Evolutionary Genetics and Admixture in African Populations

Abstract

As the ancestral homeland of our species, Africa contains elevated levels of genetic diversity and substantial population structure. Importantly, African genomes are heterogeneous: they contain mixtures of multiple ancestries, each of which have experienced different evolutionary histories. In this review, we view population genetics through the lens of admixture, highlighting how multiple demographic events have shaped African genomes. Each of these historical vignettes paints a recurring picture of population divergence followed by secondary contact. First, we give a brief overview of African genetic variation and examine deep population structure within Africa, including evidence of ancient introgression from archaic “ghost” populations. Second, we describe the genetic legacies of admixture events that have occurred during the past 10,000 years. This includes gene flow between different click-speaking Khoe-San populations, the stepwise spread of pastoralism from eastern to southern Africa, multiple migrations of Bantu speakers across the continent, as well as admixture from the Middle East and Europe into the Sahel region and North Africa. Furthermore, the genomic signatures of more recent admixture can be found in the Cape Peninsula and throughout the African diaspora. Third, we highlight how natural selection has shaped patterns of genetic variation across the continent, noting that gene flow provides a potent source of adaptive variation and that selective pressures vary across Africa. Finally, we explore the biomedical implications of African population genetic structure on health and disease and call for more ethically conducted studies of African genetic variation.

Genetic admixture predictors of fetal alcohol spectrum disorders (FASD) in the South African Cape Coloured population

“…Our findings are notably consistent with prior reports (15)(16)(17)(18)(19). de Wit et al (16) estimated admixture in 959 SACC individuals, reporting ~67% African, ~23% European, and ~10% Asian ancestry.…”

“…We used a newly-developed reference database (33), which harmonized two public databases: 1000 Genome (1000G) (34) and the Human Genome Diversity Project (HGDP) (35). Consistent with prior studies in this population (15)(16)(17)(18)(19), we conducted supervised admixture analyses utilizing African, European, South Asian, and East Asian as reference population data [African: HGDP Yoruba, Bantu Kena, Mandenka and 1000G Yoruba; European: HGDP French, Tuscan, Bergamo Italian and 1000G Great Britain, CEU (Utah, USA residents with Northern and Western European), Toscani Italian; South Asian HGDP Cambodian, Lahu (ethnic group in Myanmar, Laos, Thailand) and 1000G Bengali (in Bangladesh), Kinh (Vietnamese); East Asian (HGDP Han-Chinese, Northern Han-Chinese and 1000G Southern Han Chinese, Beijing Han Chinese]. PCA analyis of uncorrelated SNPs was then conducted on a combined dataset of 352 unrelated participants in our cohorts and the reference populations listed above to examine similarities between our SACC cohorts participants and the reference populations.…”

“…Although race is a social construct, geopolitical and institutional practices and policies over the last three centuries have heavily influenced the genetic admixture of the SACC population. Previous studies have demonstrated genetic ancestry from the African Khoe-San, African Bantu-speaking, European, South Asian, and East Asian populations (15)(16)(17)(18)(19). The SACC population may be particularly well-suited to genetic association studies for complex diseases, such FASD.…”

Uncovering the genetic architecture and evolutionary roots of androgenetic alopecia in African men

“…We note that the study sites analyzed here contain individuals from a wide range of sociolinguistic groups and genetic ancestries, and there may substantial heterogeneity in the genetic architecture of MPB and other complex traits within Africa. 62,63 Going forward, there is clear need to conduct additional studies of diverse African populations (including functional genomics experiments to infer molecular mechanisms that are due to private alleles). Because early-onset MPB is indicative of the levels of sex hormones, 64 future studies combining baldness phenotypes with genetic data may be informative about the risks of prostate cancer and other hormonal diseases.…”

Highlight: How Mixing and Matching Alleles Shaped Human Ancestry

“…Genomes of Africans contain mixtures of multiple ancestries, each of which has experienced different evolutionary histories. In the article “ Evolutionary genetics and admixture in African populations ,” researchers from two institutes—Georgia Institute of Technology and Mediclinic Precise Southern Africa—reviewed how multiple demographic events have shaped African genomes over time ( Pfennig et al 2023 ). According to Joseph Lachance, one of the review's authors, “What stands out is the sheer complexity of human demographic history, especially in Africa.…”