Abstract Multiple lines of genetic and archaeological evidence suggest that there were major demographic changes in the terminal Late Pleistocene epoch and early Holocene epoch of sub-Saharan Africa 1–4 . Inferences about this period are challenging to make because demographic shifts in the past 5,000 years have obscured the structures of more ancient populations 3,5 . Here we present genome-wide ancient DNA data for six individuals from eastern and south-central Africa spanning the past approximately 18,000 years (doubling the time depth of sub-Saharan African ancient DNA), increase the data quality for 15 previously published ancient individuals and analyse these alongside data from 13 other published ancient individuals. The ancestry of the individuals in our study area can be modelled as a geographically structured mixture of three highly divergent source populations, probably reflecting Pleistocene interactions around 80–20 thousand years ago, including deeply diverged eastern and southern African lineages, plus a previously unappreciated ubiquitous distribution of ancestry that occurs in highest proportion today in central African rainforest hunter-gatherers. Once established, this structure remained highly stable, with limited long-range gene flow. These results provide a new line of genetic evidence in support of hypotheses that have emerged from archaeological analyses but remain contested, suggesting increasing regionalization at the end of the Pleistocene epoch.
more »
« less
Genomic evidence for shared common ancestry of East African hunting-gathering populations and insights into local adaptation
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.
more » « less- NSF-PAR ID:
- 10086260
- Publisher / Repository:
- Proceedings of the National Academy of Sciences
- Date Published:
- Journal Name:
- Proceedings of the National Academy of Sciences
- Volume:
- 116
- Issue:
- 10
- ISSN:
- 0027-8424
- Page Range / eLocation ID:
- p. 4166-4175
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Admixture in Africanized honey bees ( Apis mellifera ) from Panamá to San Diego, California (U.S.A.)more » « less
Abstract The Africanized honey bee (AHB) is a New World amalgamation of several subspecies of the western honey bee (
Apis mellifera ), a diverse taxon historically grouped into four major biogeographic lineages: A (African), M (Western European), C (Eastern European), and O (Middle Eastern). In 1956, accidental release of experimentally bred “Africanized” hybrids from a research apiary in Sao Paulo, Brazil initiated a hybrid species expansion that now extends from northern Argentina to northern California (U.S.A.). Here, we assess nuclear admixture and mitochondrial ancestry in 60 bees from four countries (Panamá; Costa Rica, Mexico; U.S.A) across this expansive range to assess ancestry of AHB several decades following initial introduction and test the prediction that African ancestry decreases with increasing latitude. We find that AHB nuclear genomes from Central America and Mexico have predominately African genomes (76%–89%) with smaller contributions from Western and Eastern European lineages. Similarly, nearly all honey bees from Central America and Mexico possess mitochondrial ancestry from the African lineage with few individuals having European mitochondria. In contrast, AHB from San Diego (CA) shows markedly lower African ancestry (38%) with substantial genomic contributions from all four major honey bee lineages and mitochondrial ancestry from all four clades as well. Genetic diversity measures from all New World populations equal or exceed those of ancestral populations. Interestingly, the feral honey bee population of San Diego emerges as a reservoir of diverse admixture and high genetic diversity, making it a potentially rich source of genetic material for honey bee breeding. -
more » « less
Abstract Preserving biodiversity under rapidly changing climate conditions is challenging. One approach for estimating impacts and their magnitude is to model current relationships between genomic and environmental data and then to forecast those relationships under future climate scenarios. In this way, understanding future genomic and environmental relationships can help guide management decisions, such as where to establish new protected areas where populations might be buffered from high temperatures or major changes in rainfall. However, climate warming is only one of many anthropogenic threats one must consider in rapidly developing parts of the world. In Central Africa, deforestation, mining, and infrastructure development are accelerating population declines of rainforest species. Here we investigate multiple anthropogenic threats in a Central African rainforest songbird, the little greenbul (
Andropadus virens ). We examine current climate and genomic variation in order to explore the association between genome and environment under future climate conditions. Specifically, we estimateGenomic Vulnerability , defined as the mismatch between current and predicted future genomic variation based on genotype–environment relationships modeled across contemporary populations. We do so while considering other anthropogenic impacts. We find that coastal and central Cameroon populations will require the greatest shifts in adaptive genomic variation, because both climate and land use in these areas are predicted to change dramatically. In contrast, in the more northern forest–savanna ecotones, genomic shifts required to keep pace with climate will be more moderate, and other anthropogenic impacts are expected to be comparatively low in magnitude. While an analysis of diverse taxa will be necessary for making comprehensive conservation decisions, the species‐specific results presented illustrate how evolutionary genomics and other anthropogenic threats may be mapped and used to inform mitigation efforts. To this end, we present an integrated conceptual model demonstrating how the approach for a single species can be expanded to many taxonomically diverse species. -
more » « less
Abstract Background Curated databases of genetic variants assist clinicians and researchers in interpreting genetic variation. Yet, these databases contain some misclassified variants. It is unclear whether variant misclassification is abating as these databases rapidly grow and implement new guidelines.
