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Post by Admin on Sept 26, 2023 22:33:11 GMT
Fig. 1. Population structure in southern Africa. (A) Map showing approximate sample locations. The lightest background color shows the desert and xeric shrublands biome. All samples from Angola are marked with “(A)” in the legend, while samples from the same ethnic group collected in Namibia are marked with “(N).” (B and C) PCA of the populations shown in (A). Plots of PC1 versus PC2 (B) and PC1 versus PC3 (C), with the percentage of variance explained by each component indicated in parentheses. The centroids for each group from the Angolan Namib are shown by black dots. (D) ADMIXTURE analysis for k = 6 (k with the lowest cross-validation error) of an extended dataset of 63 African populations (fig. S3 and tables S1 and S2). The horizontal color bar below the ADMIXTURE barplot indicates the language group. CAR, Central African Rainforest. RESULTS In a principal components analysis (PCA) (31), the Angolan !Xun foragers are most similar to southern African groups speaking languages from the Ju branch of Kx’a, while all other sampled Angolan groups are closer to West Africans and to Bantu-speaking populations (Fig. 1B and fig. S3). Among those groups, the populations from the Angolan Namib display a notable substructure, forming a gradient of genetic differentiation best captured by principal component 3 (PC3), which stretches from the Kuvale and Himba cattle herders to the peripatetic Kwisi and Twa (Fig. 1C and fig. S4). In addition, the differentiation displayed in PC3 is correlated (r = 0.87; P < 0.001) with increasing amounts of an ancestry component revealed at k = 6 by the unsupervised population clustering approach implemented in ADMIXTURE (yellow in Fig. 1D and figs. S5 to S8) (32). This component overlaps with a previously identified “NW-Savannah” ancestry that was found to be especially common in northwestern Namibia among the Southwest Bantu–speaking Himba, Herero, and Ovambo (11, 12). It is also predominant in the Khoekhoe-speaking Damara who are genetically very similar to the Herero and Himba (2, 24) and probably adopted their language from Nama pastoralists with whom they had historically established a peripatetic-like association (text S1) (30). The varying proportions of this ancestry in southwestern Angola and northwestern Namibia seem to be broadly associated with subsistence strategy and socioeconomic status, being on average the lowest in the Nyaneka, Ovambo, and Ovimbundu agropastoralists (18 to 27%) and highest among the peripatetic Tjimba, Twa, and Kwisi (79 to 93%). An analysis of identity-by-descent (IBD) sharing (33) among these populations further indicates that between-group sharing of IBD segments is highest among the peripatetic communities (fig. S9). As the southwestern Angolan pastoral scene is dominated by a highly hierarchized, caste-like matriclanic organization (text S1) (24), it is conceivable that the observed genetic structure was caused by drift and inbreeding associated with the marginalization of peripatetic communities. Alternatively, it is also possible that it reflects different levels of admixture with an unsampled or no longer existing population. To investigate the role of genetic drift, we assessed the levels of genetic diversity in several populations from southwestern Angola and northwestern Namibia by computing for each group the total length of IBD (in centimorgans) segments shared between individuals (33) and the total length (in megabases) of runs of homozygosity (RoHs) per individual (34). We found that in southwestern Angola, the lowest and highest IBD and RoH lengths are found among agropastoralists and peripatetics, respectively (Fig. 2A and fig. S10A). Moreover, the peripatetic groups display significantly higher mean lengths of shared IBD segments above 10 cM than other southern African populations (Wilcoxon rank sum test, W = 0, P = 0.0016) (Fig. 2B). Estimates of effective population size (Ne) across time leveraging information from shared IBD segments (35) further reveal strong bottlenecks in peripatetic groups starting ~20 generations ago (fig. S11). Together, these results suggest that drift played a major role in the genetic differentiation of the Angolan communities with a lower socioeconomic status.
