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Ancient West African foragers in the context of African population history.

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 group^1-11. One individual carried the deeply divergent Y chromosome haplogroup A00, which today is found almost exclusively in the same region^12,13. 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.

SUBMITTER: Lipson M

PROVIDER: S-EPMC8386425 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

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Ancient West African foragers in the context of African population history.

Lipson Mark M Ribot Isabelle I Mallick Swapan S Rohland Nadin N Olalde Iñigo I Adamski Nicole N Broomandkhoshbacht Nasreen N Lawson Ann Marie AM López Saioa S Oppenheimer Jonas J Stewardson Kristin K Asombang Raymond Neba'ane RN Bocherens Hervé H Bradman Neil N Culleton Brendan J BJ Cornelissen Els E Crevecoeur Isabelle I de Maret Pierre P Fomine Forka Leypey Mathew FLM Lavachery Philippe P Mindzie Christophe Mbida CM Orban Rosine R Sawchuk Elizabeth E Semal Patrick P Thomas Mark G MG Van Neer Wim W Veeramah Krishna R KR Kennett Douglas J DJ Patterson Nick N Hellenthal Garrett G Lalueza-Fox Carles C MacEachern Scott S Prendergast Mary E ME Reich David D

Nature 20200122 7792

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 group<sup>1-11</sup>. One individual carried the deeply divergent Y chromosome haplogroup A00, wh ...[more]

PMID: 31969706

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Project description:BackgroundAfrica contains the most genetically divergent group of continental populations and several studies have reported that African populations show a high degree of population stratification. In this regard, it is important to investigate the potential for population genetic structure or stratification in genetic epidemiology studies involving multiple African populations. The presences of genetic sub-structure, if not properly accounted for, have been reported to lead to spurious association between a putative risk allele and a disease. Within the context of the Africa America Diabetes Mellitus (AADM) Study (a genetic epidemiologic study of type 2 diabetes mellitus in West Africa), we have investigated population structure or stratification in four ethnic groups in two countries (Akan and Gaa-Adangbe from Ghana, Yoruba and Igbo from Nigeria) using data from 372 autosomal microsatellite loci typed in 493 unrelated persons (986 chromosomes).ResultsThere was no significant population genetic structure in the overall sample. The smallest probability is associated with an inferred cluster of 1 and little of the posterior probability is associated with a higher number of inferred clusters. The distribution of members of the sample to inferred clusters is consistent with this finding; roughly the same proportion of individuals from each group is assigned to each cluster with little variation between the ethnic groups. Analysis of molecular variance (AMOVA) showed that the between-population component of genetic variance is less than 0.1% in contrast to 99.91% for the within population component. Pair-wise genetic distances between the four ethnic groups were also very similar. Nonetheless, the small between-population genetic variance was sufficient to distinguish the two Ghanaian groups from the two Nigerian groups.ConclusionThere was little evidence for significant population substructure in the four major West African ethnic groups represented in the AADM study sample. Ethnicity apparently did not introduce differential allele frequencies that may affect analysis and interpretation of linkage and association studies. These findings, although not entirely surprising given the geographical proximity of these groups, provide important insights into the genetic relationships between the ethnic groups studied and confirm previous results that showed close genetic relationship between most studied West African groups.

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Ancient West African foragers in the context of African population history.

Publications

Ancient West African foragers in the context of African population history.

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