Genetic history of Africa

The genetic history of Africa tells us about the ancestors and families of people who have lived on the continent for thousands of years. It helps us understand how groups of people in Africa are related to each other and where they came from.

Africa is a huge place with many different areas, like North Africa, West Africa, East Africa, Central Africa, and Southern Africa. Each of these places has its own special history and ways of life. Scientists study the DNA of people living there today to learn about their past.

One important fact is that modern humans — people like us — first appeared in Africa. This means that all people in the world today can trace their ancestors back to Africa. The Sahara desert has changed over time, sometimes being wet and green and other times being dry and sandy. When it was wetter, people could travel across it more easily. But when it became a desert, it acted like a wall, making it harder for groups of people to mix between the north and the central parts of Africa. Even so, people still found ways to stay connected during certain times in history.

Overview

Africans have different genetic backgrounds based on where they live and their language families. Populations that share the same language and ethnic background often have similar genetic makeup. Events like migration, mixing between groups, and changes in population sizes have shaped the genetic diversity in Africa. The spread of Bantu-speaking people had a big impact, leading to more genetic and linguistic similarity across the continent.

Different African groups show unique genetic patterns, but they can often be grouped together in certain ways:

• Khoisan or South African hunter-gatherers from Southern Africa are known for having one of the oldest genetic lines, diverging around 270,000 years ago.
• Central African hunter-gatherers or Rain forest hunter-gatherers are linked to deep genetic roots around 220,000 years ago.
• Ancestral Eurasians represent the group from which modern Eurasians originated, splitting off from other African groups about 70,000 years ago.
• Afroasiatic-speakers from Northern Africa and the Horn of Africa diverged from other African groups around 50,000 years ago and have mixed with West Asian groups.
• Eastern African hunter-gatherers show connections to both East and West African groups and have some mixing with Eurasian groups.
• Ancient East Africans are linked to the ancestors of modern Niger-Congo and Nilo-Saharan speakers, originating around 28,000 years ago in the Nile Valley region.
• Malagasy people in Madagascar have ancestry from both East/Southeast Asia and Africa, with mixing happening about 2,200 years ago.

Indigenous Africans

The term indigenous Africans refers to groups with mainly African ancestry, including Niger-Congo speakers, Nilo-Saharan speakers, and the Khoisan grouping, among others. The origins of Afroasiatic languages are still debated, with some thinking they started in the Middle East and others in Africa. The Austronesian languages began in southern East Asia and later spread from the Philippines.

The Niger-Congo languages likely started in West Africa or Central Africa before the Bantu expansion. Their spread may have been linked to the beginning of farming during the African Neolithic period, after the Sahara dried up around 3500 BCE. The Nilo-Saharan language family’s origin is uncertain, but it is thought to have started between Chad, Sudan, and the Central African Republic around 10,000–8,000 BCE. The Southern African hunter-gatherers (Khoisan) are believed to be the original hunter-gatherer group in southern Africa before Bantu-speakers and East African pastoralists arrived.

Out-of-Africa event

Main article: Recent African origin of modern humans

The recent African origin of modern humans suggests that all modern humans started in Africa. Recent studies show that Homo sapiens-subgroups originated in many parts of Africa, not just one area. The ancestors of all modern humans likely left Northeastern Africa between 50,000 and 100,000 years ago. All non-African populations come from one or more groups of Homo sapiens that left Africa between 70,000 and 60,000 years ago.

Studies show that West African populations have a small amount of DNA from ancient human types that lived before modern humans and Neanderthals, dating back between 360,000 and 1,020,000 years ago. All African groups also have some Neanderthal ancestry, though at lower levels than Eurasian groups.

Geneflow between Eurasian and African populations

See also: Eurasian backflow

Significant mixing with Eurasian groups is found in Northern Africa, the Horn of Africa, Northern Sudan, the Sahel region, and among the Malagasy people of Madagascar. Studies show multiple ancient movements of people from Eurasia into Africa and mixing with local groups. West Eurasian mixing reached Northern Africa during the Paleolithic period (30,000 to 15,000 years ago), followed by other migrations before and during the Neolithic period. Medieval events, like the Arab expansion, also left genetic traces in African populations. Research shows that Western Eurasian ancestry reached Southeast Africa and Southern Africa through Northeast Africa.

