AfricanNeo aDNA Study
Ontology highlight
ABSTRACT:
PROVIDER: EGAS00001007519 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Bantu languages are spoken by ~310 million Africans, yet the genetic history of Bantu-speaking populations remains largely unexplored. We generated genomic data for 1,318 individuals from 35 populations in western central Africa, where Bantu languages originated. We found that early Bantu speakers first moved southward, through the equatorial rainforest, before spreading toward eastern and southern Africa. We also found that genetic adaptation of Bantu speakers was facilitated by admixture with autochthonous populations, particularly for the HLA and LCT loci. Finally, we identified a major contribution of western central African Bantu speakers to the ancestry of African Americans, whose genomes present no strong signals of natural selection. Together, these results highlight the contribution of Bantu-speaking peoples to the complex genetic history of Africans and African Americans.
| EGAS00001002078 | EGA
Project description:We seek to investigate the genetic relationships between different Bantu-speaking populations and the migratory routes they followed during various phases of the Bantu expansion. Genomic and whole genome amplified DNA were genotyped on the Illumina InfiniumOmni2.5Exome-8v1.3 array. For quality control filtering, we used the PLINK v1.9 software and custom scripts.
2019-11-24 | E-MTAB-8450 | biostudies-arrayexpress
Project description:The genetic structure of the indigenous hunter-gatherer peoples of Southern Africa, the oldest known lineage of modern man, holds an important key to understanding humanity's early history. Previously sequenced human genomes have been limited to recently diverged populations. Here we present the first complete genome sequences of an indigenous hunter-gatherer from the Kalahari Desert and of a Bantu from Southern Africa, as well as protein-coding regions from an additional three hunter-gatherers from disparate regions of the Kalahari. We characterize the extent of whole-genome and exome diversity among the five men, reporting 1.3 million novel DNA differences genome-wide, and 13,146 novel amino-acid variants. These data allow genetic relationships among Southern African foragers and neighboring agriculturalists to be traced more accurately than was previously possible. Adding the described variants to current databases will facilitate inclusion of Southern Africans in medical research efforts.
2010-02-18 | GSE19048 | GEO
Project description:The genetic structure of the indigenous hunter-gatherer peoples of Southern Africa, the oldest known lineage of modern man, holds an important key to understanding humanity's early history. Previously sequenced human genomes have been limited to recently diverged populations. Here we present the first complete genome sequences of an indigenous hunter-gatherer from the Kalahari Desert and of a Bantu from Southern Africa, as well as protein-coding regions from an additional three hunter-gatherers from disparate regions of the Kalahari. We characterize the extent of whole-genome and exome diversity among the five men, reporting 1.3 million novel DNA differences genome-wide, and 13,146 novel amino-acid variants. These data allow genetic relationships among Southern African foragers and neighboring agriculturalists to be traced more accurately than was previously possible. Adding the described variants to current databases will facilitate inclusion of Southern Africans in medical research efforts. Copy number differences between NA18507 and KB1 were predicted from the depth of whole-genome shotgun sequence reads. These predictions were then validated using array-CGH using a a genome-wide design as well as a custom design targeted at specific regions of copy number difference
2010-02-17 | E-GEOD-19048 | biostudies-arrayexpress
Project description:Illumina single nucleotide polymorphism (SNP) array data were generated to study genome-wide patterns of genomic variation on Sumba and Timor, two small islands in eastern Indonesia. Both islands have a complex history from their initial settlement ~50,000 years ago, to admixture with Austronesian-speaking groups during the Neolithic farming expansion, and more recent intra-island gene flow and community interactions. As part of this detailed microgeographic study, we also collected associated cultural and linguistic information. The primary study location was Sumba, for which we genotyped SNPs in 235 individuals from eight communities that span the island, including groups that speak most of Sumba’s nine languages. Particular attention was paid to genomic data that are informative for recent aspects of population history, including reconstructions of past gene flow, socio-genetic interactions and possible signals of selection.
2016-07-14 | GSE76645 | GEO
Project description:Only a few scattered groups with oral traditions of Khoe-San hunter-gatherer ancestry remain in southeastern Africa. We investigate genomic variation of remaining individuals from two South African groups with oral histories connecting them to eastern San groups, i.e., the San from Lake Chrissie and the Duma San of the uKhahlamba-Drakensberg. Using ~2.2 million genetic markers, combined with comparative published datasets, we show that the Lake Chrissie San have genetic ancestry from both Khoe-San (likely the ||Xegwi San) and Bantu-speakers. Specifically, we found that the Lake Chrissie San are closely related to current southern San groups (i.e. the Karretjie People). Duma San individuals, on the other hand, were genetically similar to southeastern Bantu speakers from South Africa. Samples were genotyped on the Illumina Omni2.5M (HumanOmni25-8v1-2_A1) SNP chip. Results were analyzed using the software GenomeStudio 2011.1 and the data were exported to Plink format, aligned to Human Genome build version 37.
