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FIG. 4.
Visual summary of key admixture events in Africa. (A) The stepwise spread of lactose persistence from northeastern Africa into eastern Africa and subsequently into southern Africa. (B) Southward migration of Bantu-speaking people through the rainforest to modern-day Angola (ANG) and Zambia (ZMB) before splitting into eBSPs and seBSPs, in concordance with the late-split hypothesis. (C) Extensive admixture between Sahelian populations with European groups in the West and Middle Eastern groups in the East, but only limited gene flow among Sahelian populations. (D) Repetitive gene flow from the Middle East/Europe and sub-Saharan Africa into Northern African populations.
In line with archeological studies, genetic studies of Khoe-San confirmed that pastoralism spread from East Africa to southern Africa by demic diffusion (Breton et al. 2014; Macholdt et al. 2014; Ranciaro et al. 2014; Schlebusch et al. 2017; Skoglund et al. 2017). Khoekhoe-speaking populations (e.g., the Nama), who currently practice a pastoralist lifestyle, have a high-frequency lactase persistence (LP) allele that is also found in East African populations (Schlebusch et al. 2012; Breton et al. 2014; Macholdt et al. 2014). This “East African” LP single nucleotide polymorphism (SNP) (14010G > C) is distinct from the “European” LP SNP (1391 °C > T) and is rare in southern African Bantu-speaking groups (Breton et al. 2014; Macholdt et al. 2014). Among Khoe-San groups, this “East African” LP SNP is found at the highest frequency in the Nama with a frequency of ∼35%, which is much higher than expected given the ∼13% East African admixture fraction in the Nama, suggesting positive selection (Breton et al. 2014; Macholdt et al. 2014). Interestingly, Prendergast et al. found that the “East African” LP allele is largely absent from ancient pastoralist individuals from Kenya and Tanzania, indicating that east African pastoralists were lactose intolerant as recently as 3–1 kya (Prendergast et al. 2019). However, it is also possible that this allele has not been detected in ancient samples due to a limited number of surveyed individuals.
A direct link between Afro-Asiatic–speaking eastern African (i.e., Amhara- or Oromo-related ancestry) and southern African pastoralists has been established by showing that a 1,200-year-old individual from southern Africa, who has genetic similarities with modern Khoekhoe-speaking pastoralist groups (e.g., the Nama), traces ∼40% of their ancestry to a Eurasian admixed group related to a 3,100-year-old pastoralist individual from Luxmanda, Tanzania (Skoglund et al. 2017). Thus, this study indicates that admixture of Khoe-San groups with eastern African pastoralists occurred at least ∼1.2 kya (fig. 4A). Concordantly, another study estimated that all modern Khoe-San populations received 9–30% gene flow from an admixed East African/Eurasian pastoralist group 1.5–1.3 kya (Schlebusch et al. 2017). Furthermore, east African pastoralist contributions to Khoe-San groups are lower on X chromosomes than autosomes (Vicente et al. 2021), indicating that male-biased admixture occurred. Overall, these results suggest that eastern African pastoralists reached southern Africa prior to and independently of Bantu-speaking groups. For a detailed review of the spread of lactase persistence in Africa, see Campbell and Ranciaro (2021).
Multiple Migration Waves of Bantu Speakers
Genetic studies showed that the spread of Bantu languages, agricultural practices, and iron use 5–3 kya was accompanied by multiple migration waves of Bantu speakers from western Africa (i.e., current eastern Nigeria and western Cameroon) to other regions in sub-Saharan Africa (Tishkoff et al. 2009; Schlebusch et al. 2012; Li et al. 2014). Consequently, the Bantu expansion extensively contributed to population structure due to differential levels of admixture with and replacement of local hunter–gatherer groups over the past 3,500 years (Skoglund et al. 2017; Sengupta et al. 2021; González-Santos et al. 2022).
