The deep population history in Africa

Abstract

Africa is the continent with the greatest genetic diversity among humans and the level of diversity is further enhanced by incorporating non-majority groups, which are often understudied. Many of today’s minority populations historically practiced foraging lifestyles, which were the only subsistence strategies prior to the rise of agriculture and pastoralism, but only a few groups practicing these strategies remain today. Genomic investigations of Holocene human remains excavated across the African continent show that the genetic landscape was vastly different compared to today’s genetic landscape and that many groups that today are population isolate inhabited larger regions in the past. It is becoming clear that there are periods of isolation among groups and geographic areas, but also genetic contact over large distances throughout human history in Africa. Genomic information from minority populations and from prehistoric remains provide an invaluable source of information on the human past, in particular deep human population history, as Holocene large-scale population movements obscure past patterns of population structure. Here we revisit questions on the nature and time of the radiation of early humans in Africa, the extent of gene-flow among human populations as well as introgression from archaic and extinct lineages on the continent.

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

“…One explanation is that people began living in larger and/or more connected groups, with variations in population size and connectivity driving differences in material culture across space and time. Given the morphological variation among Late Pleistocene skeletons, interactions may have involved deeply structured populations 2,10 , consistent with some population history models based on genetics 3 .…”

“…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 Africa [1][2][3][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 populations 3,5 .…”

“…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 Africa [1][2][3][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 populations 3,5 . 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.…”

Ostrich eggshell beads reveal 50,000-year-old social network in Africa

“…4 ), requiring humans to adjust mobility and foraging strategies 36 – 38 . This in turn could have reorganized the distribution of people on the landscape, depopulating areas, and rendering some previous social networks unsustainable 1 , 39 , 40 . The breakdown between phase I and phase II also coincides with the lowest effective population size in Africa predicted by ref.…”

Following the evolution of Homo sapiens across Africa using a uniparental genetic guide

“…Furthermore, it was observed that differences between Khoisan genomes were greater than those between geographically very distant Eurasian genomes [67]. However, there is genomic evidence of secondary contacts among extant populations of Khoisan, rainforest pygmies, and click speakers Hadza and Sandawe from Tanzania which diverged by 100 – 120 kya [58,68]. In a similar vein, an ancient genomic divergence between the ancestors of the rainforest pygmies and West African Yoruba farmers was estimated to 90 – 150 Kya [69].…”