| 1. |
- Meyer, Anja, et al.
(författare)
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A reassessment of archaeological human remains recovered from rock shelters in Cathkin Peak, South Africa
- 2021
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Ingår i: Azania. - : Routledge. - 0067-270X .- 1945-5534. ; 56:4, s. 508-538
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Tidskriftsartikel (refereegranskat)abstract
- Various skeletons from the uThukela region of the uKhahlamba-Drakensberg Mountains of South Africa were excavated from rock shelters there during the early part of the twentieth century, with limited accompanying data or analysis. This paper analyses and reports on nine such graves (eight of which contained human remains), excavated during 1931 near Cathkin Peak. The remains are currently housed in the Raymond A. Dart Archaeological Human Remains Collection, University of the Witwatersrand, Johannesburg. Most of the skeletons were radiocarbon-dated to between the fourteenth and mid-seventeenth centuries, but one is older and dates to between the seventh and ninth centuries AD. Remains recovered from the various shelters included those of both adults and children, males and females, indicating that these rock shelters were used for the burials of, and were possibly occupied by, a wide variety of individuals over a long period of time. Skeletal analyses revealed several signs of disease and trauma, attesting to some hardships living in this region of South Africa. Stable isotope analyses of carbon and nitrogen indicate a predominantly plant-based diet. Originally it was thought that these individuals’ remains represented those of the historic amaZizi people, however, radiocarbon dates indicate that they are contemporaneous with the Moor Park phase of the Blackburn branch, which predates the amaZizi by several decades. Of interest is the fact that one individual predates the Moor Park phase. This is significant and sheds some light on the movement of people from KwaZulu-Natal into the interior. Future ancient DNA analysis will provide more information on the origin and genetic relationship of these individuals.
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| 2. |
- Babiker, Hiba, et al.
(författare)
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Genetic variation and population structure of Sudanese populations as indicated by 15 Identifiler sequence-tagged repeat (STR) loci.
- 2011
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Ingår i: Investigative Genetics. - : Springer Science and Business Media LLC. - 2041-2223. ; 2:1
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: 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.RESULT: 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.CONCLUSION: 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.
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| 3. |
- 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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| 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. |
- 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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| 6. |
- Hammarén, Rickard, 1989-, et al.
(författare)
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Eurasian back-migrations into Northeast Africa was a complex and multifaceted process
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Recent studies have identified Northeast Africa as an important area for human movements during the Holocene. Eurasian populations have moved back into Northeastern Africa and contributed to the genetic composition of its people. By gathering the largest reference dataset to date of Northeast, North, and East African as well as Middle Eastern populations, we give new depth to our knowledge of Northeast African demographic history. By employing local ancestry methods, we isolated the Non-African parts of modern-day Northeast African genomes and identified the best putative source populations. Egyptians and Sudanese Copts bore most similarities to Levantine populations whilst other populations in the region generally had predominantly genetic contributions from Arabian peninsula rather than Levantine populations for their Non-African genetic component. We also date admixture events and investigated which factors influenced the date of admixture and find that major linguistic families were associated with the date of Eurasian admixture. Taken as a whole we detect complex patterns of admixture and diverse origins of Eurasian admixture in Northeast African populations of today.
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| 7. |
- Hollfelder, Nina, et al.
(författare)
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Northeast African genomic variation shaped by the continuity of indigenous groups and Eurasian migrations
- 2017
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Ingår i: PLOS Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 13:8
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Tidskriftsartikel (refereegranskat)abstract
- Northeast Africa has a long history of human habitation, with fossil-finds from the earliest anatomically modern humans, and housing ancient civilizations. The region is also the gate-way out of Africa, as well as a portal for migration into Africa from Eurasia via the Middle East and the Arabian Peninsula. We investigate the population history of northeast Africa by genotyping ~3.9 million SNPs in 221 individuals from 18 populations sampled in Sudan and South Sudan and combine this data with published genome-wide data from surrounding areas. We find a strong genetic divide between the populations from the northeastern parts of the region (Nubians, central Arab populations, and the Beja) and populations towards the west and south (Nilotes, Darfur and Kordofan populations). This differentiation is mainly caused by a large Eurasian ancestry component of the northeast populations likely driven by migration of Middle Eastern groups followed by admixture that affected the local populations in a north-to-south succession of events. Genetic evidence points to an early admixture event in the Nubians, concurrent with historical contact between North Sudanese and Arab groups. We estimate the admixture in current-day Sudanese Arab populations to about 700 years ago, coinciding with the fall of Dongola in 1315/1316 AD, a wave of admixture that reached the Darfurian/Kordofanian populations some 400–200 years ago. In contrast to the northeastern populations, the current-day Nilotic populations from the south of the region display little or no admixture from Eurasian groups indicating long-term isolation and population continuity in these areas of northeast Africa.
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| 8. |
- Hollfelder, Nina, et al.
