| 1. |
- Breton, Gwenna, et al.
(författare)
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Deciphering early human history using Approximate Bayesian Computation and 74 whole genomes from Central and Southern Africa
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Human evolutionary history in Africa before and after the out-of-Africa event remains largely unexplored, due to lack of genome sequence data, limited representation of populations and limitations of presently available inference methods. We generated high-coverage genomes from 49 Central African individuals, from five rainforest hunter-gatherer populations and four neighboring populations, and from 25 Khoe-San individuals, from five populations. We analyzed these genomes jointly with 104 comparative genomes from worldwide populations. We showed that rainforest hunter-gatherers and Khoe-San populations define two distinct major axes of genetic variation both at the worldwide and Sub-Saharan scales. This new data provides unprecedented resolution to unravel complex genetic differentiation among rainforest hunter-gatherer populations in particular. Using both deterministic and Approximate Bayesian Computation inferences, we found strong support for gene flow throughout the entire history of Central and Southern Africa, and an early divergence, some 250-370 kya ago, of Khoe-San ancestors from the lineage ancestral to all Central African populations. This event was followed, still in the presence of gene-flow, some 80-240 kya, by the divergence of lineages ancestral to rainforest hunter-gatherers and their neighbors. Finally, divergence between the different Khoe-San populations likely predated that of eastern and western rainforest hunter-gatherers which occurred 16-44 kya. Altogether, our results indicate that a tree-like history of Central Africa incorporating gene-flow among ancient lineages as well as among recent lineages can explain genomic variation observed among populations today.
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| 2. |
- Breton, Gwenna, et al.
(författare)
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Lactase Persistence Alleles Reveal Partial East African Ancestry of Southern African Khoe Pastoralists
- 2014
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Ingår i: Current Biology. - : Elsevier BV. - 0960-9822 .- 1879-0445. ; 24:8, s. 852-858
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Tidskriftsartikel (refereegranskat)abstract
- The ability to digest milk into adulthood, lactase persistence (LP), as well as specific genetic variants associated with LP, is heterogeneously distributed in global populations [1-4]. These variants were most likely targets of selection when some populations converted from hunter-gatherer to pastoralist or farming lifestyles [5-7]. Specific LP polymorphisms are associated with particular geographic regions and populations [1-4, 8-10]; however, they have not been extensively studied in southern Africa. We investigate the LP-regulatory region in 267 individuals from 13 southern African populations (including descendants of hunter-gatherers, pastoralists, and agropastoralists), providing the first comprehensive study of the LP-regulatory region in a large group of southern Africans. The "East African" LP single-nucleotide polymorphism (SNP) (14010G>C) was found at high frequency (>20%) in a strict pastoralist Khoe population, the Nama of Namibia, suggesting a connection to East Africa, whereas the "European" LP SNP (13910C>T) was found in populations of mixed ancestry. Using genome-wide data from various African populations, we identify admixture (13%) in the Nama, from an Afro-Asiatic group dating to >1,300 years ago, with the remaining fraction of their genomes being from San hunter-gatherers. We also find evidence of selection around the LCT gene among Khoe-speaking groups, and the substantial frequency of the 14010C variant among the Nama is best explained by adaptation to digesting milk. These genome-local and genome-wide results support a model in which an East African group brought pastoralist practices to southern Africa and admixed with local hunter-gatherers to form the ancestors of Khoe people.
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| 3. |
- Breton, Gwenna, et al.
(författare)
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The “BaTwa” populations from remote areas in Zambia retain ancestry of past forager groups
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Sub-equatorial Africa is inhabited today predominantly by Bantu-speaking farmers of west African descent. However, before the arrival of agriculture and pastoralism ~2,000 years ago, the region was inhabited by hunter-gatherers. The incoming farmer populations replaced, displaced or admixed with local hunter-gatherer groups. In some regions such as southern and central Africa, current-day farming populations have absorbed a large local hunter-gatherer genetic component. In other regions, such as Malawi, and Mozambique current-day populations have absorbed little to none of the local component. In this study, we generated genome-wide SNP data from two populations from Zambia thought to represent former hunter-gatherers, known locally as “BaTwa”, but for which no direct evidence exists of a hunter-gatherer past, either in language or lifestyle. We compared the BaTwa data to three Bantu-speaker agropastoralist populations from Zambia, and to other African and non-African populations. We show that the two BaTwa populations harbor a hunter-gatherer-like genetic component, representing respectively ~20% and ~30% of their genetic ancestry, while the rest is similar to Bantu-speaker agropastoralists. Although the component is closest related to current-day Khoe-San populations from southern Africa, results still suggest a unique local hunter-gatherer component. These results accord with Middle and Late Holocene skeletal evidence from Zambia and Malawi for a regionally separate hunter-gatherer population, which is now only detectable among the BaTwa. A two-way admixture scenario between a Bantu-speaker agropastoralist-like source and a hunter-gatherer-like source is supported for the two populations, occurring ~40 and ~16 generations ago respectively. These estimates are consistent with archaeological records for the arrival of agropastoralists in northern and central Zambia respectively. The study demonstrate the value of studying underrepresented minority groups to better understand the complexity of regional population histories.
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| 4. |
- Fortes-Lima, Cesar A., PhD, 1985-, et al.