Two major migratory routes of Bantu-speaking populations (BSPs) have been hypothesized. The early-split hypothesis suggests that BSPs split at an early stage north of the rainforest, with one group then moving directly South through the rainforest, whereas the other migrated East, north of the rainforest, toward the Great African Lakes. In contrast, the late-split hypothesis states that BSPs first migrated South through the rainforest before splitting into two groups, with one moving further South and the other one migrating East toward the Great African Lakes. Similarly to phylolinguistics (e.g., Rexová et al. 2006), genetics are in favor of the late-split hypothesis, as eastern BSPs (eBSPs) and south-eastern BSPs (seBSPs) are genetically closer to western BSPs (wBSPs) south of the rainforest (i.e., Angola) than to wBSPs north of the rainforest (Patin et al. 2017). A subsequent study using samples from wider geographic and ethnolinguistic groups showed that eBSPs, seBSPs, and southwestern BSPs (swBSPs) are genetically closest to Bantu speakers from Zambia (Choudhury et al. 2020). Together, these findings suggest that Bantu speakers first migrated South through the rainforest to Angola and subsequently to Zambia before splitting into two groups (fig. 4B).
In western Africa, wBSPs asymmetrically mixed with resident RHG groups, with RHG groups receiving higher amounts of gene flow from wBSPs (Jarvis et al. 2012; Hsieh, Veeramah, et al. 2016; Patin et al. 2017; Lopez et al. 2018). wBSPs in Angola have small amounts of RHG-related ancestry from an admixture event that occurred after the split of BSPs ∼800 ya (Patin et al. 2017), although a recent study inferred a more ancient admixture date of ∼1.9 kya for Bantu speakers in Cabinda, Angola (Tallman et al. 2022). The amount of gene flow from wBSPs into individual RHG groups varied. Whereas the Mbuti and the Biaka have <6% wBSP-related ancestry, the Bezan and the Bongo trace as much as 38.5% and 47.5% to wBSPs, respectively (Patin et al. 2014). This gene flow from wBSPs into RHGs was inferred to have occurred ∼7 kya using models of site-frequency spectra (Hsieh, Veeramah, et al. 2016; Lopez et al. 2018), whereas methods leveraging LD patterns yielded estimates <1 kya (Patin et al. 2014, 2017). Analyses of uniparental markers as well as autosomal and X chromosomal data also showed that this gene flow from wBSPs into RHGs was male-biased (Verdu et al. 2013; Patin et al. 2014). For an excellent review of the interactions between BSPs and RHGs, see Patin and Quintana-Murci (2018).
In eastern Africa, two admixture events 1.5–1 kya and 400–150 years ago have been inferred between wBSPs (∼75% contribution) and an Afro-Asiatic–speaking population from Ethiopia (∼10%) (Patin et al. 2017). These estimates are in slight disagreement with the estimates of Skoglund et al. (2017), who estimated that admixture between Bantu speakers and eastern African pastoralists occurred 800–400 years ago, but are in agreement with 71% Bantu-related ancestry in an ancient Iron Age individual dated to ∼1,160 years ago from the Rift Valley in Kenya (Prendergast et al. 2019).
In South Africa, seBSPs received between 1.5% (e.g., the Tsonga) and 20% (e.g., the Tswana) gene flow from Khoe-San groups during independent admixture events (Sengupta et al. 2021). The exact admixture timings differ between populations (1.7 kya–700 ya), with northern groups showing older dates than southern groups (Sengupta et al. 2021; Tallman et al. 2022). However, Tallman et al. (2022) also reported an older Khoe-San admixture event in the Zulu ∼3 kya. Furthermore, uniparental markers and X chromosomal and autosomal data suggest male-biased seBSPs contributions and female-biased Khoe-San contributions (Bajić et al. 2018; Sengupta et al. 2021). In contrast to the admixture in South Africa, seBSPs appeared to have replaced resident hunter–gatherer populations in Malawi and Mozambique with present-day individuals deriving ≥97% of their ancestry from the Bantu expansion (Skoglund et al. 2017; Tallman et al. 2022). Overall, this suggests multiple migration waves of Bantu speakers or that Khoe-San admixture did not occur immediately.