(författare)
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Patterns of African and Asian admixture in the Afrikaner population of South Africa
- 2020
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Ingår i: BMC Biology. - : Springer Science and Business Media LLC. - 1741-7007. ; 18:1
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The Afrikaner population of South Africa is the descendants of European colonists who started to colonize the Cape of Good Hope in the 1600s. In the early days of the colony, mixed unions between European males and non-European females gave rise to admixed children who later became incorporated into either the Afrikaner or the Coloured populations of South Africa. Differences in ancestry, social class, culture, sex ratio and geographic structure led to distinct and characteristic admixture patterns in the Afrikaner and Coloured populations. The Afrikaner population has a predominant European composition, whereas the Coloured population has more diverse ancestries. Genealogical records previously estimated the contribution of non-Europeans into the Afrikaners to be between 5.5 and 7.2%. RESULTS: To investigate the genetic ancestry of the Afrikaner population today (11-13 generations after initial colonization), we genotyped approximately five million genome-wide markers in 77 Afrikaner individuals and compared their genotypes to populations across the world to determine parental source populations and admixture proportions. We found that the majority of Afrikaner ancestry (average 95.3%) came from European populations (specifically northwestern European populations), but that almost all Afrikaners had admixture from non-Europeans. The non-European admixture originated mostly from people who were brought to South Africa as slaves and, to a lesser extent, from local Khoe-San groups. Furthermore, despite a potentially small founding population, there is no sign of a recent bottleneck in the Afrikaner compared to other European populations. Admixture amongst diverse groups from Europe and elsewhere during early colonial times might have counterbalanced the effects of a small founding population. CONCLUSIONS: While Afrikaners have an ancestry predominantly from northwestern Europe, non-European admixture signals are ubiquitous in the Afrikaner population. Interesting patterns and similarities could be observed between genealogical predictions and our genetic inferences. Afrikaners today have comparable inbreeding levels to current-day European populations.
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| 9. |
- Hollfelder, Nina, et al.
(författare)
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The Genetic Variation of Lactase Persistence Alleles in Sudan and South Sudan
- 2021
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Ingår i: Genome Biology and Evolution. - : Oxford University Press. - 1759-6653. ; 13:5
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Tidskriftsartikel (refereegranskat)abstract
- Lactase persistence (LP) is a well-studied example of a Mendelian trait under selection in some human groups due to gene-culture coevolution. We investigated the frequencies of genetic variants linked to LP in Sudanese and South Sudanese populations. These populations have diverse subsistence patterns, and some are dependent on milk to various extents, not only from cows but also from other livestock such as camels and goats. We sequenced a 316-bp region involved in regulating the expression of the LCT gene on chromosome 2, which encompasses five polymorphisms that have been associated with LP. Pastoralist populations showed a higher frequency of LP-associated alleles compared with nonpastoralist groups, hinting at positive selection also among northeast African pastoralists. Among the LP variants, the -14009:G variant occurs at the highest frequency among the investigated populations, followed by the -13915:G variant, which is likely of Middle Eastern origin, consistent with Middle Eastern gene flow to the Sudanese populations. There was no incidence of the “East African” LP allele (-14010:C) in the Sudanese and South Sudanese groups, and only one heterozygous individual for the “European” LP allele (-13910:T), suggesting limited recent admixture from these geographic regions. The Beja population of the Beni Amer show three different LP variants at substantial and similar levels, resulting in one of the greatest aggregation of LP variants among all populations across the world.
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| 10. |
- Owers, Katharine A., et al.
(författare)
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Adaptation to infectious disease exposure in indigenous Southern African populations
- 2017
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Ingår i: Proceedings of the Royal Society of London. Biological Sciences. - : ROYAL SOC. - 0962-8452 .- 1471-2954. ; 284:1852
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Tidskriftsartikel (refereegranskat)abstract
- Genetic analyses can provide information about human evolutionary history that cannot always be gleaned from other sources. We evaluated evidence of selective pressure due to introduced infectious diseases in the genomes of two indigenous southern African San groups-the double dagger Khomani who had abundant contact with other people migrating into the region and the more isolated Ju vertical bar'hoansi. We used a dual approach to test for increased selection on immune genes compared with the rest of the genome in these groups. First, we calculated summary values of statistics that measure genomic signatures of adaptation to contrast selection signatures in immune genes and all genes. Second, we located regions of the genome with extreme values of three selection statistics and examined these regions for enrichment of immune genes. We found stronger and more abundant signals of selection in immune genes in the double dagger Khomani than in the Ju vertical bar'hoansi. We confirm this finding within each population to avoid effects of different demographic histories of the two populations. We identified eight immune genes that have potentially been targets of strong selection in the double dagger Khomani, whereas in the Juj'hoansi, no immune genes were found in the genomic regions with the strongest signals of selection. We suggest that the more abundant signatures of selection at immune genes in the double dagger Khomani could be explained by their more frequent contact with immigrant groups, which likely led to increased exposure and adaptation to introduced infectious diseases.
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| 11. |
- Schlebusch, Carina, 1977-, et al.
(författare)
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Khoe-San Genomes Reveal Unique Variation and Confirm the Deepest Population Divergence in Homo sapiens
- 2020
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 37:10, s. 2944-2954
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Tidskriftsartikel (refereegranskat)abstract
- The southern African indigenous Khoe-San populations harbor the most divergent lineages of all living peoples. Exploring their genomes is key to understanding deep human history. We sequenced 25 full genomes from five Khoe-San populations, revealing many novel variants, that 25% of variants are unique to the Khoe-San, and that the Khoe-San group harbors the greatest level of diversity across the globe. In line with previous studies, we found several gene regions with extreme values in genome-wide scans for selection, potentially caused by natural selection in the lineage leading to Homo sapiens and more recent in time. These gene regions included immunity-, sperm-, brain-, diet-, and muscle-related genes. When accounting for recent admixture, all Khoe-San groups display genetic diversity approaching the levels in other African groups and a reduction in effective population size starting around 100,000 years ago. Hence, all human groups show a reduction in effective population size commencing around the time of the Out-of-Africa migrations, which coincides with changes in the paleoclimate records, changes that potentially impacted all humans at the time.
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| 12. |
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