Ramsay et al. (2018) found evidence of significant Western Eurasian mixing in many parts of Africa, from both ancient and recent migrations. This mixing was highest among groups from Northern Africa and some in 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.

This distinctive Eurasian admixture appears to have occurred over at least three time periods with ancient admixture in central west Africa (e.g., Yoruba from Nigeria) occurring between ~7.5 and 10.5 kya, older admixture in east Africa (e.g., Ethiopia) occurring between ~2.4 and 3.2 kya and more recent admixture between ~0.15 and 1.5 kya in some east African (e.g., Kenyan) populations.

Subsequent studies based on LD decay and haplotype sharing in an extensive set of African and Eurasian populations confirmed the presence of Eurasian signatures in west, east and southern Africans. In the west, in addition to Niger-Congo speakers from The Gambia and Mali, the Mossi from Burkina Faso showed the oldest Eurasian admixture event ~7 kya. In the east, these analyses inferred Eurasian admixture within the last 4000 years in Kenya.

There is no clear agreement on when or where the original home of the Afroasiatic language family was. Some think it spread by people with West-Eurasian ancestry during the Neolithic Revolution from the Middle East, specifically the Levant. Others argue that the first speakers were in Northeast Africa because that area has the most diversity in the Afroasiatic language family. A subset of the Proto-Afroasiatic population may have moved to the Levant during the late Paleolithic period, mixing with local West-Eurasians and leading to the Natufian culture, linked to early agriculture and early Afroasiatic languages. In addition, Y-haplogroup sub-lineage E-M215 (also known as "E1b1b) and its derivative E-M35 are common among Afroasiatic speakers, and southwestern Ethiopia is a likely source of these haplogroups. Under this African model, the linguistic group and carriers of this lineage may have started and spread together from Northeast Africa in the Mesolithic period, possibly already practicing pastoralism and intensive plant usage.

The Near-Eastern agriculturalist hypothesis does not explain the domestication of plants native to the Horn of Africa such as teff, ensete, and Niger seed, nor does it explain the lack of evidence for crops like wheat, barley, or sorghum in that region before 3000 B.C. According to historian and linguist Christopher Ehret, the intensive plant collection practiced by the Proto-Afroasiatic population in Northeast Africa may have been a precursor to later agricultural practices that developed independently in the Fertile Crescent and the Horn of Africa.

David Schoenbrun, Christopher Ehret, Steven A. Brandt and Shomarka Keita (2025) have pointed out problems in how genetic haplogroups are labeled as ‘African’ and ‘Eurasian' in North African genome studies. Regarding the van de Loosdrecht et al. 2018 study on the epipalaeolithic Taforalt remains from Morocco, which identified the EM35 (primarily EM78) common in north-eastern Africa but described the mtDNA (female lineage haplogroups) of U6 and M1 as 'Eurasian', the authors questioned this classification despite the long-established presence of these maternal haplogroups in ancient African populations. In their view, identifying African populations may still be challenging “since the idea of ‘African’ can still be stereotyped or limited. (Accepting the southwestern Asian/Levantine geographical continuity with Africa eliminates a conceptual barrier related to racio-typological thinking permitting an Africasian construct analogous to Eurasian.)”.

