| 1. |
- Meyer, Anja, et al.
(author)
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A reassessment of archaeological human remains recovered from rock shelters in Cathkin Peak, South Africa
- 2021
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In: Azania. - : Routledge. - 0067-270X .- 1945-5534. ; 56:4, s. 508-538
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Journal article (peer-reviewed)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. |
- Steyn, Maryna, et al.
(author)
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African Farmers, Not Stone Age Foragers : Reassessment of Human Remains from the Mumbwa Caves, Zambia
- 2023
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In: African Archaeological Review. - : Springer Nature. - 0263-0338 .- 1572-9842. ; 40:1, s. 53-72
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Journal article (peer-reviewed)abstract
- In this article, we reassess the human remains from the Mumbwa Caves housed in the Raymond A. Dart Archaeological Human Remains Collection at the University of the Witwatersrand, South Africa. Based on new radiocarbon dates from human bone collagen and stable isotope analysis, our results revealed that the poorly preserved remains, comprising mostly crania and teeth, represent at least 16 individuals. Some of them have culturally modified anterior teeth. Enamel hypoplastic lesions were seen in a few individuals, which indicates disease and malnutrition during childhood. Radiocarbon dating revealed that all the individuals were buried at Mumbwa sometime between the late tenth and early twentieth century CE, with most dates clustering between the early sixteenth and the late nineteenth century. With the exception of a single individual who seems to have had a hunter-gatherer/forager diet, the carbon and nitrogen isotope values of others are consistent with what would be expected from a low-trophic farmer diet based on foodplants with C4 photosynthetic pathways. It is, therefore, our contention that, rather than being associated with the Stone Age as previously suggested, these individuals lived in more recent agricultural communities around the Mumbwa Caves.
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| 3. |
- Alva, Omar, et al.
(author)
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The loss of biodiversity in Madagascar is contemporaneous with major demographic events
- 2022
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In: Current Biology. - : Elsevier. - 0960-9822 .- 1879-0445. ; 32:23, s. 4997-
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Journal article (peer-reviewed)abstract
- Only 400 km off the coast of East Africa, the island of Madagascar is one of the last large land masses to have been colonized by humans. While many questions surround the human occupation of Madagascar, recent studies raise the question of human impact on endemic biodiversity and landscape transformation. Previous genetic and linguistic analyses have shown that the Malagasy population has emerged from an admixture that happened during the last millennium, between Bantu-speaking African populations and Austronesian-speaking Asian populations. By studying the sharing of chromosome segments between individuals (IBD determination), local ancestry information, and simulated genetic data, we inferred that the Malagasy ancestral Asian population was isolated for more than 1,000 years with an effective size of just a few hundred individuals. This isolation ended around 1,000 years before present (BP) by admixture with a small African population. Around the admixture time, there was a rapid demographic expansion due to intrinsic population growth of the newly admixed population, which coincides with extensive changes in Madagascar's landscape and the extinction of all endemic large- bodied vertebrates. Therefore, our approach can provide new insights into past human demography and associated impacts on ecosystems.
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| 4. |
- Avila-Arcos, Maria C., et al.
(author)
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Going local with ancient DNA : A review of human histories from regional perspectives
- 2023
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 382:6666, s. 53-58
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Research review (peer-reviewed)abstract
- Ancient DNA (aDNA) has added a wealth of information about our species' history, including insights on genetic origins, migrations and gene flow, genetic admixture, and health and disease. Much early work has focused on continental-level questions, leaving many regional questions, especially those relevant to the Global South, comparatively underexplored. A few success stories of aDNA studies from smaller laboratories involve more local aspects of human histories and health in the Americas, Africa, Asia, and Oceania. In this Review, we cover some of these contributions by synthesizing finer-scale questions of importance to the archaeogenetics field, as well as to Indigenous and Descendant communities. We further highlight the potential of aDNA to uncover past histories in regions where colonialism has neglected the oral histories of oppressed peoples.
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| 5. |
- Babiker, Hiba, et al.
(author)
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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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In: Investigative Genetics. - : Springer Science and Business Media LLC. - 2041-2223. ; 2:1
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Journal article (peer-reviewed)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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| 6. |
- Breton, Gwenna, et al.
(author)
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Comparison of sequencing data processing pipelines and application to underrepresented African human populations
- 2021
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In: BMC Bioinformatics. - : BioMed Central (BMC). - 1471-2105. ; 22:1
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Journal article (peer-reviewed)abstract
- Background Population genetic studies of humans make increasing use of high-throughput sequencing in order to capture diversity in an unbiased way. There is an abundance of sequencing technologies, bioinformatic tools and the available genomes are increasing in number. Studies have evaluated and compared some of these technologies and tools, such as the Genome Analysis Toolkit (GATK) and its "Best Practices" bioinformatic pipelines. However, studies often focus on a few genomes of Eurasian origin in order to detect technical issues. We instead surveyed the use of the GATK tools and established a pipeline for processing high coverage full genomes from a diverse set of populations, including Sub-Saharan African groups, in order to reveal challenges from human diversity and stratification. Results We surveyed 29 studies using high-throughput sequencing data, and compared their strategies for data pre-processing and variant calling. We found that processing of data is very variable across studies and that the GATK "Best Practices" are seldom followed strictly. We then compared three versions of a GATK pipeline, differing in the inclusion of an indel realignment step and with a modification of the base quality score recalibration step. We applied the pipelines on a diverse set of 28 individuals. We compared the pipelines in terms of count of called variants and overlap of the callsets. We found that the pipelines resulted in similar callsets, in particular after callset filtering. We also ran one of the pipelines on a larger dataset of 179 individuals. We noted that including more individuals at the joint genotyping step resulted in different counts of variants. At the individual level, we observed that the average genome coverage was correlated to the number of variants called. Conclusions We conclude that applying the GATK "Best Practices" pipeline, including their recommended reference datasets, to underrepresented populations does not lead to a decrease in the number of called variants compared to alternative pipelines. We recommend to aim for coverage of > 30X if identifying most variants is important, and to work with large sample sizes at the variant calling stage, also for underrepresented individuals and populations.
