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Sökning: WFRF:(Jakobsson Mattias) > Schlebusch Carina 1977

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1.
  • Babiker, Hiba, et al. (författare)
  • Genetic variation and population structure of Sudanese populations as indicated by 15 Identifiler sequence-tagged repeat (STR) loci.
  • 2011
  • Ingår i: Investigative Genetics. - : Springer Science and Business Media LLC. - 2041-2223. ; 2:1
  • 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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2.
  • Breton, Gwenna, et al. (författare)
  • Comparison of sequencing data processing pipelines and application to underrepresented African human populations
  • 2021
  • Ingår i: BMC Bioinformatics. - : BioMed Central (BMC). - 1471-2105. ; 22:1
  • Tidskriftsartikel (refereegranskat)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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3.
  • Breton, Gwenna, et al. (författare)
  • Comparison of sequencing data processing pipelines and application to underrepresented human populations
  • Ingår i: BMC Bioinformatics. - 1471-2105.
  • Tidskriftsartikel (refereegranskat)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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4.
  • Breton, Gwenna, et al. (författare)
  • Deciphering early human history using Approximate Bayesian Computation and 74 whole genomes from Central and Southern Africa
  • 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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5.
  • Breton, Gwenna (författare)
  • Human demographic history : Insights on the human past based on genomes from Southern through Central Africa
  • 2020
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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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6.
  • Breton, Gwenna, et al. (författare)
  • The “BaTwa” populations from remote areas in Zambia retain ancestry of past forager groups
  • 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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7.
  • Coutinho, Alexandra, et al. (författare)
  • Later Stone Age human hair from Vaalkrans Shelter, Cape Floristic Region of South Africa, reveals genetic affinity to Khoe groups
  • 2021
  • Ingår i: American Journal of Physical Anthropology. - : John Wiley & Sons. - 0002-9483 .- 1096-8644. ; 174:4, s. 701-713
  • Tidskriftsartikel (refereegranskat)abstract
    • Previous studies show that the indigenous people of the southern Cape of South Africa were dramatically impacted by the arrival of European colonists starting ~400 years ago and their descendants are today mixed with Europeans and Asians. To gain insight on the occupants of the Vaalkrans Shelter located at the southernmost tip of Africa, we investigated the genetic make-up of an individual who lived there about 200 years ago. We further contextualize the genetic ancestry of this individual among prehistoric and current groups. From a hair sample excavated at the shelter, which was indirectly dated to about 200 years old, we sequenced the genome (1.01 times coverage) of a Later Stone Age individual. We analyzed the Vaalkrans genome together with genetic data from 10 ancient (pre-colonial) individuals from southern Africa spanning the last 2000 years. We show that the individual from Vaalkrans was a man who traced ~80% of his ancestry to local southern San hunter–gatherers and ~20% to a mixed East African-Eurasian source. This genetic make-up is similar to modern-day Khoekhoe individuals from the Northern Cape Province (South Africa) and Namibia, but in the southern Cape, the Vaalkrans man's descendants have likely been assimilated into mixed-ancestry “Coloured” groups. The Vaalkrans man's genome reveals that Khoekhoe pastoralist groups/individuals lived in the southern Cape as late as 200 years ago, without mixing with non-African colonists or Bantu-speaking farmers. Our findings are also consistent with the model of a Holocene pastoralist migration, originating in Eastern Africa, shaping the genomic landscape of historic and current southern African populations.
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8.
  • Coutinho, Alexandra, et al. (författare)
  • The Evolution of Adaptive traits in Indigenous human populations in Sub-Saharan Africa
  • Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
    • Several well-known genetic variants that confer disease resistance or other adaptive advantages have been investigated in modern-day populations across the globe. In particular, sub-Saharan African populations display variation for many of these loci. In this study, we investigate allele frequencies underlying functional variants of interest in sub-Saharan African populations. By also investigating sequence data from ancient human remains from excavated sites in sub-Saharan Africa, we can start to get an indication of the allele frequency trajectories of adaptive variants, how they have diffused through the African genetic landscape, and how much migration and admixture played a role in the distribution of these variants in modern-day African populations. Our results show that as well as selection, migration has had a large influence on changing allele frequency through time in variants associated with disease resistance, salt sensitivity and metabolism. Yet in other variants, such as some associated with skin pigmentation, allele frequencies have changed little over time. Lastly, this study emphasizes the need for continued study of African populations, as due to the sheer genetic diversity present in Africa, different functional variants may confer similar means of adaptation than those we know for out-of-Africa populations. This study is the first to comprehensively investigate adaptive variants in both ancient and modern Africans, and further research will continue to reveal how the genetic landscape of modern humans has changed, and continues to change through time.
