The genetic history of Africa summarizes the genetic makeup and population history of Africans in living on the African continent, including the recent origin of modern humans in Africa, as well as the regional genetic histories of Africa's generally recognized subdivisions: North Africa, West Africa, East Africa, Central Africa, and Southern Africa.
The genetic history of Africa has been influenced by the various migrations, modes of economy, and social practices of its peoples; as well as by major historical events. In addition, various major geographical features of the continent have influenced Africans' genetic history, with the Sahara famously serving as both a trans-regional passageway and place of dwelling for people in Africa during various humid phases and periods throughout the history of Africa; as well as a physical barrier restricting (but not preventing) geneflow between the northernmost and Sub-Saharan parts of the continent.
Overview
The peoples of Africa are characterized by regional genetic substructure and heterogeneity, reflecting to some degree respective ethno-linguistic identity, and, in part, explainable by the "multiregional evolution" of modern human lineages in various multiple regions of the African continent, as well as later admixture events, including back-migrations from Eurasia, of both highly differentiated West and East Eurasian components.
Africans' genetic ancestry is largely partitioned by geography and language family, with populations belonging to the same ethno-linguistic groupings showing high genetic homogeneity and coherence. Gene flow, consistent with both short- and long-range migration events followed by extensive admixture and bottleneck events, have influenced the regional genetic makeup and demographic structure of Africans. The historical Bantu expansion had lasting impacts on the modern demographic make up of Africa, resulting in a greater genetic and linguistic homogenization.
Overall, different African populations display genetic diversity and substructure, but can be clustered in distinct but partially overlapping groupings:
Khoisan or 'South African hunter-gatherers' from Southern Africa represented by the Khoisan peoples; they are associated with the deepest divergence (c. 270,000 years ago) of human genetic diversity, forming a distinct cluster of their own. They subsequently diverged into a Northern and Southern subgroup, c. 30,000 years ago. 'Central African hunter-gatherers' or 'Rain forest hunter-gatherers' (Pygmies) of Central Africa, represented by the Biaka and Mbuti; associated with another deep divergence (c. 220,000 years ago). They subsequently diverged into an Eastern and Western subgroup, c. 20,000 years ago. "Ancestral Eurasians" represent the ancestral population of modern Eurasians shortly before the Out-of-Africa expansion; they are inferred to have diverged from other African populations, most likely somewhere in Northeast Africa, c. 70,000 years ago. The various Afroasiatic-speakers from Northern Africa and the Horn of Africa, are suggested to have diverged from other African groups c. 50,000 years ago, but currently insufficient data and geneflow from other groups complicate an accurate estimation of the divergence date. Afroasiatic-speaking populations also display variable amounts of West Asian (primarily Natufian-like, but also Neolithic Anatolian and Iranian) admixtures from Eurasian backflow movements, with the remainder being primarily from autochthonous African genetic clusters, associated with Nilotic-like ancestry. They also display affinity for the Paleolithic North African Taforalt specimens of the Iberomaurusian culture. 'Eastern African hunter-gatherers', represented by Hadza, Sandawe, Omotic-speakers, and the ancient Mota specimen; their phylogenetic relationship to other populations is not clear, but they display affinity to modern East and West African populations, and harbor Khoesan-like geneflow along a Northeast to Southwest cline, as well as later (West) Eurasian admixtures, but at lower amounts than among Afroasiatic-speakers. "Ancient East Africans" or "Ancestral West/East Africans" associated with the common ancestor of modern Niger-Congo and Nilo-Saharan-speakers originated around 28,000 years ago, likely in the Nile Valley region. They subsequently diverged at c. 18,000 years ago into the ancestors of West and West-Central African Niger-Congo and Bantu-speakers, and into the East African Nilo-Saharan/Nilotic-speakers. They represent the dominant and most widespreaded ancestry component of modern Africa, and are associated with relative recent population expansions linked to agriculture and pastoralist lifestyles. Genetic data indicates affinity for older hunter-gatherer groups in East Africa, but their exact relationship remains unclear. There is evidence for limited geneflow (9–13%) from a human ghost lineage, referred to as 'West African foragers' with a deeper or equally deep divergence time than 'Khoisan hunter-gatherers', into modern West Africans. Austronesian-speaking Malagasy people in Madagascar have received significant East/Southeast Asian admixture associated with the Austronesian expansion, with the remainder ancestry being primarily associated with West-Central and East African components. The estimated date of geneflow between these sources is c. 2,200 years ago.
Out-of-Africa event
The "recent African origin" model proposes that all modern non-African populations descend from one or several waves of H. sapiens that left Africa 70,000–60,000 years ago. Notably, recent genetic and archeologic data suggests that H. sapiens originated from interactions in multiple regions of Africa, instead of emerging from a singular sub-region, as descendants of the last common ancestor of all modern humans expanded into, absorbed, and/or replaced various other deep lineages (described as "archaic"). The H. sapiens ancestral to non-Africans would have most likely left Northeastern Africa.
