The genetic legacy of the expansion of Bantu-speaking peoples in Africa

Fortes-Lima, César; Burgarella, Concetta; Hammarén, Rickard; Eriksson, Anders; Vicente, Mário; Jolly, Cécile; Semo, Armando; Gunnink, Hilde; Pacchiarotti, Sara; Mundeke, Leon; Matonda, Igor; Muluwa, Joseph Koni; Coutros, Peter R.; Nyambe, Terry S.; Cikomola, Cirhuza; Coetzee, Vinet; Castro, Minique de; Ebbesen, Peter; Delanghe, Joris; Stoneking, Mark; Barham, Lawrence; Lombard, Marlize; Meyer, Anja; Steyn, Maryna; Malmström, Helena; Rocha, Jorge; Soodyall, Himla; Pakendorf, Brigitte; Bostoen, Koen; Schlebusch, Carina M.

doi:10.1101/2023.04.03.535432

Cited by 4 publications

References 49 publications

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Hunter–gatherer genetics research: Importance and avenues

Padilla-Iglesias,

Derkx

2024

Evolut. Hum. Sci.

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Major developments in the field of genetics in the past few decades have revolutionised notions of what it means to be human. Although currently only a few populations around the world practise a hunting and gathering lifestyle, this mode of subsistence has characterised members of our species since its very origins and allowed us to migrate across the planet. Therefore, the geographical distribution of hunter-gatherer populations, dependence on local ecosystems, and connections to past populations and neighbouring groups has provided unique insights into our evolutionary origins. However, given the vulnerable status of hunter-gatherers worldwide, the development of the field of anthropological genetics requires that we reevaluate how we conduct research with these communities. Here, we review how the inclusion of hunter-gatherer populations in genetics studies has advanced our understanding of human origins, ancient population migrations and interactions as well as phenotypic adaptations and adaptability to different environments, and the important scientific and medical applications of these advancements. At the same time, we highlight the necessity to address yet unresolved questions and identify areas in which the field may benefit from improvements.

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Hunter–gatherer genetics research: Importance and avenues

Padilla-Iglesias,

Derkx

2024

Evolut. Hum. Sci.

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Dated Holocene Human Remains From South Africa: Recalibration and Broad Contextualization

Loftus,

Lombard,

Steyn

2024

Radiocarbon

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The study of human remains can provide valuable information about aspects of past populations. Here we present an updated database consisting of 590 radiocarbon (14C) dates for human remains from Holocene South Africa before European contact. We calibrated or recalibrated all the previously published dates using the most recent calibration curve for the southern hemisphere. Each date is roughly georeferenced and plotted according to their Stone Age or Iron Age contexts, revealing the broad distribution pattern of dated Holocene human remains across South Africa—perhaps reflecting aspects of past population distribution and densities, but also underscoring historical collection practices, archaeological research focus, and preservation conditions. We use Kernel Density Estimation models to show peaks and troughs of dated remains through time, with Later Stone Age peaks at ∼5.5 ka cal BP, ∼2 ka cal BP and ∼0.5 ka cal BP, and Iron Age peaks ∼1.1 ka cal BP and ∼0.5 ka cal BP, some of which show broad correspondence to climatic data. Our data, based on dated remains only, do not provide a full reflection of past populations, and our large-scale, coarse-grained analysis cannot yet assess the reasons for the peaks in dated human remains in detail. Yet, the study provides a new resource, and a data-driven overview that highlights aspects to be explored with further contextual analyses against the available archaeological records, population histories and climatic indicators through time and across space.

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Imputation Accuracy Across Global Human Populations

Cahoon,

Rui,

Tang

et al. 2023

Preprint

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Genotype imputation is now fundamental for genome-wide association studies but lacks fairness due to the underrepresentation of populations with non-European ancestries. The state-of-the-art imputation reference panel released by the Trans-Omics for Precision Medicine (TOPMed) initiative contains a substantial number of admixed African-ancestry and Hispanic/Latino samples to impute these populations with nearly the same efficacy as European-ancestry cohorts. However, imputation for populations primarily residing outside of North America may still fall short in performance due to persisting underrepresentation. To illustrate this point, we curated genome-wide array data from 23 publications published between 2008 to 2021. In total, we imputed over 43k individuals across 123 populations around the world. We identified a number of populations where imputation accuracy paled in comparison to that of European-ancestry populations. For instance, the mean imputation r-squared (Rsq) for 1-5% alleles in Saudi Arabians (N=1061), Vietnamese (N=1264), Thai (N=2435), and Papua New Guineans (N=776) were 0.79, 0.78, 0.76, and 0.62, respectively. In contrast, the mean Rsq ranged from 0.90 to 0.93 for comparable European populations matched in sample size and SNP content. Outside of Africa and Latin America, Rsq appeared to decrease as genetic distances to European reference increased, as predicted. Further analysis using sequencing data as ground truth suggested that imputation software may inflate imputation quality for non-European populations, implying that these quality estimates may be lower than initially estimated. To improve imputation quality, we assessed a strategy using meta-imputation to combine results from TOPMed with smaller population-specific reference panels, using 1496 whole genome sequenced individuals from Taiwan Biobank as an example reference. While we found that meta-imputation in this design did not improve Rsq genome-wide, Southeast Asian populations such as Filipino and Vietnamese experience a 0.16 and 0.11 increase in average imputation Rsq, respectively, for alleles extremely rare in Europeans (< 0.1% frequency) but more common (>1%) in East Asians. Taken together, our analysis suggests that meta-imputation may complement a large reference panel such as that of TOPMed for underrepresented cohorts. Nevertheless, reference panels must ultimately strive to increase diversity and size to promote equity within genetics research.

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The genetic legacy of the expansion of Bantu-speaking peoples in Africa

Cited by 4 publications

References 49 publications

Hunter–gatherer genetics research: Importance and avenues

Hunter–gatherer genetics research: Importance and avenues

Dated Holocene Human Remains From South Africa: Recalibration and Broad Contextualization

Imputation Accuracy Across Global Human Populations

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