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| 7. |
- Breton, Gwenna, et al.
(author)
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Comparison of sequencing data processing pipelines and application to underrepresented human populations
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In: BMC Bioinformatics. - 1471-2105.
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Journal article (peer-reviewed)abstract
- Population genetic studies of humans make increasing use of high-throughput sequencing in order to capture human diversity in an unbiased way. There is an abundance of sequencing technologies, bioinformatic tools and the available genomes are increasing in number. Studies have evaluated and compared some of these technologies and tools, such as the Genome Analysis Toolkit (GATK) and its “Best Practices” bioinformatic pipelines. However, studies often focus on few genomes of Eurasian origin in order to detect technical issues. We instead surveyed the use of the GATK tools and established a pipeline for processing high coverage full genomes from a diverse set of populations, including Sub-Saharan African groups, in order to reveal challenges from human diversity and stratification.We started by surveying 29 studies using high-throughput sequencing data, and compared their strategies for data pre-processing and variant calling. We found that processing of data is very variable across studies, that the GATK “Best Practices” are seldom followed strictly and that processing pipelines are often not reported in full details. We then compared three versions of the GATK pipeline, differing in the inclusion of an indel realignment step and with a modification of the base quality score recalibration step. We applied the pipelines on a diverse set of 28 individuals. We compared the pipelines in terms of count of called variants and overlap of the callsets. We found that the pipelines resulted in similar callsets, in particular after callset filtering. We also ran one of the pipeline on a larger dataset of 179 individuals. We noted that including more individuals at the joint genotyping step resulted in different counts of variants. At the individual level, we observed that the average genome coverage was correlated to the number of variants called.We conclude that applying the GATK “Best Practices” pipeline, including their recommended reference datasets, to underrepresented populations does not lead to a decrease in the number of called variants compared to alternative pipelines. We recommend to aim for a coverage of >30X, and to work with large sample sizes at the variant calling stage, also for underrepresented individuals and populations.
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| 8. |
- Breton, Gwenna, et al.
(author)
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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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Other publication (other academic/artistic)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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| 9. |
- Breton, Gwenna
(author)
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Human demographic history : Insights on the human past based on genomes from Southern through Central Africa
- 2020
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Doctoral thesis (other academic/artistic)abstract
- Evidence from paleontology, archaeology and population genetics support that modern humans originated in Africa. While the out-of-Africa event and subsequent colonization of all continents are well documented, human history in Africa at that time and before is less studied. Some current-day hunter-gatherer populations trace most of their genetic lineages to populations who inhabited Sub-Saharan Africa until the arrival of farming. They are informative about human history before and after the arrival of farming.I studied high-coverage genomes from two such groups, the Khoe-San from Southern Africa and the rainforest hunter-gatherers from Central Africa. I generated a total of 74 genomes, significantly increasing the number of genomes from Sub-Saharan African hunter-gatherers. I compared several versions of a commonly used pipeline for high-coverage genomes and showed that using standard ascertained reference datasets has no significant impact on variant calling in populations from Sub-Saharan Africa. Using the full genome information, I described the genetic diversity in the Khoe-San and in the rainforest hunter-gatherers and showed that gene flow from agropastoralist groups increased the Khoe-San genetic diversity. I also detected a signal of population size decline in the Khoe-San around the time of the out-of-Africa event, and I evaluated the power of the method to detect bottlenecks by applying it to simulated data. I investigated the history of modern humans in Africa by estimating divergence times between populations and applying an Approximate Bayesian Computation analysis. We confirmed that the earliest divergence event was between the Khoe-San ancestral lineage and the rest of modern humans, ~250-350 kya. I also showed that the possibility of high gene flow should be incorporated in models of human evolution.I furthermore examined SNP array data for two BaTwa populations from Zambia and showed that 20-30% of their autosomal diversity is hunter-gatherer-like. The estimated times for the admixture between a presumably local hunter-gatherer population and incoming agropastoralist groups are consistent with archaeological records.In this thesis, I investigated questions related to human history in Sub-Saharan Africa, from the emergence of modern humans ~300 kya to recent events related to the expansion of farming.
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| 10. |
- Breton, Gwenna, et al.
(author)
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The “BaTwa” populations from remote areas in Zambia retain ancestry of past forager groups
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Other publication (other academic/artistic)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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