Reconstructing Prehistoric African Population Structure

Abstract

Summary We assembled genome-wide data from 16 prehistoric Africans. We show that the anciently divergent lineage that comprises the primary ancestry of the southern African San had a wider distribution in the past, contributing ~2/3 of the ancestry of Malawi hunter-gatherers ~8100–2500 years ago, and ~1/3 of Tanzanian hunter-gatherers ~1400 years ago. We document how the spread of farmers from western Africa involved complete replacement of local hunter-gatherers in some regions, and we track the spread of herders by showing that the population of a ~3100 year-old pastoralist from Tanzania contributed ancestry to people from northeast to southern Africa, including a ~1200-year-old southern African pastoralist. The deepest diversifications of African lineages were complex, involving long-distance gene flow, or a lineage more deeply diverging than that of the San contributing more to some western Africans than others. We finally leverage ancient genomes to document episodes of natural selection in southern African populations.

Models of archaic admixture and recent history from two-locus statistics

“…Modeling archaic admixture worldwide resolved this discrepancy. We recovered the signal of Neanderthal admixture in Eurasian populations, and found evidence for substantial and long-lasting admixture from a deeply diverged lineage in two African populations that is consistent with evidence from previous studies (Plagnol and Wall, 2006;Skoglund et al, 2017;Hey et al, 2018;Durvasula and Sankararaman, 2018).…”

“…could also contribute to Eurasians through admixture prior to the OOA event (Figure 4(A)). Many human lineages coexisted on the African continent, possibly until quite recently (Rightmire, 2009;Harvati et al, 2011;Berger et al, 2017), and genetic evidence points to a history of archaic admixture or deep structure across many modern African populations (Hammer et al, 2011;Lachance et al, 2012;Hsieh et al, 2016;Skoglund et al, 2017;Durvasula and Sankararaman, 2018;Hey et al, 2018). It is likely that modern humans have met and mixed with diverged lineages many times through history, rather than receiving just a single pulse of migrants (Browning et al, 2018;Villanea and Schraiber, 2019).…”

Unraveling African diversity from a cross‐disciplinary perspective

“…In eastern Africa, novel research of archeological, biomolecular, and ancient genomic data sets have begun to shed more light on the arrival of food producing populations and their integration with autochthonous foragers during the Bantu expansion . Other research projects are studying environmental and social consequences of intensive agriculture over the last 500 years to investigate the extent of human‐induced environmental changes in eastern African landscapes…”

Ancient human DNA: How sequencing the genome of a boy from Ballito Bay changed human history

“…In contrast to approaches targeting a limited number of markers found polymorphic in some modern populations, 2,3 whole genomesequence data from ancient remains include the complete and unbiased genetic information carried by an individual. The data potentially also incorporate genetic variants unique to the individual or population.…”