2016-09-21 | E-MTAB-5119 | biostudies-arrayexpress
Project description:Modern genetic data combined with appropriate statistical methods have the potential to contribute substantially to our understanding of human history. We have developed an approach that exploits the genomic structure of admixed populations to date and characterize historical mixture events at fine scales. We used this to produce an atlas of worldwide human admixture history, constructed using genetic data alone and encompassing over 100 events occurring over the past 4,000 years. We identify events whose dates and participants suggest they describe genetic impacts of the Mongol Empire, Arab slave trade, Bantu expansion, first millennium CE migrations in eastern Europe, and European colonialism, as well as unrecorded events, revealing admixture to be an almost universal force shaping human populations.
2014-02-14 | GSE53626 | GEO
Project description:Modern genetic data combined with appropriate statistical methods have the potential to contribute substantially to our understanding of human history. We have developed an approach that exploits the genomic structure of admixed populations to date and characterize historical mixture events at fine scales. We used this to produce an atlas of worldwide human admixture history, constructed using genetic data alone and encompassing over 100 events occurring over the past 4,000 years. We identify events whose dates and participants suggest they describe genetic impacts of the Mongol Empire, Arab slave trade, Bantu expansion, first millennium CE migrations in eastern Europe, and European colonialism, as well as unrecorded events, revealing admixture to be an almost universal force shaping human populations. 158 indviduals of Eurasian descent included as part of a global analysis of admixture
2014-02-14 | E-GEOD-53626 | biostudies-arrayexpress
Project description:Linguistic and cultural evidence suggests that Madagascar was the final point of two major dispersals of Austronesian and Bantu speaking populations. Today, Mikea are described as the last known Malagasy population reported to be still practising a hunter-gatherer life-style. It is unclear, however, whether Mikea descend from a remnant population that existed before the arrival of Austronesian and Bantu agriculturalists or whether it is only their life-style that separates them from the other contemporary populations of South Madagascar. In order to address these questions we have performed a genome wide analysis of >700,000 SNP markers on 21 Mikea, 24 Vezo and 24 Temoro individuals together with 50 individuals from Bajo and Lebbo populations from Indonesia. Our analyses of these data in the context of data available from other Southeast Asian and African populations reveal that all three Malagasy populations are derived from the same admixture event involving Austronesian and Bantu sources. In contrast to the fact that most of the vocabulary of the Malagasy speakers is derived from the Barito group of the Austronesian language family we observe that only one third of their genetic ancestry is related to the populations of Java-Kalimantan-Sulawesi area. Because no additional ancestry components distinctive to for the Mikea were found, it is likely that they have adopted their hunter-gatherer way of life by through cultural reversion.
2013-12-19 | GSE53445 | GEO
Project description:Linguistic and cultural evidence suggests that Madagascar was the final point of two major dispersals of Austronesian and Bantu speaking populations. Today, Mikea are described as the last known Malagasy population reported to be still practising a hunter-gatherer life-style. It is unclear, however, whether Mikea descend from a remnant population that existed before the arrival of Austronesian and Bantu agriculturalists or whether it is only their life-style that separates them from the other contemporary populations of South Madagascar. In order to address these questions we have performed a genome wide analysis of >700,000 SNP markers on 21 Mikea, 24 Vezo and 24 Temoro individuals together with 50 individuals from Bajo and Lebbo populations from Indonesia. Our analyses of these data in the context of data available from other Southeast Asian and African populations reveal that all three Malagasy populations are derived from the same admixture event involving Austronesian and Bantu sources. In contrast to the fact that most of the vocabulary of the Malagasy speakers is derived from the Barito group of the Austronesian language family we observe that only one third of their genetic ancestry is related to the populations of Java-Kalimantan-Sulawesi area. Because no additional ancestry components distinctive to for the Mikea were found, it is likely that they have adopted their hunter-gatherer way of life by through cultural reversion. 69 samples were analysed with the Illumina platform OmniExpress BeadChips and are described herein.
2013-12-19 | E-GEOD-53445 | biostudies-arrayexpress