In contrast to seBSPs, swBSPs appear to have reached southern Africa more recently (∼750 ya), as indicated by more recent admixture of a western African-related source in the Khoisan-speaking Khwe and !Xun from Angola (Busby et al. 2016). This suggests that swBSPs took a different route directly south along the western coast and thus have different recent population histories than seBSPs (fig. 4B).
Genetic studies of uniparental and autosomal markers initially suggested that BSPs are largely genetically homogenous groups of people (i.e., FST ≤ 0.02) (Coelho et al. 2009; Ansari-Pour et al. 2013; Gurdasani et al. 2015; Busby et al. 2016). Despite the modest FST values, fine-scale population structure of BSPs has recently been emphasized (Semo et al. 2020; Sengupta et al. 2021; Tallman et al. 2022). Semo et al. (2020) showed that eBSPs from Mozambique and Angola form a North–South genetic cline of relatedness along the coast from Kenya/Tanzania to South Africa. They also found that genetic homogeneity increases east- and southward, indicating serial founder effects and little admixture with local populations until Bantu speakers reached South Africa. Additionally, Sengupta et al. (2021) found that fine-scale genetic substructure among seBSPs in South Africa correlates well with geography and linguistics and persists even after accounting for differential levels of Khoe-San admixture.
Overall, recent genetic studies highlight the spatially and temporally complex dynamics of the Bantu expansion, with differential levels of admixture among sub-Saharan populations and multiple migration waves. Increasing sample sizes, as well as the number of sampled BSPs and additional ancient genomes, may allow for clarifying the exact migratory route, dating major events, and revealing further fine-scale population structure among BSPs. For a comprehensive review of the population history of Bantu speakers, see Schlebusch and Jakobsson (2018) as well as Choudhury et al. (2021).
Visual summary of key admixture events in Africa. (A) The stepwise spread of lactose persistence from northeastern Africa into eastern Africa and subsequently into southern Africa. (B) Southward migration of Bantu-speaking people through the rainforest to modern-day Angola (ANG) and Zambia (ZMB) before splitting into eBSPs and seBSPs, in concordance with the late-split hypothesis. (C) Extensive admixture between Sahelian populations with European groups in the West and Middle Eastern groups in the East, but only limited gene flow among Sahelian populations. (D) Repetitive gene flow from the Middle East/Europe and sub-Saharan Africa into Northern African populations.
In line with archeological studies, genetic studies of Khoe-San confirmed that pastoralism spread from East Africa to southern Africa by demic diffusion (Breton et al. 2014; Macholdt et al. 2014; Ranciaro et al. 2014; Schlebusch et al. 2017; Skoglund et al. 2017). Khoekhoe-speaking populations (e.g., the Nama), who currently practice a pastoralist lifestyle, have a high-frequency lactase persistence (LP) allele that is also found in East African populations (Schlebusch et al. 2012; Breton et al. 2014; Macholdt et al. 2014). This “East African” LP single nucleotide polymorphism (SNP) (14010G > C) is distinct from the “European” LP SNP (1391 °C > T) and is rare in southern African Bantu-speaking groups (Breton et al. 2014; Macholdt et al. 2014). Among Khoe-San groups, this “East African” LP SNP is found at the highest frequency in the Nama with a frequency of ∼35%, which is much higher than expected given the ∼13% East African admixture fraction in the Nama, suggesting positive selection (Breton et al. 2014; Macholdt et al. 2014). Interestingly, Prendergast et al. found that the “East African” LP allele is largely absent from ancient pastoralist individuals from Kenya and Tanzania, indicating that east African pastoralists were lactose intolerant as recently as 3–1 kya (Prendergast et al. 2019). However, it is also possible that this allele has not been detected in ancient samples due to a limited number of surveyed individuals.