Horn of Africa

While many studies on Horn of Africa populations estimate West-Eurasian mixing around 3,000 years ago, Hodgson et al. (2014) found a distinct West-Eurasian ancestral component among Afroasiatic-speaking groups in the Horn of Africa (and to a lesser extent in North Africa and West Asia), most common among the ethnic Somali. This component, called "Ethio-Somali", is most closely related to the "Maghrebi" component and is believed to have split from other non-African ancestries around 23,000 years ago, and moved back to Africa before agriculture developed (12–23 ka) from the Near East. This population may have crossed through the Sinai Peninsula and split into two, with one branch moving west across North Africa and the other heading south into the Horn of Africa. The authors suggest that the "Ethio-Somali" component may have been a major ancestral part of the Proto-Afroasiatic-speaking population. Later migrations from Arabia into the Horn of Africa beginning around 3 ka may explain the origin of Ethiosemitic languages at that time. A mtDNA study by Gandini et al. (2016) provided additional evidence for a pre-agricultural back-migration from West-Eurasia into the Horn of Africa, with an estimated arrival in the early Holocene, possibly due to obsidian exchange networks across the Red Sea. Hodgson et al. also confirmed the existence of an ancestral component unique to the Horn of Africa - "Ethiopic" or "Omotic" (Pagani et al.) - most common among Omotic branch Afroasiatic speakers in southwestern Ethiopia. This lineage is linked to a 4,500 year-old fossil (Mota) found in a cave in southwestern Ethiopia, which has strong genetic ties to modern Ethiopian groups, especially the blacksmith caste of the Omotic Aari people. Like Mota, Aari blacksmiths show no evidence of mixing with West-Eurasians, showing a degree of population continuity in this region for at least 4,500 years. In a comparison of Mota's genome with modern populations, Gallego et al. (2016) concluded that the split of Omotic from other Afroasiatic languages may have resulted from the relative isolation of its speakers from outside groups.

Another 2004 mtDNA study included samples from Gurna, Upper Egypt and grouped them with Ethiopian and Yemeni groups, between Near Eastern and other African sample groups.

The E-M35 haplogroup subclade is found among all Afro-Asiatic speaking regions, with the M-78 clade now thought to have originated in Sudan or Egypt, "or further south in the northeastern quadrant of Africa".

In an analysis of 68 Ethiopian ethnic groups, Lopez et al. (2021) found that several groups belonging to the three AA classifications of Cushitic, Omotic and Semitic show high genetic similarity on average. Furthermore, Nilo-Saharan speakers in the southwest share more recent ancestry with Bantu and Nilotics, while Afro-Asiatic speakers in the northeast share more recent ancestry with Egyptians and other West Eurasians. The data also supports widespread recent mixing among various ethnic groups.

Madagascar

Specific East Asian-related ancestry is found among Malagasy speakers of Madagascar at a medium frequency. This is mostly linked to the Austronesian peoples' expansion from Southeast Asia. The peoples of Borneo were identified as resembling the East Asian voyagers who arrived in Madagascar. East Asian ancestry among Malagasy people is estimated at a mean average of 33%, but as high as ~75% among some Highlander groups and upper caste groups.

Northern Africa

Genetic studies have identified a high frequency of E haplogroup subclades across Egypt, including among Egyptian Copts in Adaima, Upper Egypt and émigré Coptic communities in Sudan. Other haplogroups notably occurring in Egyptian populations have included the J and R haplogroups.

A 2005 study found that populations in Somalia, Sudan, Egypt and Oromos in Ethiopia share the same Y chromosome haplogroup E3b1, defined by E-M78.

A 2005 genetic study found close links of eastern sub-Saharan populations with Egypt in phylogenetic trees through analysis of short DNA sequences. The authors suggested that the influential role of the Nile River served as a migratory route and an agent of genetic flow which contributed to present-day heterogeneity in Egypt.

Dobon et al. (2015) identified an autosomal ancestral component commonly found among modern Afroasiatic-speaking populations (as well as Nubians) in Northeast Africa. This Coptic component peaks among Copts in Sudan, differentiated by its lack of Arab influence, but shares common ancestry with North African/Middle Eastern populations. It appears alongside a component that defines Nilo-Saharan speakers of southwestern Sudan and South Sudan. Arauna et al. (2017), analyzing existing genetic data from Northern African populations, such as Berbers, described them as a mix of North African (Taforalt), Middle Eastern, European (Early European Farmers), and Sub-Saharan African-related ancestries.

