Genetic structure correlates with ethnolinguistic diversity in eastern and southern Africa

• Published in: American journal of human genetics Vol. 109; no. 9; pp. 1667 - 1679
• Main Authors: Atkinson, Elizabeth G., Dalvie, Shareefa, Pichkar, Yakov, Kalungi, Allan, Majara, Lerato, Stevenson, Anne, Abebe, Tamrat, Akena, Dickens, Alemayehu, Melkam, Ashaba, Fred K., Atwoli, Lukoye, Baker, Mark, Chibnik, Lori B., Creanza, Nicole, Daly, Mark J., Fekadu, Abebaw, Gelaye, Bizu, Gichuru, Stella, Injera, Wilfred E., James, Roxanne, Kariuki, Symon M., Kigen, Gabriel, Koen, Nastassja, Koenen, Karestan C., Koenig, Zan, Kwobah, Edith, Kyebuzibwa, Joseph, Musinguzi, Henry, Mwema, Rehema M., Neale, Benjamin M., Newman, Carter P., Newton, Charles R.J.C., Ongeri, Linnet, Ramachandran, Sohini, Ramesar, Raj, Shiferaw, Welelta, Stein, Dan J., Stroud, Rocky E., Teferra, Solomon, Yohannes, Mary T., Zingela, Zukiswa, Martin, Alicia R.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.09.2022; Elsevier
• Subjects: Africa; Africa, Southern; Black People - genetics; diverse populations; Genetic Structures; Genetic Variation - genetics; Genetics, Population; genotypes; Humans; linguistics; population genetics; population structure; Africa, Southern; genotypes; population genetics; linguistics; diverse populations; population structure; Africa
• ISSN: 0002-9297; 1537-6605
• DOI: 10.1016/j.ajhg.2022.07.013

African populations are the most diverse in the world yet are sorely underrepresented in medical genetics research. Here, we examine the structure of African populations using genetic and comprehensive multi-generational ethnolinguistic data from the Neuropsychiatric Genetics of African Populations-Psychosis study (NeuroGAP-Psychosis) consisting of 900 individuals from Ethiopia, Kenya, South Africa, and Uganda. We find that self-reported language classifications meaningfully tag underlying genetic variation that would be missed with consideration of geography alone, highlighting the importance of culture in shaping genetic diversity. Leveraging our uniquely rich multi-generational ethnolinguistic metadata, we track language transmission through the pedigree, observing the disappearance of several languages in our cohort as well as notable shifts in frequency over three generations. We find suggestive evidence for the rate of language transmission in matrilineal groups having been higher than that for patrilineal ones. We highlight both the diversity of variation within Africa as well as how within-Africa variation can be informative for broader variant interpretation; many variants that are rare elsewhere are common in parts of Africa. The work presented here improves the understanding of the spectrum of genetic variation in African populations and highlights the enormous and complex genetic and ethnolinguistic diversity across Africa. [Display omitted] Africa has immense genetic, linguistic, and cultural diversity. Here, we examine how languages relate to genetics across individuals from Ethiopia, Kenya, Uganda, and South Africa. We find self-reported language tags genetic variation, and we observe shifts in language transmission through three generations. African genetic variation is informative for broader variant interpretation.