The evolution of human genetic and phenotypic variation in Africa

Abstract

Africa is the birthplace of modern humans, and is the source of the geographic expansion of ancestral populations into other regions of the world. Indigenous Africans are characterized by high levels of genetic diversity within and between populations. The pattern of genetic variation in these populations has been shaped by demographic events occurring over the last 200,000 years. The dramatic variation in climate, diet, and exposure to infectious disease across the continent has also resulted in novel genetic and phenotypic adaptations in extant Africans. This review summarizes some recent advances in our understanding of the demographic history and selective pressures that have influenced levels and patterns of diversity in African populations.

Figure 1. Classification of major language families and proposed historic and prehistoric migration events within Africa

African languages have been classified into four major linguistic families as follows: Niger-Kordofanian (spoken predominantly by agriculturalist populations across a broad geographic distribution in Africa), Afroasiatic (spoken predominantly by northern and eastern African pastoralists and agropastoralists), Nilo-Saharan (spoken predominantly by central and eastern African pastoralists) and Khoesan (a language containing click-consonants, spoken by eastern and southern African hunter-gatherers). This map also shows a number of key migration events that occurred in Africa, most notably the expansion of Bantu-speakers from a homeland in Nigeria and Cameroon first into the equatorial rainforests and then into eastern and southern Africa, as well as the migration of Nilo-Saharan-speakers both westward and eastward from a Sudanese homeland. Additionally, Cushitic-speakers from the Ethiopian highlands migrated northward to the Red Sea coast of Sudan (where their modern-day descendants, the Beja, presently live) as well as southward into Kenya and Tanzania [6]. (based on Figure 1 from reference [2]).

Figure 2. The ‘Recent African Origin’ model of modern humans and population substructure in Africa

A study of genome-wide polymorphic markers in 121 ethnically diverse African populations indicated the presence of 14 genetically distinct ancestral population clusters in Africa [18]. According to the Recent African Origin model of modern human origins, anatomically modern humans evolved in Africa around 200 kya, migrated to Eurasia within the last 40,000–80,000 years and then migrated to the Americas within the last 15,000–30,000 years. The geographic expansion from Africa is thought to have been accompanied by a population bottleneck and a concomitant loss of genetic diversity. Studies have also suggested that a serial founder model of migration occurred in the history of non-Africans in which the migration of populations across much of the globe occurred in many small steps, with each migration event involving a sampling of variation from the previous population [25, 29, 33, 46]. In this figure, decreasing intensity of color represents the concomitant loss of genetic diversity as populations migrated in an eastward direction from Africa. Solid horizontal lines indicate gene-flow between ancestral human populations and the dashed horizontal line indicates recent gene-flow between Asian and Australian/Melanesian populations (based on Figure 2 from reference [1]).

Figure 3. Map of African climate, vegetation and culture in the early Holocene (adapted from Maps 5 and 6 in reference [6])

Following a period of dramatic increase in rainfall ~10.5 kya, the expansion of both rainforest vegetation in the Congo Basin and woodland savanna farther north and south of the rainforest belt, as well as the expansion of tropical steppe and grassland vegetation into the Sahara region occurred. New lakes also appeared, while old lakes grew in size along the southern edges of the Sahara [6]. Between 10.5 – 8.5 kya, several key demographic events occurred among culturally distinct ancestral African populations, including the migration of Nilo-Saharan-speakers from their homeland in Sudan northward to the dry tropical steppe vegetation of the eastern Sahara where they practiced agropastoralism [6]. Northern Erythraites (Afroasiatic-speakers) also lived mainly in the Mediterranean climate of the northern Sahara where they engaged in herding and wild grain collection[6]. The distributions of these cultural groups, among others depicted on this map, roughly correspond to the present-day distribution of major linguistic groups in Africa (Refer to Figure 1). The shift from dry to wetter climatic conditions in the early Holocene likely provided an opportunity for ancestral Africans to develop cultural traditions, such as agriculture and herding, in a more favorable environment leading to further technological developments in Africa [6].