Khoe-San genomes reveal unique variation and confirm the deepest population divergence in Homo sapiens

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

Human demographic history : Insights on the human past based on genomes from Southern through Central Africa

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

Archaeogenetics

Movie produced for the outreach event SciFest (scifest.se) in Uppsala. Film about the investigation of an archaeological site where different approaches were used, including ancient DNA study. Everything starts with the excavation of a funeral mound: who was buried there? When did they leave? What were their function in society or their relationship to others? Archaeologists and geneticists investigate the remains with surprising results. Each discovery contributes an additional piece to the puzzle for the reconstruction of our past. Watch and find out about the person buried in the funeral mound! The movie was made by archaeologists and geneticists working with ancient DNA. For more information and activities on this topic follow the links below. The scenario of the animation movie was partially inspired by the story of the “Birka lady”, a skeleton found at the Viking locality of Birka, on Björkö (close to Stockholm).Read more about it on Wikipedia (https://en.wikipedia.org/wiki/Birka_female_Viking_warrior) or have a look at the ancient DNA research article (https://onlinelibrary.wiley.com/doi/full/10.1002/ajpa.23308)

Archaeogenetics

Movie produced for the outreach event SciFest (scifest.se) in Uppsala. Film about the investigation of an archaeological site where different approaches were used, including ancient DNA study. Everything starts with the excavation of a funeral mound: who was buried there? When did they leave? What were their function in society or their relationship to others? Archaeologists and geneticists investigate the remains with surprising results. Each discovery contributes an additional piece to the puzzle for the reconstruction of our past. Watch and find out about the person buried in the funeral mound! The movie was made by archaeologists and geneticists working with ancient DNA. For more information and activities on this topic follow the links below. The scenario of the animation movie was partially inspired by the story of the “Birka lady”, a skeleton found at the Viking locality of Birka, on Björkö (close to Stockholm).Read more about it on Wikipedia (https://en.wikipedia.org/wiki/Birka_female_Viking_warrior) or have a look at the ancient DNA research article (https://onlinelibrary.wiley.com/doi/full/10.1002/ajpa.23308)