Admixture events with archaic hominins
According to Durvasula et al. (2020), there are indications that 2% to 19% (≃6.6 to 7.0%) of the DNA of West African populations may have come from an unknown archaic hominin which split from the ancestor of humans and Neanderthals between 360 kya to 1.02 mya. However, Durvasula et al. (2020) also suggests that at least part of this archaic admixture is also present in Eurasians/non-Africans, and that the admixture event or events range from 0 to 124 ka B.P, which includes the period before the Out-of-Africa migration and prior to the African/Eurasian split (thus affecting in part the common ancestors of both Africans and Eurasians/non-Africans). "Non-African populations (Han Chinese in Beijing and Utah residents with northern and western European ancestry) also show analogous patterns in the CSFS, suggesting that a component of archaic ancestry was shared before the split of African and non-African populations...One interpretation of the recent time of introgression that we document is that archaic forms persisted in Africa until fairly recently. Alternately, the archaic population could have introgressed earlier into a modern human population, which then subsequently interbred with the ancestors of the populations that we have analyzed here. The models that we have explored here are not mutually exclusive, and it is plausible that the history of African populations includes genetic contributions from multiple divergent populations, as evidenced by the large effective population size associated with the introgressing archaic population...Given the uncertainty in our estimates of the time of introgression, we wondered whether jointly analyzing the CSFS from both the CEU (Utah residents with Northern and Western European ancestry) and YRI genomes could provide additional resolution. Under model C, we simulated introgression before and after the split between African and non-African populations and observed qualitative differences between the two models in the high-frequency–derived allele bins of the CSFS in African and non-African populations (fig. S40). Using ABC to jointly fit the high-frequency–derived allele bins of the CSFS in CEU and YRI (defined as greater than 50% frequency), we find that the lower limit on the 95% credible interval of the introgression time is older than the simulated split between CEU and YRI (2800 versus 2155 generations B.P.), indicating that at least part of the archaic lineages seen in the YRI are also shared with the CEU..." Supplementary Materials for Recovering signals of ghost archaic introgression in African populations", section "S8.2" "We simulated data using the same priors in Section S5.2, but computed the spectrum for both YRI [West African Yoruba] and CEU [a population of European origin] . We found that the best fitting parameters were an archaic split time of 27,000 generations ago (95% HPD: 26,000–28,000), admixture fraction of 0.09 (95% HPD: 0.04–0.17), admixture time of 3,000 generations ago (95% HPD: 2,800–3,400), and an effective population size of 19,700 individuals (95% HPD: 19,300–20,200). We find that the lower bound of the admixture time is further back than the simulated split between CEU and YRI (2155 generations ago), providing some evidence in favor of a pre-Out-of-Africa event. This model suggests that many populations outside of Africa should also contain haplotypes from this introgression event, though detection is difficult because many methods use unadmixed outgroups to detect introgressed haplotypes [Browning et al., 2018, Skov et al., 2018, Durvasula and Sankararaman, 2019] (5, 53, 22). It is also possible that some of these haplotypes were lost during the Out-of-Africa bottleneck." Chen et al. (2020) found that Africans have higher Neanderthal ancestry than previously thought. 2,504 African samples from all over Africa were analyzed and tested on Neanderthal ancestry. All African samples showed evidence for minor Neanderthal ancestry, but always at lower levels than observed in Eurasians.
Geneflow between Eurasian and African populations
Significant Eurasian admixture is found in Northern Africa, and among specific ethnic groups of the Horn of Africa, Northern Sudan, the Sahel region, as well as among the Malagasy people of Madagascar. Various genome studies found evidence for multiple prehistoric back-migrations from various Eurasian populations and subsequent admixture with native groups. West Eurasian-associated geneflow arrived to Northern Africa during the Paleolithic (30,000 to 15,000 years ago), followed by other pre-Neolithic and Neolithic migration events. Genetic data on the Taforalt samples "demonstrated that Northern Africa received significant amounts of gene-flow from Eurasia predating the Holocene and development of farming practices". Medieval geneflow events, such as the Arab expansion also left traces in various African populations. Pickrell et al. (2014) indicated that Western Eurasian ancestry eventually arrived through Northeast Africa (particularly the Horn of Africa) to Southeast Africa and Southern Africa.
Ramsay et al. (2018) also found evidence for significant Western Eurasian admixture in various parts of Africa, from both ancient and more recent migrations, being highest among populations from Northern Africa, and some groups of the Horn of Africa:
In addition to the intrinsic diversity within the continent due to population structure and isolation, migration of Eurasian populations into Africa has emerged as a critical contributor to the genetic diversity. These migrations involved the influx of different Eurasian populations at different times and to different parts of Africa. Comprehensive characterization of the details of these migrations through genetic studies on existing populations could help to explain the strong genetic differences between some geographically neighbouring populations.