Ancient DNA and deep population structure in sub-Saharan African foragers
Author:
Lipson Mark, Sawchuk Elizabeth A.ORCID, Thompson Jessica C.ORCID, Oppenheimer Jonas, Tryon Christian A.ORCID, Ranhorn Kathryn L.ORCID, de Luna Kathryn M.ORCID, Sirak Kendra A.ORCID, Olalde IñigoORCID, Ambrose Stanley H.ORCID, Arthur John W.ORCID, Arthur Kathryn J. W., Ayodo George, Bertacchi AlexORCID, Cerezo-Román Jessica I.ORCID, Culleton Brendan J., Curtis Matthew C.ORCID, Davis Jacob, Gidna Agness O., Hanson Annalys, Kaliba Potiphar, Katongo MaggieORCID, Kwekason Amandus, Laird Myra F.ORCID, Lewis JasonORCID, Mabulla Audax Z. P., Mapemba Fredrick, Morris Alan, Mudenda George, Mwafulirwa Raphael, Mwangomba Daudi, Ndiema Emmanuel, Ogola Christine, Schilt FloraORCID, Willoughby Pamela R., Wright David K.ORCID, Zipkin AndrewORCID, Pinhasi RonORCID, Kennett Douglas J.ORCID, Manthi Fredrick Kyalo, Rohland Nadin, Patterson Nick, Reich DavidORCID, Prendergast Mary E.ORCID
Abstract
AbstractMultiple 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.
Publisher
Springer Science and Business Media LLC
Subject
Multidisciplinary
Reference76 articles.
1. Tryon, C. A. The Middle/Later Stone Age transition and cultural dynamics of late Pleistocene East Africa. Evol. Anthropol. Issues News Rev. 28, 267–282 (2019). 2. Mirazón Lahr, M. The shaping of human diversity: filters, boundaries and transitions. Philos. Trans. R. Soc. B 371, 20150241 (2016). 3. Hollfelder, N., Breton, G., Sjödin, P. & Jakobsson, M. The deep population history in Africa. Hum. Mol. Genet. 30, R2–R10 (2021). 4. Miller, J. M. & Wang, Y. V. Ostrich eggshell beads reveal 50,000-year-old social network in Africa. Nature 601, 234–239 (2021). 5. Vicente, M. & Schlebusch, C. M. African population history: an ancient DNA perspective. Curr. Opin. Genet. Dev. 62, 8–15 (2020).
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