Ancient West African foragers in the context of African population history

[Angoliga]

(Lipson et al., 2020)

Mark Lipson, Isabelle Ribot, Swapan Mallick, Nadin Rohland, Iñigo Olalde, Nicole Adamski, Nasreen Broomandkhoshbacht, Ann Marie Lawson, Saioa López, Jonas Oppenheimer, Kristin Stewardson, Raymond Neba’ane Asombang, Hervé Bocherens, Neil Bradman, Brendan J. Culleton, Els Cornelissen, Isabelle Crevecoeur, Pierre de Maret, Forka Leypey Mathew Fomine, Philippe Lavachery, Christophe Mbida Mindzie, Rosine Orban, Elizabeth Sawchuk, Patrick Semal, Mark G. Thomas, Wim Van Neer, Krishna R. Veeramah, Douglas J. Kennett, Nick Patterson, Garrett Hellenthal, Carles Lalueza-Fox, Scott MacEachern, Mary E. Prendergast & David Reich et. al (paper link)


Abstract

Our knowledge of ancient human population structure in sub-Saharan Africa, particularly prior to the advent of food production, remains limited. Here we report genome-wide DNA data from four children—two of whom were buried approximately 8,000 years ago and two 3,000 years ago—from Shum Laka (Cameroon), one of the earliest known archaeological sites within the probable homeland of the Bantu language group1,2,3,4,5,6,7,8,9,10,11. One individual carried the deeply divergent Y chromosome haplogroup A00, which today is found almost exclusively in the same region12,13. However, the genome-wide ancestry profiles of all four individuals are most similar to those of present-day hunter-gatherers from western Central Africa, which implies that populations in western Cameroon today—as well as speakers of Bantu languages from across the continent—are not descended substantially from the population represented by these four people. We infer an Africa-wide phylogeny that features widespread admixture and three prominent radiations, including one that gave rise to at least four major lineages deep in the history of modern humans.

Fig. 1-4

 

Fig.1 Y chromosome phylogeny

 

Fig.2 PCA Results

 

Fig.3 Allele-sharing statistics

 

Fig.4 Admixture graph results

 

Extended Data Fig. 1-5

 

Extended Data Fig. 1 | Overview of the site of Shum Laka

 

Extended Data Fig. 2 | Kinship analysis

 

Extended Data Fig. 3 | Alternative PCA and allele-sharing analyses

 

Extended Data Fig. 4 | Primary inferred admixture graph with full parameters

 

Extended Data Fig. 5 | Schematic of first alternative admixture graph

 

Extended Data Table 1-3

 

Extended Data Table 1 | Populations in the study

 

Extended Data Table 2 | Allele-sharing statistics for deep ancestry

 

Extended Data Table 3 | Admixture graph parameter estimates

 

[Michalis Moriopoulos]

The Tropical African ancestry in the pygmy samples is interesting. Each population has it but different types and in different amounts. The Shum Laka samples are modelled as 64% Basal West African, but the Biaka are 59% Bantu West African. The Mbuti are 26% Bantu and 17% Ancestral East African (Nilote-like). If these models are somewhat accurate, then it's possible there were still "pure" Central African hunter-gatherers living in the Congo before the Bantu expansion. Shum Laka's admixture is probably of older vintage (maybe even Pleistocene) given that it's not Bantu-related. Central African HG ancestry is probably as old as the South African HG split, but all the Tropical African ancestry modern pygmies have has given us the impression that it's a younger ancestry type. In truth, pygmies are just very mixed.