Genetic structure correlates with ethnolinguistic diversity in eastern and southern Africa

Abstract

African populations are the most diverseinthe world yetare sorelyunderrepresented inmedicalgeneticsresearch. Here, we examine the structure of African populations using genetic and comprehensive multi-generational ethnolinguistic data from the Neuropsychiatric GeneticsofAfricanPopulations-Psychosisstudy(NeuroGAP-Psychosis)consistingof900individualsfromEthiopia,Kenya,SouthAfrica, andUganda.Wefindthatself-reportedlanguageclassificationsmeaningfullytagunderlyinggeneticvariationthatwouldbemissedwith 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 languagetransmission in matrilineal groupshaving been higherthan that for patrilinealones. We highlight both the diversityof vari ation 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.