPs were combined in different datasets and analysed using two different approaches allowing for genotype and haplotype analyses. Data from these three marker systems were analysed using different analytical methods (distance based phylogenetic analysis, network analysis, dating of lineages, principal components analysis, phylogeographic analysis, AMOVA analysis, population structure analysis, and population genetic summary statistics) to asses the ancestral associations and the genetic affinities of the various San, Khoe and Coloured populations. The most striking observation from this study was the high frequencies of the oldest mtDNA haplogroups (L0d and L0k) and Y-chromosome haplogroups (haplogroups A and B) found in Khoe-San and Coloured groups. The sub-haplogroups were, however, differentially distributed in the different Khoe-San and Coloured groups which suggested different demographic histories. The current distribution of Khoe-San groups comprises a wide geographic region extending from southern Angola in the north to the Cape Province (South Africa) in the south. Linguistically Khoe-San groups are also divided into northern Khoisan-speaking groups (Ju division) and southern Khoisan-speaking groups (Tuu division) with an additional linguistic group (Khoe) associated with some Khoe-speaking San groups in Botswana and the Khoe herders of South Africa and Namibia (such as the Nama). For all three genetic marker systems, northern groups (Ju speaking - !Xun, Ju\’hoansi and Khoe-speaking San - /Gui + //Gana) grouped into one cluster and southern groups (historically Tuu speaking - ‡Khomani and Coloured groups) grouped into a second cluster with the Khoe group (Nama) clustering with the southern Khoe-San and Coloured groups. The Khwe genetic profile was very different from the other Khoe-San groups. Although high proportions of Bantu-speaking admixture were identified in the Khwe group, they also contained a unique distribution of other mtDNA and Y-chromosome lineages. A previously published theory suggested that, based on the presence of a specific E-M35 Ychromosome haplotype, the Khwe might be descendants of an east African pastoralist group that introduced the pastoralist culture to a region located in the present day northern Botswana. This pattern also mirrors what archaeologists have found with respect to the introduction of pastoralism to southern Africa. The theory was further supported and elaborated on in the present thesis. Considering the frequency and distribution of E-M35, the highest frequency (46%) was found in the Khwe with a present-day distribution in northern Botswana and southern Angola while a decrease in frequency is observed towards the south with low frequencies (<10%) in the Karoo Coloured groups. Conversely, none of the mtDNA (female) L0k and L0d lineages observed in the Khwe group were observed in the southern Khoe-San and Coloured groups. From these observations a theory was proposed that after introduction into the region of northern Botswana, the southwards spread of pastoralism was not a clear-cut demic or cultural diffusion. Rather some male individuals integrated with the southern tribes and took with them the pastoralist practice and likely also their Khoe-language. Altogether this thesis presented new insights into the multifaceted demographic history that shaped the existing genetic landscape of the Khoe-San and Coloured populations of southern Africa

DNA is the key to unlocking our ancient African past

Abstract: Each region of the world, and the human groups living in them, have unique histories of migration, genetic mixing (admixture) and adaptation that have shaped their past. While archaeology has been of extreme value in elucidating this complex, multifaceted past, the genesis of DNA studies has enriched their story, and now ancient DNA (aDNA) has helped answer even more questions surrounding our prehistory. aDNA offers a unique opportunity to access genetic variation of past populations and enables us to contextualize past populations in present-day genetic variation. By linking the past to the present in this way, we now have a deeper understanding of our prehistory, and how our genetic landscape has changed from the past to the present. However, the study of aDNA is complex and there are various factors that need to be considered to yield successful aDNA results

Genetic variation and population structure of Sudanese populations as indicated by 15 Identifiler sequence-tagged repeat (STR) loci

<p>Abstract</p> <p>Background</p> <p>There is substantial ethnic, cultural and linguistic diversity among the people living in east Africa, Sudan and the Nile Valley. The region around the Nile Valley has a long history of succession of different groups, coupled with demographic and migration events, potentially leading to genetic structure among humans in the region.</p> <p>Result</p> <p>We report the genotypes of the 15 Identifiler microsatellite markers for 498 individuals from 18 Sudanese populations representing different ethnic and linguistic groups. The combined power of exclusion (PE) was 0.9999981, and the combined match probability was 1 in 7.4 × 10¹⁷. The genotype data from the Sudanese populations was combined with previously published genotype data from Egypt, Somalia and the Karamoja population from Uganda. The Somali population was found to be genetically distinct from the other northeast African populations. Individuals from northern Sudan clustered together with those from Egypt, and individuals from southern Sudan clustered with those from the Karamoja population. The similarity of the Nubian and Egyptian populations suggest that migration, potentially bidirectional, occurred along the Nile river Valley, which is consistent with the historical evidence for long-term interactions between Egypt and Nubia.</p> <p>Conclusion</p> <p>We show that despite the levels of population structure in Sudan, standard forensic summary statistics are robust tools for personal identification and parentage analysis in Sudan. Although some patterns of population structure can be revealed with 15 microsatellites, a much larger set of genetic markers is needed to detect fine-scale population structure in east Africa and the Nile Valley.</p