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9.
  • Coutinho, Alexandra (författare)
  • Where our feet have taken us : Examples of human contact, migration, and adaptation as revealed by ancient DNA
  • 2019
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • In spite of our extensive knowledge of the human past, certain key questions remain to be answered about human prehistory. One involves the nature of cultural change in material culture through time from the perspective of how different ancient human groups interacted with one another. The other is how humans have adapted to the different environments as they migrated and populated the rest of the world from their origin in Africa. For my thesis I have investigated examples of human evolutionary history using genetic information from ancient human remains. Chapter 1 focused on the nature of possible interaction between the Pitted Ware Culture (PWC) and Battle Axe Culture (BAC) on the island of Gotland, in the Baltic Sea. Through the analysis of 4500 year old human remains from three PWC burial sites, I found that the existence of BAC influences in these burial sites was the result of cultural and not demic influence from the BAC. In chapter 2, I investigated the ancestry of a Late Stone Age individual from the southwestern Cape of South Africa. Population genetic analyses revealed that this individual was genetically affiliated with Khoe groups in southern Africa, a genetic make-up that is today absent from the Cape. Chapter 3 investigated the genetic landscape of prehistoric individuals from southern Africa. Specifically, I explored frequencies of adaptive variants between Late Stone Age and Iron Age individuals. I found an increase in disease resistance alleles in Iron Age individuals and attributed this to the effects of the Bantu expansion. Chapter 4 incorporated a wider range of trait-associated variants among a greater number of modern-day populations and ancient individuals in Africa. I found that many allele frequency patterns found in modern populations follow the routes of major migrations which took place in the African Holocene. The thesis attests to the complexity of human demographic history in general, and how migration contributes to adaptation by dispersing novel adaptive variants to populations.
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10.
  • Hammarén, Rickard, 1989- (författare)
  • From the migrations of herders and farmers to the colonial era and the modern-day : Genetic inferences on African demographic history
  • 2022
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • Africa is the birthplace of the human species and home to great linguistic, cultural, and genetic diversity. Despite this, the genetics of the peoples of the continent remains understudied. In this thesis, I apply population genetic approaches, to contribute to the knowledge of human demographic history in Africa. Specifically, I investigated three events that have had major impacts on human population genetics in Africa. Paper I, investigated Eurasian back migrations into Northeast Africa and what genetic patterns this has left in the current-day populations of the area. I identified complex demography and linguistic stratification of Eurasian admixture in the region. These genetic patterns coincide in time with historical events such as the spread of Islam, the fall of the Kingdom of Aksum, and trade routes across the Red Sea. Paper II focused on the Bantu expansion, the different migratory routes of Bantu-speakers out of West Africa, and how they shaped the genetic makeup of the peoples of sub-equatorial Africa. We compiled the most comprehensive geographically distributed genetic dataset of Bantu-speaking individuals to date. I investigated the spatial patterns of migrations and the decline of genetic diversity from their homeland. I find evidence for serial founder events and migrations across Zambia and the Congo basin to the rest of sub-equatorial Africa. Paper III and IV involved South Africa and the effects that European colonialism and 20:th century policies have had on the country's genetic landscape. Paper III focuses on the Afrikaner population of South Africa, descendants of the first European settlers of the Cape colony, I describe the extent of African and Asian admixture in this population and investigate evidence of selection and adaptive admixture. Paper IV focuses on the Coloured population of South Africa, an emergent cultural identity. The Coloured population traces their origin primarily to Khoe-San women, manumitted slaves, and European men from the Cape colony. The term Coloured was also used for admixed individuals under the Apartheid racial classification system. The Coloured has one of the most complex admixture histories in the world, with genetic ancestry from Europe, East and South Asia, West and East Africa, as well as southern African Khoe-San. In our paper, we describe these complex patterns, the differences in sex-biased admixture, and determine the admixture dates across an extensive collection of Coloured, across South Africa. My work thus highlights complex genetic patterns within African human demographic history and shows how profoundly it has been shaped by the movement of people in the last 5 000 years.
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