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Origin: reconstructing African prehistory using ancient DNA

Periodic Reporting for period 1 - ORIGIN (Origin: reconstructing African prehistory using ancient DNA)

Reporting period: 2019-11-01 to 2021-10-31

Human history in Africa over the last tens of thousands of years is an integral part of understanding the origins of our species. For example, African populations harbour more genetic diversity than what is found in populations of all the other continents combined. However, the history shaping this diversity remains largely unknown, providing a barrier to populations with African ancestry benefiting from future advances in medical genetics and precision medicine. The vast majority of the current population structure in Africa was shaped by the expansions of food producers, mainly agriculturalists and pastoralists, over just the last few thousand years. Still, relative contributions of diverse populations that formed past genetic landscapes are to a large extent still unknown, as these expansions across the African continent erased the genetic footprint of previous populations and obscured signatures of older demographic processes.

The genomes of present-day humans are directly shaped by the changes in human populations in the past and thus hold considerable information about past processes. Nevertheless, making inferences about human evolutionary history from present-day genomes alone is extremely challenging. Ancient DNA (aDNA), or DNA extracted from long dead organisms, has filled some of this gap and provided invaluable insights into prehistoric events and population history that would otherwise not be accessible. Even though aDNA transformed our understanding of the past demography of different human groups reaching as far back as ~430,000 years ago (ka) in Europe, Africa remained largely underrepresented in aDNA studies. The project “Origin: Reconstructing African prehistory using ancient DNA” aimed to reconstruct the genetic diversity of ancient African populations from across the continent by applying cutting-edge methods developed for the retrieval of aDNA from very poorly preserved human specimens stemming from difficult environments. These genome-wide data allow us to directly investigate past populations and hold the potential of addressing many of the most urgent questions in human origins.
ORIGIN was carried out in the Ancient Genomics group led by Dr. Pontus Skoglund at the Francis Crick Institute in London, United Kingdom. With an international network of researchers from Africa and Europe, including archaeologists, palaeoanthropologists, curators and aDNA geneticists, we studied human skeletal remains from in total 23 archaeological sites from ten African countries. After the death of an individual, the amount of their DNA, or endogenous DNA, decreases over time, accumulating damage such as nucleotide modifications, and these processes are largely accelerated in warm and humid environments such as Africa. Thus, in the first stage of this project, we assessed the levels of endogenous DNA preservation in the selected specimens of human bones, bone fragments, hair and teeth. To increase the amounts of genetic data that can be recovered from these ancient specimens and to minimize the impacts of present-day human DNA contamination, which, if introduced, can be detrimental for downstream analyses, all of the work was conducted in the clean-room facility at the Francis Crick Institute. To further maximise our chances of the recovery of genomic material for downstream computational and population genetic analyses, we used most up-to-date extraction and library preparation methods for the recovery of ultra-short and degraded DNA molecules.

In total, more than 62% of the screened specimens had evidence of endogenous DNA preservation with high enough overall DNA content and low enough levels of present-day human DNA contamination for genome-wide data production at three levels of completion. For the specimens with lowest amounts of detectable DNA, we used highly efficient hybridization-based method that allows for the enrichment of specific genomic regions of interest even in the cases where 99.9% of the total DNA stems from microorganisms that colonise the remains after the death of an individual. For this purpose we designed a new capture array spanning thousands of sites across the genome which are highly informative for reconstructing population history of individuals with African ancestry in an unbiased way. For the specimens with intermediate amounts of endogenous DNA, we are able to obtain between 1- and 3-fold coverage genomes, i.e. low-coverage genomes where each position in the genome is covered with on average one to three unique DNA fragments. In addition, we were able to recover a high quality (>20-fold coverage) genome of an ancient individual from South Africa which pre-dates the arrival of food producers ~2ka.

These genome-wide data allow us to reconstruct the genetic ancestry of ancient African individuals prior to the spread of the food producers which transformed the genetic ancestry across the continent, test for the hypotheses of gene-flow between west Eurasia and Africa starting as early as ~20ka, and reconstruct the ancestry of the African source populations for the out-of-Africa expansion which gave rise to all present-day non-Africans. Moreover, during the course of this fellowship, I obtained and analysed genome-wide data from currently the oldest securely dated modern humans in Eurasia, results of which were published in Nature. Even though not directly from Africa, these individuals are currently closest in time to the major out-of-Africa migration of modern humans and are thus crucial for addressing one of the main objectives of this fellowship, directly related to reconstructing the ancestry of the African source population which ~60-50ka gave rise to all present-day non-Africans.

Throughout the course of this fellowship I worked closely with curators, archaeologists and paleoanthropologists to bridge over increasing tensions between these disciplines and aDNA genetics research, as well as ethical issues over doing aDNA research on human remains in diverse environments. The latter resulted in a set of globally applicable guidelines published in Nature. Moreover, I took an active role in forming a Discussion Series of “Current Issues in Ancient DNA Research” which brings together ECRs, young and senior PIs from across the world working with aDNA from human remains, and in order to discuss main issues our research faces and come with direct outputs to address those problems, provide training for young researchers, build networks and open up conversations within a highly competitive field.
This fellowship specifically aimed to investigate migrations, interactions, admixture and population structure of different human groups within Africa prior to the major genetic transformation of the African continent, as well as between Africa and other parts of the world. The power of aDNA is that it can provide insights not only on population history, but also on how human biology has changed over time and how certain mutations that proved to be beneficial for population survival arose either through different evolutionary processes such as adaptation or admixture between different groups. Reconstructing the origins of present-day African diversity is therefore important beyond aDNA field, and can prove vital for future medical genetics and precision medicine of people with African ancestry, as well as understanding the emergence of and susceptibility to diseases that originated in these populations.
Evaluation of ancient DNA preservation in MSCA Origin specimens