Genomic evidence for shared common ancestry of East African hunting-gathering populations and insights into local adaptation

Abstract

Anatomically modern humans arose in Africa ∼300,000 years ago, but the demographic and adaptive histories of African populations are not well-characterized. Here, we have generated a genome-wide dataset from 840 Africans, residing in western, eastern, southern, and northern Africa, belonging to 50 ethnicities, and speaking languages belonging to four language families. In addition to agriculturalists and pastoralists, our study includes 16 populations that practice, or until recently have practiced, a hunting-gathering (HG) lifestyle. We observe that genetic structure in Africa is broadly correlated not only with geography, but to a lesser extent, with linguistic affiliation and subsistence strategy. Four East African HG (EHG) populations that are geographically distant from each other show evidence of common ancestry: the Hadza and Sandawe in Tanzania, who speak languages with clicks classified as Khoisan; the Dahalo in Kenya, whose language has remnant clicks; and the Sabue in Ethiopia, who speak an unclassified language. Additionally, we observed common ancestry between central African rainforest HGs and southern African San, the latter of whom speak languages with clicks classified as Khoisan. With the exception of the EHG, central African rainforest HGs, and San, other HG groups in Africa appear genetically similar to neighboring agriculturalist or pastoralist populations. We additionally demonstrate that infectious disease, immune response, and diet have played important roles in the adaptive landscape of African history. However, while the broad biological processes involved in recent human adaptation in Africa are often consistent across populations, the specific loci affected by selective pressures more often vary across populations.

Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa

“…These individuals fall in an intermediate position between Ethiopian and Tanzanian foragers on a genetic cline that is well correlated (among sampled ancient individuals) with geographical location (22). Broadly, however, the similarity of foragers buried in the Victoria and Eyasi Basins to individuals living on the Kenya coast and in Ethiopia and coastal Tanzania (22, 24) suggests that shared forager ancestry extended widely across the region, as also attested by present-day genetic data (20).…”

The genetic landscape of Ethiopia: diversity, intermixing and the association with culture

“…While the relationships of Beta Israel with other Jewish communities have been the subject of focused research following their migration to Israel (Non et al, 2011, Behar et al, 2010, Thomas et al, 2002, studies involving genomic analyses of the history of wider sets of Ethiopian groups have been more limited (Tadesse et al, 2014, Poloni et al, 2009. Although as early as 1988 Cavalli-Sforza et al (1988) drew attention to the importance of bringing together genetic, archaeological and linguistic data, there have been few attempts to do so in studies of Ethiopia (Boattini et al, 2013, Pagani et al, 2012, Gallego-Llorente et al, 2015, Baker et al 2017, Scheinfeldt et al 2019, Gopalan et al 2019. Generally, studies have been limited to analysing data from single autosomal loci, non-recombining portion of the Y chromosome and mitochondrial DNA (Semino et al, 2002, Kivisild et al, 2004, Poloni et al, 2009, Boattini et al, 2013, Messina et al, 2017 and/or relatively few ethnic groups (Scheinfeldt et al, 2012, Pagani et al, 2012, Pagani et al, 2015, Scheinfeldt et al, 2019, Gopalan et al, 2019, Prendergast et al, 2019, which has severely limited the inferences that can be drawn.…”

“…Although as early as 1988 Cavalli-Sforza et al (1988) drew attention to the importance of bringing together genetic, archaeological and linguistic data, there have been few attempts to do so in studies of Ethiopia (Boattini et al, 2013, Pagani et al, 2012, Gallego-Llorente et al, 2015, Baker et al 2017, Scheinfeldt et al 2019, Gopalan et al 2019. Generally, studies have been limited to analysing data from single autosomal loci, non-recombining portion of the Y chromosome and mitochondrial DNA (Semino et al, 2002, Kivisild et al, 2004, Poloni et al, 2009, Boattini et al, 2013, Messina et al, 2017 and/or relatively few ethnic groups (Scheinfeldt et al, 2012, Pagani et al, 2012, Pagani et al, 2015, Scheinfeldt et al, 2019, Gopalan et al, 2019, Prendergast et al, 2019, which has severely limited the inferences that can be drawn. Furthermore, hitherto there has been little exploration of how genetic similarity is associated with shared cultural practices (see however van Dorp et al, 2015) despite the considerable variation known to exist in cultural practices, particularly in the southern part of the country (The Council of Nationalities, Southern Nations and Peoples Region, 2017).…”

Genomic landscape of the signals of positive natural selection in populations of Northern Eurasia: A view from Northern Russia

“…Such SNPs were further annotated using the snpEff program (v.4.3p) [72]. Additionally, genes or genomics regions subjected to selective pressure were searched in 100 kb non-overlapping genomic windows contained SNPs found in the 0.1% tail of the empirical distribution of the test statistics [27,73,74]. Windows with two or more such SNPs were filtered and SNPs from them were annotated.…”