A direct link between Afro-Asiatic–speaking eastern African (i.e., Amhara- or Oromo-related ancestry) and southern African pastoralists has been established by showing that a 1,200-year-old individual from southern Africa, who has genetic similarities with modern Khoekhoe-speaking pastoralist groups (e.g., the Nama), traces ∼40% of their ancestry to a Eurasian admixed group related to a 3,100-year-old pastoralist individual from Luxmanda, Tanzania (Skoglund et al. 2017). Thus, this study indicates that admixture of Khoe-San groups with eastern African pastoralists occurred at least ∼1.2 kya (fig. 4A). Concordantly, another study estimated that all modern Khoe-San populations received 9–30% gene flow from an admixed East African/Eurasian pastoralist group 1.5–1.3 kya (Schlebusch et al. 2017). Furthermore, east African pastoralist contributions to Khoe-San groups are lower on X chromosomes than autosomes (Vicente et al. 2021), indicating that male-biased admixture occurred. Overall, these results suggest that eastern African pastoralists reached southern Africa prior to and independently of Bantu-speaking groups. For a detailed review of the spread of lactase persistence in Africa, see Campbell and Ranciaro (2021).
Multiple Migration Waves of Bantu Speakers
Genetic studies showed that the spread of Bantu languages, agricultural practices, and iron use 5–3 kya was accompanied by multiple migration waves of Bantu speakers from western Africa (i.e., current eastern Nigeria and western Cameroon) to other regions in sub-Saharan Africa (Tishkoff et al. 2009; Schlebusch et al. 2012; Li et al. 2014). Consequently, the Bantu expansion extensively contributed to population structure due to differential levels of admixture with and replacement of local hunter–gatherer groups over the past 3,500 years (Skoglund et al. 2017; Sengupta et al. 2021; González-Santos et al. 2022).
Two major migratory routes of Bantu-speaking populations (BSPs) have been hypothesized. The early-split hypothesis suggests that BSPs split at an early stage north of the rainforest, with one group then moving directly South through the rainforest, whereas the other migrated East, north of the rainforest, toward the Great African Lakes. In contrast, the late-split hypothesis states that BSPs first migrated South through the rainforest before splitting into two groups, with one moving further South and the other one migrating East toward the Great African Lakes. Similarly to phylolinguistics (e.g., Rexová et al. 2006), genetics are in favor of the late-split hypothesis, as eastern BSPs (eBSPs) and south-eastern BSPs (seBSPs) are genetically closer to western BSPs (wBSPs) south of the rainforest (i.e., Angola) than to wBSPs north of the rainforest (Patin et al. 2017). A subsequent study using samples from wider geographic and ethnolinguistic groups showed that eBSPs, seBSPs, and southwestern BSPs (swBSPs) are genetically closest to Bantu speakers from Zambia (Choudhury et al. 2020). Together, these findings suggest that Bantu speakers first migrated South through the rainforest to Angola and subsequently to Zambia before splitting into two groups (fig. 4B).
In western Africa, wBSPs asymmetrically mixed with resident RHG groups, with RHG groups receiving higher amounts of gene flow from wBSPs (Jarvis et al. 2012; Hsieh, Veeramah, et al. 2016; Patin et al. 2017; Lopez et al. 2018). wBSPs in Angola have small amounts of RHG-related ancestry from an admixture event that occurred after the split of BSPs ∼800 ya (Patin et al. 2017), although a recent study inferred a more ancient admixture date of ∼1.9 kya for Bantu speakers in Cabinda, Angola (Tallman et al. 2022). The amount of gene flow from wBSPs into individual RHG groups varied. Whereas the Mbuti and the Biaka have <6% wBSP-related ancestry, the Bezan and the Bongo trace as much as 38.5% and 47.5% to wBSPs, respectively (Patin et al. 2014). This gene flow from wBSPs into RHGs was inferred to have occurred ∼7 kya using models of site-frequency spectra (Hsieh, Veeramah, et al. 2016; Lopez et al. 2018), whereas methods leveraging LD patterns yielded estimates <1 kya (Patin et al. 2014, 2017). Analyses of uniparental markers as well as autosomal and X chromosomal data also showed that this gene flow from wBSPs into RHGs was male-biased (Verdu et al. 2013; Patin et al. 2014). For an excellent review of the interactions between BSPs and RHGs, see Patin and Quintana-Murci (2018).