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Post by Admin on Sept 27, 2023 21:16:28 GMT
Southern Africa holds possibly the greatest human genetic diversity on Earth and new research reveals that diversity is in better shape than had been suspected. When some languages from the Namib Desert died out, anthropologists feared the populations that spoke them had gone too, but new research indicates the people have maintained a genetic identity even without their native tongue. It is a common pattern that biological diversity is greatest in the place where a species or family originated. Although some non-scientists beg to differ, anthropologists would know humans evolved in Africa even without the fossil record simply by looking at how much greater our diversity is there. This can be seen most dramatically among the inhabitants of the Kalahari and Namib Deserts of south-eastern Africa. The Namib is a long, thin desert hugging the coast of Namibia and parts of Angola and South Africa. Wars disrupted the northern part for decades and interfered with attempts to study this diversity. Stabilization allowed representatives of the Portuguese-Angolan TwinLab to fill in some of the gaps, identifying patterns in ancient human prehistory in the process. “We were able to locate groups which were thought to have disappeared more than 50 years ago,” Dr Jorge Rocha of the University of Porto said in a statement. One of these is the Kwepe, who used to speak Kwadi, a language whose disappearance was thought to mark the end of their separation from neighboring populations. “Kwadi was a click language that shared a common ancestor with the Khoe languages spoken by foragers and herders across southern Africa,” said Dr Ann-Maria Fehn of the Centro de Investigação em Biodiversidade e Recursos Genéticos. As part of the project, the team found two survivors who can remember much of the language living near the mouth of the Kuroka River, whom Fehn was able to interview. Using a combination of genetic and linguistic analysis the researchers investigated the relationships between Angolan Namib dwellers. They found the biggest genetic differences between populations with contrasting lifestyles – farmers versus herders versus more traditional hunter-gatherers for example. Kwadi may be almost gone, but the team found the descendants of those who spoke it retain their genetic distinctiveness that traces back to a time before Bantu-speaking farmers moved into the area. “A lot of our efforts were placed in understanding how much of this local variation and global eccentricity was caused by genetic drift – a random process that disproportionately affects small populations and by admixtures from vanished populations,” said Dr Sandra Oliverira of the University of Bern. "Previous studies revealed that foragers from the Kalahari desert descend from an ancestral population who was the first to split from all other extant humans,” added Professor Mark Stoneking of the Max Plank Institute for Evolutionary Anthropology, who pioneered genome-wide studies of southern African desert populations. “Our results consistently place the newly identified ancestry within the same ancestral lineage but suggest that the Namib-related ancestry diverged from all other southern African ancestries, followed by a split of northern and southern Kalahari ancestries." The Angolan Namib and northern areas of Namibia are the only regions where this genetic heritage survives in any numbers. The research allowed the team to reconstruct the migrations of the region’s populations. The Khoe-Kwadi speakers dispersed across the area around 2,000 years ago, possibly from what is now Tanzania. This makes them relative late-comers compared to the first inhabitants, who spoke Khoe languages and may have been in the area for hundreds of thousands of years. The Bantu speakers arrived 200-500 years late from West and Central Africa. Khoe language speakers survive in the area, and share ancestry with the more heavily studied Kalahari populations, while the Bantu speakers diverge much less from the rest of humanity. The populations that once spoke Kwadi, before adopting Bantu languages in recent decades, are the missing piece in humanity’s jigsaw identified in this study. The study is open access in Science Advances. www.science.org/doi/10.1126/sciadv.adh3822
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Post by Admin on Sept 30, 2023 16:09:45 GMT
Fig. 2. IBD sharing in southern Africa. (A) Violin plots showing the distribution of total IBD length (in centimorgans) shared within groups. The thick and thin black lines represent the interquartile range and the upper and lower adjacent values, respectively; the central dot shows the median. (B) Mean total IBD length for different length categories. We next used CHROMOPAINTER to investigate the genetic differentiation of the peripatetic groups while accounting for the effects of genetic drift (Fig. 3 and fig. S12). In CHROMOPAINTER, haploid genomes from recipient individuals are decomposed into chunks, each copied from the best-matching haplotype in a pool of donor populations (36). In populations where high levels of differentiation are mainly due to genetic drift, recipients tend to copy most DNA chunks from donors belonging to their own or closely related groups, obscuring ancestry shared with other groups (37). As outlined by van Dorp et al. (37), if recipients are prevented from finding their best-matching haplotypes inside their own group, the effects of drift are attenuated and genetic relationships to other groups can be better evaluated. Mimicking this approach, we did not allow pastoralists and peripatetics from southwestern Angola and northwestern Namibia to copy haplotypes from each other to evaluate whether their genetic distinctiveness could be attributed to differences in their ancestry composition before recent isolation. Under these conditions, the Kwepe, Twa, and Kwisi display very similar copying profiles that are clearly differentiated from the profiles of their pastoralist (Fig. 3, C and D) and agropastoralist (fig. S12, C and D) neighbors. The profile of the Tjimba is close but not identical to the other peripatetics, while the Damara fully align with the Bantu-speaking pastoralists (Fig. 3, C and D, and fig. S11, C and D). Comparisons of profile differences between each group and representative pastoralist (Kuvale) and agropastoralist (Ovimbundu) populations further show that peripatetic groups have decreased amounts of Bantu and West African–related ancestries, while copying elevated numbers of haplotypes from groups carrying southern African forager ancestry and, to a lesser extent, the Mbuti rain forest hunter-gatherers and several East African groups (Fig. 3, A and B, and fig. S12, A and B). This finding highlights the impact of differential admixture with pre-Bantu populations and suggests that drift and inbreeding were not the only factors influencing their genetic differentiation.
