Genetic history of Southern Africa

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The genetic history of Southern Africa encompasses the genetic history of the people of Southern Africa. The Sahara served as a trans-regional passageway and place of dwelling for people in Africa during various humid phases [1] [2] [3] and periods throughout the history of Africa. [4] [5]

Contents

Archaic human DNA

While Denisovan and Neanderthal ancestry in non-Africans outside of Africa are more certain, archaic human ancestry in Africans is less certain and is too early to be established with certainty. [6]

Ancient DNA

Three Later Stone Age hunter-gatherers carried ancient DNA similar to Khoisan-speaking hunter-gatherers. [7] Prior to the Bantu migration into the region, as evidenced by ancient DNA from Botswana, East African herders migrated into Southern Africa. [7] Out of four Iron Age Bantu agriculturalists of West African origin, two earlier agriculturalists carried ancient DNA similar to Tsonga and Venda peoples and the two later agriculturalists carried ancient DNA similar to Nguni people; this indicates that there were various movements of peoples in the overall Bantu migration, which resulted in increased interaction and admixing between Bantu-speaking peoples and Khoisan-speaking peoples. [7]

Botswana

At Nqoma, in Botswana, an individual, dated to the Early Iron Age (900 BP), carried haplogroup L2a1f. [8] [9]

At Taukome, in Botswana, an individual, dated to the Early Iron Age (1100 BP), carried haplogroups E1b1a1 (E-M2, E-Z1123) and L0d3b1. [8] [9]

At Xaro, in Botswana, there were two individuals, dated to the Early Iron Age (1400 BP); one carried haplogroups E1b1a1a1c1a and L3e1a2, and another carried haplogroups E1b1b1b2b (E-M293, E-CTS10880) and L0k1a2. [8] [9]

Malawi

Fingira

At Fingira rockshelter, in Malawi, an individual, dated between 6179 BP and 2341 BP, carried haplogroups B2 and L0d1. [10]

At Fingira, in Malawi, an individual, estimated to date between 6175 BP and 5913 BP, carried haplogroups BT and L0d1b2b. [11]

At Fingira, in Malawi, an individual, estimated to date between 6177 BP and 5923 BP, carried haplogroups BT and L0d1c. [11]

At Fingira, in Malawi, an individual, estimated to date between 2676 BP and 2330 BP, carried haplogroup L0f. [11]

Chencherere

At Chencherere, in Malawi, an individual, estimated to date between 5400 BP and 4800 BP, carried haplogroup L0k2. [11]

At Chencherere, in Malawi, an individual, estimated to date between 5293 BP and 4979 BP, carried haplogroup L0k1. [11]

Hora

At Hora 1 rockshelter, in Malawi, an individual, dated between 16,897 BP and 15,827 BP, carried haplogroups B2b and L5b. [10]

At Hora 1 rockshelter, in Malawi, an individual, dated between 16,424 BP and 14,029 BP, carried haplogroups B2b1a2~ and L0d3/L0d3b. [10]

At Hora, in Malawi, an individual, estimated to date between 10,000 BP and 5000 BP, carried haplogroups BT and L0k2. [11]

At Hora, in Malawi, an individual, estimated to date between 8173 BP and 7957 BP, carried haplogroup L0a2. [11]

South Africa

At Doonside, in South Africa, an individual, estimated to date between 2296 BP and 1910 BP, carried haplogroup L0d2. [12] [13]

At Champagne Castle, in South Africa, an individual, estimated to date between 448 BP and 282 BP, carried haplogroup L0d2a1a. [12] [13]

At Eland Cave, in South Africa, an individual, estimated to date between 533 BP and 453 BP, carried haplogroup L3e3b1. [12] [13]

At Mfongosi, in South Africa, an individual, estimated to date between 448 BP and 308 BP, carried haplogroup L3e1b2. [12] [13]

At Newcastle, in South Africa, an individual, estimated to date between 508 BP and 327 BP, carried haplogroup L3e2b1a2. [12] [13]

At St. Helena, in South Africa, an individual, estimated to date between 2241 BP and 1965 BP, carried haplogroups A1b1b2a and L0d2c1. [11]

At Faraoskop Rock Shelter, in South Africa, an individual, estimated to date between 2017 BP and 1748 BP, carried haplogroups A1b1b2a and L0d1b2b1b. [11]

