Ancient genomics and early modern human population lineages in Africa

by Pontus Skoglund

Ancient DNA sequencing has yet to be comprehensively brought to benefit the study of Africa's past. I will discuss our current state of understanding of the genomic record of past African populations, and how this record can be interpreted together with the archaeological, fossil and climatic records. I will present inference of population genetic models of prehistoric African population history based on both ancient genome sequences and present-day genetic diversity. Analysis of ancient genomes from Africa now emphasize long-distance interconnectivity between early Holocene southern African and eastern African populations, and new evidence of deep human population structure in Africa around the time of emergence of anatomically modern humans. Specifically, new results provide evidence for deep structure in west Africa that may reflect some of the earliest diversifications of population lineages contributing to present-day populations. We also consider a new class of models for continuous genetic structure that may provide alternative explanations. These continuous models can be fitted as one-dimensional stepping stone “chains” of up multiple populations, and allow predictions of the model to be explicitly tested and deviations identified. Regardless of the promises and limitations of models of the deep human past, the ancient genomic record obtained so far reveals substantial impacts of expansions of food-production on early Holocene hunter-gatherer metapopulations in Africa. Together, the preliminary ancient genomic record of Africa cautions against extrapolating genetic models of the deep past from more recent data, and highlight the need for further ancient DNA studies in Africa.