Chen et al. (2020) analyzed 2,504 African samples from all over Africa, and found Neanderthal ancestry among all tested African samples at low frequency. They also identified a European-related (West-Eurasian) ancestry segment, which seems to largely match the detected Neanderthal ancestry components. European-related mixing among Africans was estimated to be between ~0% to up to ~30%, peaking among Northern Africans. According to Chen et al. (2020), "These data are consistent with the hypothesis that back-migration contributed to the signal of Neanderthal ancestry in Africans. Furthermore, the data indicates that this back-migration came after the split of Europeans and East Asians, from a population related to the European lineage."

There is minor gene flow from North Africa into parts of Southern Europe, supported by the presence of an African-specific mitochondrial haplogroup among one of four 4,000 year old samples. Multiple studies have also found evidence for gene flow of African ancestry towards Eurasia, specifically Europe and the Middle East. Analysis of 40 different West-Eurasian populations found African mixing at a frequency of 0% to up to ~15%.

Western Africa

Hollfelder et al. (2021) concluded that West African Yoruba people, previously used as an "unmixed reference population" for indigenous Africans, have minor levels of Neanderthal ancestry, which can be largely linked to back-migration of an "Ancestral European-like" source population.

A genome-wide study of a Fulani community from Burkina Faso inferred two major mixing events in this group, dating to ~1800 ya, and 300 ya. The first mixing event was between the West African ancestors of the Fula and ancestral North African nomadic groups. The second mixing event, more recent, inferred a source from Southwestern Europe, or suggests additional gene flow between the Fulani and Northern African groups, who carry mixing proportions from Europeans. Sahelian populations like the Toubou also showed mixing coming from Eurasians.

Southern Africa

Low levels of West Eurasian ancestry (European or Middle Eastern) are found in Khoe–Kwadi Khoesan-speakers. This may have been acquired indirectly by mixing with migrating pastoralists from East Africa. This hypothesis of gene flow from eastern to southern Africa is supported by other genetic and archaeological data showing the spread of pastoralism from East to South Africa.

Regional genomic overview

The genetic history of Africa shows the diverse makeup and population history of African groups. Modern humans originated in Africa, and the Sahara Desert played a key role as both a passageway and a barrier, influencing gene flow between different regions.

North Africa

Main article: Genetic history of North Africa

Further information: DNA history of Egypt and Genetic studies on Moroccans

Ancient genetic studies show that people in North Africa have links to both nearby African populations and those farther away. Over time, movements and changes in climate affected the genetic mix in this area.

West Africa

Main article: Genetic history of West Africa

Further information: Genetic history of the African diaspora

West Africa’s genetic history includes ancient connections and later influences from other regions. Studies of DNA from modern and ancient peoples help show these links and changes over time.

Central Africa

Main article: Genetic history of Central Africa

Further information: Genetic history of the African diaspora

See also: African Pygmies § Genetics

Central Africa’s genetic history reflects a mix of ancient local groups and later influences. DNA studies reveal connections to both nearby and distant populations.

Eastern Africa

Main article: Genetic history of Eastern Africa

Further information: Genetic history of the African diaspora

Eastern Africa has been a key area for human history, with ancient DNA showing links to many other populations. Studies help trace these connections and changes over time.

Southern Africa

Main article: Genetic history of Southern Africa

Further information: Genetic history of the African diaspora

See also: San people § Genetics, and Khoekhoe

Southern Africa’s genetic history includes some of the oldest human groups. DNA studies show both ancient local connections and later influences from other regions.

Recent African origin of modern humans

Main article: Recent African origin of modern humans

Further information: Early human migrations, Basal Eurasian, and Human genetic variation

Between 500,000 and 300,000 years ago, modern humans first appeared in Africa. Over time, they spread from Africa to other parts of the world. Many scientists think humans may have come from many places in Africa, not just one spot.

Africans have more genetic differences among themselves than people from other parts of the world. This shows that most genetic variety started in Africa. Africans have also adapted to their environments in many ways, such as developing resistance to diseases like malaria. These adaptations help protect them from illnesses common in Africa.