At Kasteelberg, in South Africa, an individual, estimated to date between 1282 BP and 1069 BP, carried haplogroup L0d1a1a. [11]

At Vaalkrans Shelter, in South Africa, an individual, estimated to date to 200 BP, is predominantly related to Khoisan speakers, partly related (15–32%) to East Africans, and carried haplogroups L0d3b1. [14]

Ballito Bay

At Ballito Bay, South Africa, an individual, estimated to date between 2149 BP and 1932 BP, carried haplogroups A1b1b2 and L0d2a1. [12] [13]

At Ballito Bay, South Africa, an individual, estimated to date between 1986 BP and 1831 BP, carried haplogroups A1b1b2 and L0d2c1. [12] [13]

At Ballito Bay, South Africa, Ballito Boy, estimated to date 1,980 ± 20 cal BP, was found to have Rickettsia felis. [15] [16]

Zambia

At Kalemba rockshelter, in Zambia, an individual, dated between 5285 BP and 4975 BP, carried haplogroup L0d1b2b. [10]

Y-chromosomal DNA

Various Y chromosome studies show that the San carry some of the most divergent (oldest) human Y-chromosome haplogroups. These haplogroups are specific sub-groups of haplogroups A and B, the two earliest branches on the human Y-chromosome tree. [17] [18] [19]

Mitochondrial DNA

In 200,000 BP, Africans (e.g., Khoisan of Southern Africa) bearing haplogroup L0 diverged from other Africans bearing haplogroup L1′6, which tend to be northward of Southern Africa. [20] Between 130,000 BP and 75,000 BP, behavioral modernity emerged among Southern Africans and long-term interactions between the regions of Southern Africa and Eastern Africa became established. [20]

Mitochondrial DNA studies also provide evidence that the San carry high frequencies of the earliest haplogroup branches in the human mitochondrial DNA tree. This DNA is inherited only from one's mother. The most divergent (oldest) mitochondrial haplogroup, L0d, has been identified at its highest frequencies in the southern African San groups. [17] [21] [22] [23]

Autosomal DNA

From the region of Kenya and Tanzania to South Africa, eastern Bantu-speaking Africans constitute a north to south genetic cline; additionally, from eastern Africa to toward southern Africa, evidence of genetic homogeneity is indicative of a serial founder effect and admixture events having occurred between Bantu-speaking Africans and other African populations by the time the Bantu migration had spanned into South Africa. [24]

Henn et al. (2011) found that the ǂKhomani San, as well as the Sandawe and Hadza peoples of Tanzania, were the most genetically diverse of any living humans studied. This high degree of genetic diversity hints at the origin of anatomically modern humans. [25] [26]

Medical DNA

Among the ancient DNA from three hunter-gatherers sharing genetic similarity with San people and four Iron Age agriculturalists, their SNPs indicated that they bore variants for resistance against sleeping sickness and Plasmodium vivax. [27] In particular, two out of the four Iron Age agriculturalists bore variants for resistance against sleeping sickness and three out of the four Iron Age agriculturalists bore Duffy negative variants for resistance against malaria. [27] In contrast to the Iron Age agriculturalists, from among the San-related hunter-gatherers, a six-year-old boy may have died from schistosomiasis. [27] In Botswana, a man, who dates to 1400 BP, may have also carried the Duffy negative variant for resistance against malaria. [27]

The genomes of Africans commonly found to undergo adaptation are regulatory DNA, and many cases of adaptation found among Africans relate to diet, physiology, and evolutionary pressures from pathogens. [24] Throughout Sub-Saharan Africa, genetic adaptation (e.g., rs334 mutation, Duffy blood group, increased rates of G6PD deficiency, sickle cell disease) to malaria has been found among Sub-Saharan Africans, which may have initially developed in 7300 BP. [24] Sub-Saharan Africans have more than 90% of the Duffy-null genotype. [28] In the Kalahari Desert region of Africa, various possible genetic adaptations (e.g., adiponectin, body mass index, metabolism) have been found among the ǂKhomani people. [24] Sub-Saharan Africans have more than 90% of the Duffy-null genotype. [28] In South Africa, genetic adaptation (e.g., rs28647531 on chromosome 4q22) and strong susceptibility to tuberculosis has been found among Coloureds. [24]

