Admixture into and within sub-Saharan Africa

Abstract

Similarity between two individuals in the combination of genetic markers along their chromosomes indicates shared ancestry and can be used to identify historical connections between different population groups due to admixture. We use a genome-wide, haplotype-based, analysis to characterise the structure of genetic diversity and gene-flow in a collection of 48 sub-Saharan African groups. We show that coastal populations experienced an influx of Eurasian haplotypes over the last 7000 years, and that Eastern and Southern Niger-Congo speaking groups share ancestry with Central West Africans as a result of recent population expansions. In fact, most sub-Saharan populations share ancestry with groups from outside of their current geographic region as a result of gene-flow within the last 4000 years. Our in-depth analysis provides insight into haplotype sharing across different ethno-linguistic groups and the recent movement of alleles into new environments, both of which are relevant to studies of genetic epidemiology.DOI: http://dx.doi.org/10.7554/eLife.15266.001

Reconstructing Prehistoric African Population Structure

“…Today, some of the earliest branching African lineages are present only in populations with relatively small census sizes, including the southern African Khoe-San (see STAR Methods for terminology), central African rainforest hunter-gatherers, and Hadza of Tanzania (Gronau et al, 2011; Schlebusch et al, 2012; Veeramah et al, 2012). However, the population structure of Africa prior to the expansion of food producers (pastoralists and agriculturalists) remains unknown (Busby et al, 2016; Gurdasani et al, 2015; Patin et al, 2017). Bantu-speaking agriculturalists originating in western Africa are thought to have brought farming to eastern Africa by ~2000 years calBP (calibrated radiocarbon years Before Present, defined by convention as years before 1950 CE) and to southern Africa by ~1500 BP, thereby spreading the largest single ancestry component to African genomes today (Russell et al, 2014; Tishkoff et al, 2009).…”

Mozambican genetic variation provides new insights into the Bantu expansion

“…6E) populations are successively removed from the list of donors. Nevertheless, the fact that Angola still represents a better proxy for the ancestry of southeastern Bantu speakers than populations closer to the Bantu homeland provides additional evidence in favor of a "late-split" between southwestern and southeastern Bantu-speaking groups after a single passage through the rainforest, as suggested in previous studies (20,21).…”

“…Some interpretations of the archaeological data have proposed that, in contrast with the "late split" between East and West Bantu suggested by linguistic evidence, East Bantu peoples introduced the Urewe tradition into the Great Lakes by migrating out of the proto-Bantu heartland along the northern fringes of the rainforest after an early separation from Bantu speakers occupying the western half of Africa (18,19). This model, however, is not supported by recent genetic studies showing that Bantu-speaking populations from eastern and southern Africa are more closely related to West Bantu speakers that migrated to the south of the rainforest than they are to West Bantu speakers that remained in the north (20)(21)(22).…”

Complete genome sequence and analysis of nine Egyptian females with clinical information from different geographic regions in Egypt

“…Overall, both mtDNA and ADMIXTURE studies suggested a diverse and admixed background of Egyptians sharing genetic signature and metabolic phenotypes with other Mediterranean nations. Although largely debated, into-Africa migration hypothesis [75] [76,77] seems to be supported by our largely diverse mtDNA haplotype collection demonstrated by just nine random samples. Egypt standing at the crossroad of different continents could have served as a gateway that allowed circulating people from Eurasia towards Africa since at least Holoscene [75]and lead to admixtures in east and sub-Saharan Africa that were reported before [76,77] and in this case lead to shared genetic predisposition to complex diseases such as obesity.…”