(författare)
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Population structure and admixture during the expansion of Bantu-speaking peoples across sub-Saharan Africa
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The migration of Bantu-speaking groups out of West Africa, thought to have started around 4 000 years ago, is known as the Bantu expansion. This movement of people changed the genetic landscape of sub-equatorial Africa. To investigate the demographic history and population structure in Bantu-speaking populations (BSP), we genotyped 1,740 individuals, including 1,487 Bantu speakers from 143 populations across 13 sub-Saharan African countries. We find patterns of fine-scale population structure that correlate with linguistics and geography. Bantu speakers received significant amounts of admixture through interaction with local groups from the regions that they expanded into. Spatial modeling indicated possible migration corridors during the Bantu-expansion. Inferences based on modern-day genomes, however, need to be supported by ancient DNA studies. We demonstrated the utility of our dataset as an exhaustive modern-day African comparative dataset for ancient DNA studies by comparing our data to published aDNA studies. By gathering the largest set of genome-wide data to date, enriched with new data from previously unsampled regions and people, we shed new light on the intricacies of the Bantu expansion.
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| 5. |
- Fortes-Lima, Cesar A., PhD, 1985-, et al.
(författare)
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The genetic legacy of the expansion of Bantu-speaking peoples in Africa
- 2024
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Ingår i: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 625:7995, s. 540-547
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Tidskriftsartikel (refereegranskat)abstract
- The expansion of people speaking Bantu languages is the most dramatic demographic event in Late Holocene Africa and fundamentally reshaped the linguistic, cultural and biological landscape of the continent1-7. With a comprehensive genomic dataset, including newly generated data of modern-day and ancient DNA from previously unsampled regions in Africa, we contribute insights into this expansion that started 6,000-4,000 years ago in western Africa. We genotyped 1,763 participants, including 1,526 Bantu speakers from 147 populations across 14 African countries, and generated whole-genome sequences from 12 Late Iron Age individuals8. We show that genetic diversity amongst Bantu-speaking populations declines with distance from western Africa, with current-day Zambia and the Democratic Republic of Congo as possible crossroads of interaction. Using spatially explicit methods9 and correlating genetic, linguistic and geographical data, we provide cross-disciplinary support for a serial-founder migration model. We further show that Bantu speakers received significant gene flow from local groups in regions they expanded into. Our genetic dataset provides an exhaustive modern-day African comparative dataset for ancient DNA studies10 and will be important to a wide range of disciplines from science and humanities, as well as to the medical sector studying human genetic variation and health in African and African-descendant populations.
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| 6. |
- Hammarén, Rickard, et al.
(författare)
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Ancestry contributions within geographically dispersed South African Coloured groups
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The South African Coloured people (SAC) are the most prominent admixed population in the country. They are descendants of local Khoe-San, and Bantu-speaking populations, European settlers, and enslaved people from the East and West Coast of Africa, South and East Asia, brought during the slave trade period. The term "Coloured" was an artificial category used by the South African apartheid government to group various groups with mixed ancestry. The term is still widely used today and is one of the ethnic categories in the South African government census. While the term is embraced by some people categorised as Coloured, it is rejected by others. This study aimed to investigate the remnant Khoekhoe and San genetic ancestry within various Coloured groups together with other ancestries introduced during colonial times. We generated novel genotyping, mtDNA, and Y-chromosome data for 65 individuals at two locations and, together with data from previously published studies, we assembled a dataset of 222 SAC individuals from 17 different geographic locations. This study has gathered the most extensive dataset of SAC individuals sampled from the largest number of sites to date. At 14 out of the 17 locations, Khoe-San was the majority ancestry. The Coloured populations display genetic ancestry from Khoe-San, West African, East African, East Asian, South Asian, and European groups at vastly varying amounts across the sampled locations, reflecting the history of South Africa, apartheid laws, and socio-cultural groupings. The ancestry proportions from different source populations differ by large fractions between the autosomes and uni-parental markers, which points to sex-biased admixture in the Coloured.This research highlights the importance of studying the South African Coloured population to comprehend the impact of complex migration patterns and historical systems of segregation in South Africa.
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| 7. |
- Lombard, Marlize, et al.
(författare)
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Bridging disciplines to better elucidate the evolution of early Homo sapiens in southern Africa
- 2013
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Ingår i: South African Journal of Science. - : Academy of Science of South Africa. - 0038-2353 .- 1996-7489. ; 109:11-12
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Tidskriftsartikel (refereegranskat)abstract
- Elucidating the history of Homo sapiens has been a passion shared by many researchers spanning several decades. There are now overwhelming lines of evidence from genetic, archaeological, palaeoanthropological and, to some extent, palaeoenvironmental research, that place Africa as the region of origin of our species. The different fields of study use diverse types of data, and methods are subject to variances introduced by mutation rates, time estimates and/or sampling biases. All of these approaches have their respective shortcomings and error ranges and are accompanied by intense debate. Yet, it is timeous to review the most recent and salient highlights that the different approaches are contributing towards explaining our deep history and ancestry. It is, after all, one history, and consequently, there ought to be several convergent patterns between data sets. Our focus is to present an updated regional synthesis from each discipline for a specific window in time within the southern African context, namely between similar to 160 ka and 85 ka, and to speculate about possible connections between data sets for this period. Even though our focus is specific in time and space, it is not intended to consider southern Africa in isolation from the rest of Africa or to suggest a singular 'origins' locale for modern Homo sapiens. We hope that this integrated approach will stimulate discussions to include broader time periods within Africa and between continents.
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| 8. |
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| 9. |
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| 10. |
- Naidoo, Thijessen, et al.
(författare)
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Y-Chromosome Variation in Southern African Khoe-San Populations Based on Whole-Genome Sequences
- 2020
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Ingår i: Genome Biology and Evolution. - : Oxford University Press (OUP). - 1759-6653. ; 12:7, s. 1031-1039
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Tidskriftsartikel (refereegranskat)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 comparison with existing whole Y-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 Y-chromosome phylogeny. The distribution of major 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 African migrations, B-M112 linked to earlier east-south gene flow, A-M14 linked to shared ancestry with central African rainforest hunter-gatherers, and A-M51 potentially unique to the Khoe-San.
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