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The African Neolithic: A genetic perspective

Periodic Reporting for period 3 - AfricanNeo (The African Neolithic: A genetic perspective)

Reporting period: 2020-11-01 to 2022-04-30

The spread of farming practices in various parts of the world had a marked influence on how humans live today and how we are distributed around the globe. Around 10,000 years ago, warmer conditions lead to population increases, coinciding with the invention of farming in several places around the world. Archaeological evidence attest to the spread of these practices to neighbouring regions. In many cases this lead to whole continents being converted from hunter-gatherer to farming societies. It is however difficult to see from archaeological records if only the farming culture spread to other places or whether the farming people themselves migrated. Investigating patterns of genetic variation for farming populations and for remaining hunter-gatherer groups can help to resolve questions on population movements co-occurring with the spread of farming practices. It can further shed light on the routes of migration and dates when migrants arrived.

The spread of farming to Europe has been thoroughly investigated in the fields of archaeology, linguistics and genetics, while on other continents these events have been less investigated. In Africa, mainly linguistic and archaeological studies have attempted to elucidate the spread of farming and herding practices. The AfricanNeo ERC project will investigate the movement of farmer and pastoral groups in Africa, by typing densely spaced genome-wide variant positions in a large number of African populations. The data will be used to infer how farming and pastoralism was introduced to various regions, where the incoming people originated from and when these (potential) population movements occurred. Through this study, the Holocene history of Africa will be revealed and placed into a global context of migration, mobility and cultural transitions. Additionally the project will give due credence to one of the largest Neolithic expansion events, the Bantu-expansion, which caused a pronounced change in the demographic landscape of the African continent.
Overall the project has proceeded well. I assembled a team to work on the project in early 2018 by employing a PhD student, postdoc and a research engineer. An existing PhD student also joined the project. During 2018 and the start of 2019 we applied for permits, assembled the samples and prepared samples for genotyping. We also assembled a large electronic repository of comparative data that will be used in the study.

In 2018 and 2019, we analysed the datasets already available and three papers for these studies have been published (Vicente et al 2019a, Vicente et al 2019b, Semo et al 2020). These papers respectively discussed the genetic composition of the Fulani herding groups of the African Sahel, the genetic history of southern African Khoekhoe herders and San hunter-gatherers, and the population structure and diversity of Mozambican and Angolan Bantu-speakers. In addition I published a review in 2018 in Annual Review of Genomics and Human Genetics and a book chapter in an edited book. During 2019 and 2020 we successfully genotyped several sample batches for the project and are busy analyzing the results at the moment. Another PhD student joined the project and we started to assess a long range sequencing method to do the targeted genome sequencing. During 2020 we published another review on genetic inferences about African history, this time in Current Opinion in Genetics and Development.

The Schlebusch group hosted a large conference at Uppsala University during May 2019 - where several of the AfricanNeo collaborators participated as speakers. The time during the conference was also used to discuss ongoing projects. The international conference “Africa, the cradle of human diversity. Joining cultural and biological approaches to uncover African diversity” was held at the Evolutionary Biology Centre, Uppsala University (Sweden) from May 22nd to 25th 2019. The conference assembled leading researchers from different fields to present and discuss long-standing questions about past and present human diversity in Africa. Over 160 people attended the conference, including thirty-tree invited speakers, twenty poster presenters, and four speakers for short-talks. The scientific content of the conference included nine plenary sessions, two poster sessions, and four short-talks by young researchers. We published a News item about the conference in Evolutionary Anthropology. This News item has been recognized as one of the most read in the journal for the 2018/2019 period. We are also working on an edited book that will include papers from conference participants.

Additionally, the team attended various international conferences and workshops where ERC associated project work have been presented.

We are looking forward to the next stage of the project where the main body of data generated for the project will be analysed and shared with the research community.
This study will represent the first in-depth genetic study that use genome-wide data to specifically investigate the spread of farming populations in sub-Saharan Africa.It represents the first in-depth investigation of the Bantu-expansions, using high density genome-wide SNP data, the first study highlighting the genetic evidence underlying the southern African KhoeKhoe-herder culture, as well as the genetic structure of the farmers and herders from the African Sahel. Through this study the history of African farmers and herders will be elucidated and placed into a global context of population diffusion.

A thorough understanding of current genetic variation in Africa will not only help inferences about human history based on modern day genetic variation but is also crucial to inform ancient DNA (aDNA) studies. The rapid developments in the aDNA field, extended the power of genetics to make direct inferences about the genetics of ancient humans. Ancient DNA from humans have the potential to answer a number of important questions, including pinpointing the origin of modern humans and assessing genetic variability of humans in pre-historic times. For more recent remains, it has the ability of directly studying population movements; i.e. it can confirm/disprove population continuity, identify in-moving groups and quantify resulting fractions of admixture in descending groups. However, it is crucial that we extend our geographic coverage of modern day genetic data across the whole of sub-Saharan Africa. The genetic data generated from the farmers and herders included in this study will be added to the database of present day sub-Saharan African genetic variation to, in the end, map aDNA studies more effectively against present day genetic variation.

Although the current project does not have direct clinical significance, data generated by the project will be made available online for research use, through the European Genome-phenome Archive, under controlled access policies consistent with consent agreements. Research access to these datasets will facilitate and encourage the inclusion of African genetic variation in medical research and clinical studies.

Through the research done in my group, I aim to provide inferences from the field of genetics to test and contribute to existing theories that originated in the fields of archaeology, linguistics and ethnography and furthermore contribute to the development of novel hypotheses. The scope of expansion and original research in the field of African human genetics is large and the next few years will prove to be exciting times for genetic research in Africa.