Related Research Articles

<span class="mw-page-title-main">Khoisan</span> African ethnic group

KhoisanKOY-sahn, or Khoe-Sān, is a catch-all term for the indigenous peoples of Southern Africa who traditionally speak non-Bantu languages, combining the Khoekhoen and the Sān peoples. Khoisan populations traditionally speak click languages and are considered to be the historical communities throughout Southern Africa, remaining predominant until European colonisation in areas climatically unfavorable to Bantu (sorghum-based) agriculture, such as the Cape region, through to Namibia, where Khoekhoe populations of Nama and Damara people are prevalent groups, and Botswana. Considerable mingling with Bantu-speaking groups is evidenced by prevalence of click phonemes in many especially Xhosa Southern African Bantu languages.

Haplogroup A is a human Y-chromosome DNA haplogroup, which includes all living human Y chromosomes. Bearers of extant sub-clades of haplogroup A are almost exclusively found in Africa, in contrast with haplogroup BT, bearers of which participated in the Out of Africa migration of early modern humans. The known branches of haplogroup A are A00, A0, A1a, and A1b1; these branches are only very distantly related, and are not more closely related to each other than they are to haplogroup BT.

Haplogroup E-M96 is a human Y-chromosome DNA haplogroup. It is one of the two main branches of the older and ancestral haplogroup DE, the other main branch being haplogroup D. The E-M96 clade is divided into two main subclades: the more common E-P147, and the less common E-M75.

Haplogroup E-V38, also known as E1b1a-V38, is a major human Y-chromosome DNA haplogroup. E-V38 is primarily distributed in Africa. E-V38 has two basal branches, E-M329 and E-M2. E-M329 is a subclade mostly found in East Africa. E-M2 is the predominant subclade in West Africa, Central Africa, Southern Africa, and the region of African Great Lakes; it also occurs at moderate frequencies in North Africa, West Asia, and Southern Europe.

<span class="mw-page-title-main">Haplogroup R1b</span> Type of paternal lineage

Haplogroup R1b (R-M343), previously known as Hg1 and Eu18, is a human Y-chromosome haplogroup.

Haplogroup E-M75 is a human Y-chromosome DNA haplogroup. Along with haplogroup E-P147, it is one of the two main branches of the older haplogroup E-M96.

Haplogroup E-P2, also known as E1b1, is a human Y-chromosome DNA haplogroup. E-P2 has two basal branches, E-V38 and E-M215. E-P2 had an ancient presence in East Africa and the Levant; presently, it is primarily distributed in Africa where it may have originated, and occurs at lower frequencies in the Middle East and Europe.

The genetic history of North Africa encompasses the genetic history of the people of North Africa. The most important source of gene flow to North Africa was from the Middle East, although the Sahara desert to the south and the Mediterranean Sea to the North were also important barriers to gene flow from sub-Saharan Africa and parts of Europe in prehistory. However, North Africa is connected to Western Asia via the Isthmus of Suez and the Sinai peninsula, while at the Straits of Gibraltar, North Africa and Europe are separated by only 15 km (9 mi), similarly Malta, Sicily, Canary Islands, and Crete are close to the coasts of North Africa.

<span class="mw-page-title-main">African Pygmies</span> Group of ethnicities native to Central Africa

The African Pygmies are a group of ethnicities native to Central Africa, mostly the Congo Basin, traditionally subsisting on a forager and hunter-gatherer lifestyle. They are divided into three roughly geographic groups:

<span class="mw-page-title-main">Genetic history of Egypt</span>

The genetic history of Egypt reflects its geographical location at the crossroads of several major biocultural areas: North Africa, the Sahara, the Middle East, the Mediterranean and sub-Saharan Africa.

<span class="mw-page-title-main">Haplogroup E-M2</span> Human Y-chromosome DNA haplogroup

Haplogroup E-M2, also known as E1b1a1-M2, is a human Y-chromosome DNA haplogroup. E-M2 is primarily distributed within Africa followed by West Asia. More specifically, E-M2 is the predominant subclade in West Africa, Central Africa, Southern Africa, and the region of the African Great Lakes; it also occurs at moderate frequencies in North Africa, and the Middle East. E-M2 has several subclades, but many of these subhaplogroups are included in either E-L485 or E-U175. E-M2 is especially common among indigenous Africans who speak Niger-Congo languages, and was spread to Southern Africa and East Africa through the Bantu expansion.