Multiple migrations to the Philippines during the last 50,000 years

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Development of a single base extension method to resolve Y chromosome haplogroups in sub-Saharan African populations

<p>Abstract</p> <p>Background</p> <p>The ability of the Y chromosome to retain a record of its evolution has seen it become an essential tool of molecular anthropology. In the last few years, however, it has also found use in forensic genetics, providing information on the geographic origin of individuals. This has been aided by the development of efficient screening methods and an increased knowledge of geographic distribution. In this study, we describe the development of single base extension assays used to resolve 61 Y chromosome haplogroups, mainly within haplogroups A, B and E, found in Africa.</p> <p>Results</p> <p>Seven multiplex assays, which incorporated 60 Y chromosome markers, were developed. These resolved Y chromosomes to 61 terminal branches of the major African haplogroups A, B and E, while also including a few Eurasian haplogroups found occasionally in African males. Following its validation, the assays were used to screen 683 individuals from Southern Africa, including south eastern Bantu speakers (BAN), Khoe-San (KS) and South African Whites (SAW). Of the 61 haplogroups that the assays collectively resolved, 26 were found in the 683 samples. While haplogroup sharing was common between the BAN and KS, the frequencies of these haplogroups varied appreciably. Both groups showed low levels of assimilation of Eurasian haplogroups and only two individuals in the SAW clearly had Y chromosomes of African ancestry.</p> <p>Conclusions</p> <p>The use of these single base extension assays in screening increased haplogroup resolution and sampling throughput, while saving time and DNA. Their use, together with the screening of short tandem repeat markers would considerably improve resolution, thus refining the geographic ancestry of individuals.</p

Y-Chromosome variation in Southern African Khoe-San populations based on whole-genome sequences

Abstract: Although the human Y chromosome has effectively shown utility in uncovering facets of human evolution and population histories, the ascertainment bias present in early Y-chromosome variant data sets limited the accuracy of diversity and TMRCA estimates obtained from them. The advent of next-generation sequencing, however, has removed this bias and allowed for the discovery of thousands of new variants for use in improving the Y-chromosome phylogeny and computing estimates that are more accurate. Here, we describe the high-coverage sequencing of the whole Y chromosome in a data set of 19 male Khoe-San individuals in comparisonwith existingwholeY-chromosome sequence data.Due to the increased resolution,we potentially resolve the source of haplogroup B-P70 in the Khoe-San, and reconcile recently published haplogroup A-M51 data with the most recent version of the ISOGG Y-chromosome phylogeny. Our results also improve the positioning of tentatively placed new branches of the ISOGG Ychromosome phylogeny. The distribution ofmajor Y-chromosome haplogroups in the Khoe-San and other African groups coincide with the emerging picture of African demographic history;with E-M2 linked to the agriculturalist Bantu expansion, E-M35 linked to pastoralist eastern Africanmigrations, B-M112 linked to earlier east-south gene flow, A-M14 linked to shared ancestrywith central African rainforest hunter-gatherers, and A-M51 potentially unique to the Khoe-San

Rickettsia felis DNA recovered from a child who lived in southern Africa 2000 years ago

DATA AVAILABILITY : Raw reads from Ballito Bay A samples are available under the NCBI BioProject PRJEB22660. The R. felis BBayA mapped reads and the metagenome-assembled genome are available under the NCBI BioProject PRJNA930765. The NCBI WGS accession number is JAQQRK000000000.The Stone Age record of South Africa provides some of the earliest evidence for the biological and cultural origins of Homo sapiens. While there is extensive genomic evidence for the selection of polymorphisms in response to pathogen-pressure in sub-Saharan Africa, e.g., the sickle cell trait which provides protection against malaria, there is inadequate direct human genomic evidence for ancient human-pathogen infection in the region. Here, we analysed shotgun metagenome libraries derived from the sequencing of a Later Stone Age hunter-gatherer child who lived near Ballito Bay, South Africa, c. 2000 years ago. This resulted in the identification of ancient DNA sequence reads homologous to Rickettsia felis, the causative agent of typhus-like flea-borne rickettsioses, and the reconstruction of an ancient R. felis genome.A National Geographic Society Scientific Exploration Grant, the Oppenheimer Endowed Fellowship in Molecular Archaeology, the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme and the Knut and Alice Wallenberg Foundation.https://www.nature.com/commsbiohj2023BiochemistryGeneticsMicrobiology and Plant Patholog

Later Stone Age human hair from Vaalkrans Shelter, Cape Floristic Region of South Africa, reveals genetic affinity to Khoe groups

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