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Post by Admin on Oct 1, 2023 19:23:28 GMT
Fig. 3. Chromopainter profiles for southwestern Angolan and northwestern Namibian groups. Bantu-speaking agropastoralists (Ovimbundu, Nyaneka, and Ovambo) are included as donors, together with more distantly related African groups. (A) Chromopainter coancestry matrix. The color gradient indicates the average number of DNA chunks a recipient group (y axis) copies from the donor populations [x axis in (B)]. (B) Differences between the number of DNA chunks copied by each recipient group from the donor populations in the x axis, and the number of DNA chunks copied by the Kuvale—used here as a baseline. (C) Average distance (TVDxy) between copying profiles. (D) Multidimensional scaling calculated on the TVDxy distances. The stress value (0.0073) indicates low distortion of population relationships by the two-dimensional plot (75). To further assess the role of pre-Bantu admixture while including ancient individuals as potential sources (16), we used qpAdm (38). By testing the fit of different mixture models, we confirm that the peripatetic peoples (Kwepe, Kwisi, Tjimba, and Twa) diverge from their neighbors (Himba, Kuvale, and Nyaneka) by displaying higher amounts (10 to 14%) of southern African forager ancestry [here represented by an ancient South Africa 2000 before the present (B.P.) genome] and a detectable contribution (4 to 5%) from East Africa, best matched by an ancient genome retrieved from a pastoral context in Tanzania (Luxmanda 3100 B.P.) (Fig. 4, text S2, fig. S13, and tables S3 and S4).
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Post by Admin on Oct 2, 2023 21:17:45 GMT
Fig. 4. Ancestry proportions estimated with qpAdm in southern African populations. SEs (black bars) were calculated with a weighted block jackknife. BP, before the present. Our inference of the relative order of mixing of the Bantu-, autochthonous southern African–, and East African–related ancestries in southwestern Angola and northwestern Namibian groups, based on ancestry covariances (39), indicates that the first admixture event involved southern African– and East African–related ancestries (table S5), in accordance with the archaeological data suggesting that pastoralism was introduced from eastern into southern Africa before the Bantu expansion (40). While we could not obtain reliable estimates for this admixture event (text S3), we detected signals of admixture between Bantu and the previously admixed pre-Bantu ancestries dating to ~600 to 1100 years ago by using Wavelets, GLOBETTROTER, and ALDER (fig. S14 and tables S5 to S7). As these estimates postdate the arrival of the first Bantu speakers in southern Africa (~1.8 to 1.5 ka ago), they may either point toward a delayed colonization of areas in and around the Namib Desert or to a delayed onset of admixture between resident and incoming populations. Alternatively, multiple pulses of admixture might have occurred at different times, in which case the inferred dates would be intermediate between the oldest and the most recent admixture events (41). Similar to the Angolan Namib, other areas where languages of the Khoe-Kwadi family are spoken today were strongly shaped by contact and display highly variable amounts of southern African–, East African–, and Bantu-related ancestries (Fig. 4). To reconstruct the contact histories of the Khoe-Kwadi following their arrival to southern Africa, we carried out local ancestry decomposition (42) and analyzed the population relationships within each of the three major settlement layers of southern Africa (figs. S15 to S18). On the basis of PCA projections, we found that the East African ancestry identified in the genomes of Khoe-Kwadi speakers and other southern Africans is related to pastoralist groups clustering around the ancient Tanzania Luxmanda individual (3100 B.P.) (fig. S16). Some Nama and ǂKhomani individuals are additionally related to East African groups with high amounts of Eurasian ancestry, likely due to admixture with Europeans during colonial times. Ancestry-specific PCA (figs. S17 and S18) and clustering analysis based on average pairwise differences (fig. S19) further show that southern African– and Bantu-related ancestries of Khoe-Kwadi groups are highly heterogeneous and mirror the genetic composition of their neighbors. This pattern becomes especially clear when the local ancestry information is combined with IBD inferences to obtain southern African– and Bantu-specific IBD sharing (Fig. 5 and fig. S20). For example, the Khwe from the northern Kalahari Basin fringe have southern African– and Bantu-related ancestries that are similar to those of !Xun foragers and Southwest Bantu agropastoral groups living in the same area (Fig. 5 and fig. S20). To their south, Khoe speakers from the Central Kalahari share southern African–related ancestry with the neighboring Taa and ǂHoan, and Bantu-related ancestry with local East Bantu speakers (Fig. 5 and fig. S20). The southern African– and Bantu-related ancestries of the Khoekhoe-speaking Nama reflect their migration history along the Atlantic coast of southern Africa. While their southern African–related ancestry resembles that of the ǂKhomani, who inhabit the southernmost areas of the Kalahari, their Bantu ancestry is similar to that of Southwest Bantu–speaking groups from northwestern Namibia (Fig. 5 and fig. S20). As the Nama are known to be a branch of Khoekhoe-speaking groups who migrated northward from South Africa (43), it is likely that they first acquired their southern African–related ancestry in the South and admixed with Bantu populations only later after reaching Namibia.
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