Ancient DNA and deep population structure in sub-Saharan African foragers

Mark Lipson,Nick Patterson,John W Arthur,David K Wright,Potiphar Kaliba,Alan Morris,George Mudenda,Jason Lewis,Jessica I Cerezo-Román,Jacob Davis,Maggie Katongo,Raphael Mwafulirwa,Kathryn Weedman Arthur ,Ïñigo Olalde ,Audax Mabulla ,George Ayodo,Christian A Tryon,Agness Gidna ,Ron Pinhasi,Stanley H Ambrose,Fredrick Mapemba,Daudi Mwangomba,David Reich,Flora Schilt,Kendra Sirak ,Christine Ogola,Pamela R Willoughby,Douglas J Kennett,Myra F Laird,Brendan J Culleton,De Luna ,Alex Bertacchi,Emmanuel Ndiema,Jonas Oppenheimer,Annalys Hanson,Amandus Kwekason,Jessica C Thompson,Fredrick K Manthi ,Elizabeth A Sawchuk,Nadin Rohland,Andrew M Zipkin ,Kathryn L Ranhorn,Matthew C Curtis,Mary E Prendergast

doi:10.1038/s41586-022-04430-9

Abstract

Multiple lines of genetic and archaeological evidence suggest that there were major demographic changes in the terminal Late Pleistocene epoch and early Holocene epoch of sub-Saharan Africa1–4. Inferences about this period are challenging to make because demographic shifts in the past 5,000 years have obscured the structures of more ancient populations3,5. Here we present genome-wide ancient DNA data for six individuals from eastern and south-central Africa spanning the past approximately 18,000 years (doubling the time depth of sub-Saharan African ancient DNA), increase the data quality for 15 previously published ancient individuals and analyse these alongside data from 13 other published ancient individuals. The ancestry of the individuals in our study area can be modelled as a geographically structured mixture of three highly divergent source populations, probably reflecting Pleistocene interactions around 80–20 thousand years ago, including deeply diverged eastern and southern African lineages, plus a previously unappreciated ubiquitous distribution of ancestry that occurs in highest proportion today in central African rainforest hunter-gatherers. Once established, this structure remained highly stable, with limited long-range gene flow. These results provide a new line of genetic evidence in support of hypotheses that have emerged from archaeological analyses but remain contested, suggesting increasing regionalization at the end of the Pleistocene epoch.

Highlights

The advent of genome-wide ancient DNA technology holds promise for better understanding major changes in material culture and hypothesized demographic shifts among ancient African foragers (Supplementary Notes 1, 2)
Individuals from Mlambalasi (I13976; about 20–17 ka) and Hora 1 (I19528, I19529; 17–14 ka) are well constrained to the Late Pleistocene based on multiple indirect dates (Supplementary Table 4 and Supplementary Note 3)
The authenticity of the new ancient DNA (aDNA) data was assessed through a combination of several criteria; detectable contamination was observed for only two samples (Methods, Extended Data Fig. 1a, Supplementary Table 2 and Supplementary Note 5)

Summary

Introduction

The advent of genome-wide ancient DNA (aDNA) technology holds promise for better understanding major changes in material culture and hypothesized demographic shifts among ancient African foragers (Supplementary Notes 1, 2). Direct and indirect dates range from around 18 ka to 5 ka, doubling the time depth of aDNA reported from sub-Saharan Africa We analyse these data together with the published sequences of 28 other ancient African individuals recovered from contexts spanning the past 8,000 years and largely associated with foraging at 17 sites in eastern, central and southern Africa. Analysis of the ancient data together with sequences from present-day groups, aided by new statistical methods, enables a reconstruction of changes in regional- and continental-scale population structures among people who lived before the sweeping demographic changes of the past approximately 5,000 years It enables comparisons of Pleistocene forager population dynamics between the tropics and more temperate regions.

Methods

Findings

Discussion

Conclusion