<span class="mw-page-title-main">Genetic history of Africa</span>

The genetic history of Africa is composed of the overall genetic history of African populations in Africa, including the regional genetic histories of North Africa, West Africa, East Africa, Central Africa, and Southern Africa, as well as the recent origin of modern humans in Africa. The Sahara served as a trans-regional passageway and place of dwelling for people in Africa during various humid phases and periods throughout the history of Africa.

<span class="mw-page-title-main">History of East Africa</span> History of the east African region

The history of East Africa has been divided into its prehistory, the major polities flourishing, the colonial period, and the post-colonial period, in which the current nations were formed. East Africa is the eastern region of Africa, bordered by North Africa, Central Africa, Southern Africa, the Indian Ocean, and the Sahara Desert. Colonial boundaries are reflected in the modern boundaries between contemporary East African states, cutting across ethnic and cultural lines, often dividing single ethnic groups between two or more states.

<span class="mw-page-title-main">History of Southern Africa</span> History of Southern African region

The history of Southern Africa has been divided into its prehistory, its ancient history, the major polities flourishing, the colonial period, and the post-colonial period, in which the current nations were formed. Southern Africa is bordered by Central Africa, East Africa, the Atlantic Ocean, the Indian Ocean, and the Sahara Desert. Colonial boundaries are reflected in the modern boundaries between contemporary Southern African states, cutting across ethnic and cultural lines, often dividing single ethnic groups between two or more states.

<span class="mw-page-title-main">Genetic history of the African diaspora</span>

The genetic history of the African diaspora is composed of the overall genetic history of the African diaspora, within regions outside of Africa, such as North America, Central America, the Caribbean, South America, Europe, Asia, and Australia; this includes the genetic histories of African Americans, Afro-Canadians, Afro-Caribbeans, Afro-Latinos, Afro-Europeans, Afro-Asians, and African Australians.

<span class="mw-page-title-main">Prehistoric East Africa</span> Prehistory of the East African subregion of the African continent

The prehistory of East Africa spans from the earliest human presence in the region until the emergence of the Iron Age in East Africa. Between 1,600,000 BP and 1,500,000 BP, the Homo ergaster known as Nariokotome Boy resided near Nariokotome River, Kenya. Modern humans, who left behind remains, resided at Omo Kibish in 233,000 BP. Afro-Asiatic speakers and Nilo-Saharan speakers expanded in East Africa, resulting in transformation of food systems of East Africa. Prehistoric West Africans may have diverged into distinct ancestral groups of modern West Africans and Bantu-speaking peoples in Cameroon, and, subsequently, around 5000 BP, the Bantu-speaking peoples migrated into other parts of Sub-Saharan Africa.

<span class="mw-page-title-main">Prehistoric Southern Africa</span> Prehistory of the Southern African subregion of the African continent

The prehistory of Southern Africa spans from the earliest human presence in the region until the emergence of the Iron Age in Southern Africa. In 1,000,000 BP, hominins controlled fire at Wonderwerk Cave, South Africa. Ancestors of the Khoisan may have expanded from East Africa or Central Africa into Southern Africa before 150,000 BP, possibly as early as before 260,000 BP. Prehistoric West Africans may have diverged into distinct ancestral groups of modern West Africans and Bantu-speaking peoples in Cameroon, and, subsequently, around 5000 BP, the Bantu-speaking peoples migrated into other parts of Sub-Saharan Africa.

The genetic history of West Africa encompasses the genetic history of the people of West Africa. The Sahara served as a trans-regional passageway and place of dwelling for people in Africa during various humid phases and periods throughout the history of Africa.

The genetic history of Central Africa encompasses the genetic history of the people of Central Africa. The Sahara served as a trans-regional passageway and place of dwelling for people in Africa during various humid phases and periods throughout the history of Africa.

The genetic history of Eastern Africa encompasses the genetic history of the people of Eastern Africa. The Sahara served as a trans-regional passageway and place of dwelling for people in Africa during various humid phases and periods throughout the history of Africa.

References

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