Methods Using archives of ClinVar and HGMD, we investigated how variant misclassification has changed over 6 years, across different ancestry groups. We considered inborn errors of metabolism (IEMs) screened in newborns as a model system because these disorders are often highly penetrant with neonatal phenotypes. We used samples from the 1000 Genomes Project (1KGP) to identify individuals with genotypes that were classified by the databases as pathogenic. Due to the rarity of IEMs, nearly all such classified pathogenic genotypes indicate likely variant misclassification in ClinVar or HGMD.
Results While the false-positive rates of both ClinVar and HGMD have improved over time, HGMD variants currently imply two orders of magnitude more affected individuals in 1KGP than ClinVar variants. We observed that African ancestry individuals have a significantly increased chance of being incorrectly indicated to be affected by a screened IEM when HGMD variants are used. However, this bias affecting genomes of African ancestry was no longer significant once common variants were removed in accordance with recent variant classification guidelines. We discovered that ClinVar variants classified as Pathogenic or Likely Pathogenic are reclassified sixfold more often than DM or DM? variants in HGMD, which has likely resulted in ClinVar’s lower false-positive rate.
Conclusions Considering misclassified variants that have since been reclassified reveals our increasing understanding of rare genetic variation. We found that variant classification guidelines and allele frequency databases comprising genetically diverse samples are important factors in reclassification. We also discovered that ClinVar variants common in European and South Asian individuals were more likely to be reclassified to a lower confidence category, perhaps due to an increased chance of these variants being classified by multiple submitters. We discuss features for variant classification databases that would support their continued improvement.
-
more » « less
Abstract Forests are being converted to agriculture throughout the Afrotropics, driving declines in sensitive rainforest taxa such as understorey birds. The ongoing expansion of cocoa agriculture, a common small‐scale farming commodity, has contributed to the loss of 80% rainforest cover in some African countries. African cocoa farms may provide habitat for biodiversity, yet little is known about their suitability for vertebrate fauna, or the effect of farm management on animal communities.
Here, we report the first in‐depth investigation into avian diversity and community composition in African cocoa, by assembling a dataset of 9,566 individual birds caught across 83 sites over 30 years in Southern Cameroon. We compared bird diversity in mature forest and cocoa using measures of alpha, beta and gamma diversity, and we investigated the effect of cocoa farm shade and forest cover on bird communities.
Gamma diversity was higher in cocoa than forest, though alpha diversity was similar, indicating a higher dissimilarity (beta diversity) between cocoa farms. Cocoa farms differed from forest in community composition, with a distinctive decrease in relative abundance of insectivores, forest specialists and ant‐followers and an increase in frugivores.
Within cocoa farms, we found that farms with high shade cover in forested landscapes resulted in higher relative abundance and richness of sensitive forest species; shady farms contained up to five times the proportion of forest specialists than sunny farms.
Synthesis and applications . Sunny African cocoa farms were less able to support sensitive bird guilds compared with shaded farms in forested landscapes. Our findings support the notion that certain ecological and dietary guilds, such as ant‐followers and forest specialists are disproportionately affected by land‐use change. In light of the current push to increase cocoa production in sub‐Saharan Africa, our results provide policymakers opportunities for more wildlife‐friendly cocoa schemes that maximize avian diversity.