In eastern Africa, two admixture events 1.5–1 kya and 400–150 years ago have been inferred between wBSPs (∼75% contribution) and an Afro-Asiatic–speaking population from Ethiopia (∼10%) (Patin et al. 2017). These estimates are in slight disagreement with the estimates of Skoglund et al. (2017), who estimated that admixture between Bantu speakers and eastern African pastoralists occurred 800–400 years ago, but are in agreement with 71% Bantu-related ancestry in an ancient Iron Age individual dated to ∼1,160 years ago from the Rift Valley in Kenya (Prendergast et al. 2019).
In South Africa, seBSPs received between 1.5% (e.g., the Tsonga) and 20% (e.g., the Tswana) gene flow from Khoe-San groups during independent admixture events (Sengupta et al. 2021). The exact admixture timings differ between populations (1.7 kya–700 ya), with northern groups showing older dates than southern groups (Sengupta et al. 2021; Tallman et al. 2022). However, Tallman et al. (2022) also reported an older Khoe-San admixture event in the Zulu ∼3 kya. Furthermore, uniparental markers and X chromosomal and autosomal data suggest male-biased seBSPs contributions and female-biased Khoe-San contributions (Bajić et al. 2018; Sengupta et al. 2021). In contrast to the admixture in South Africa, seBSPs appeared to have replaced resident hunter–gatherer populations in Malawi and Mozambique with present-day individuals deriving ≥97% of their ancestry from the Bantu expansion (Skoglund et al. 2017; Tallman et al. 2022). Overall, this suggests multiple migration waves of Bantu speakers or that Khoe-San admixture did not occur immediately.
In contrast to seBSPs, swBSPs appear to have reached southern Africa more recently (∼750 ya), as indicated by more recent admixture of a western African-related source in the Khoisan-speaking Khwe and !Xun from Angola (Busby et al. 2016). This suggests that swBSPs took a different route directly south along the western coast and thus have different recent population histories than seBSPs (fig. 4B).
Genetic studies of uniparental and autosomal markers initially suggested that BSPs are largely genetically homogenous groups of people (i.e., FST ≤ 0.02) (Coelho et al. 2009; Ansari-Pour et al. 2013; Gurdasani et al. 2015; Busby et al. 2016). Despite the modest FST values, fine-scale population structure of BSPs has recently been emphasized (Semo et al. 2020; Sengupta et al. 2021; Tallman et al. 2022). Semo et al. (2020) showed that eBSPs from Mozambique and Angola form a North–South genetic cline of relatedness along the coast from Kenya/Tanzania to South Africa. They also found that genetic homogeneity increases east- and southward, indicating serial founder effects and little admixture with local populations until Bantu speakers reached South Africa. Additionally, Sengupta et al. (2021) found that fine-scale genetic substructure among seBSPs in South Africa correlates well with geography and linguistics and persists even after accounting for differential levels of Khoe-San admixture.
Overall, recent genetic studies highlight the spatially and temporally complex dynamics of the Bantu expansion, with differential levels of admixture among sub-Saharan populations and multiple migration waves. Increasing sample sizes, as well as the number of sampled BSPs and additional ancient genomes, may allow for clarifying the exact migratory route, dating major events, and revealing further fine-scale population structure among BSPs. For a comprehensive review of the population history of Bantu speakers, see Schlebusch and Jakobsson (2018) as well as Choudhury et al. (2021).