Genetic affinities among southern Africa hunter-gatherers and the impact of admixing farmer and herder populations
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PROVIDER: PRJEB31751 | ENA |
REPOSITORIES: ENA
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Project description:Southern African indigenous groups, traditionally hunter-gatherers (San) and herders (Khoekhoe), are commonly referred to as "Khoe-San" populations and have a long history in southern Africa. Their ancestors were largely isolated up until ∼2,000 years ago before the arrival of pastoralists and farmers in southern Africa. Assessing relationships among regional Khoe-San groups has been challenging due to admixture with immigrant populations that obscure past population affinities and gene flow among these autochthonous communities. We re-evaluate a combined genome-wide data set of previously published southern Africa Khoe-San populations in conjunction with novel data from Khoe-San individuals collected in Xade (Central Kalahari Game Reserve, Botswana) prior to their resettlement outside the reserve. After excluding regions in the genome that trace their ancestry to recent migrant groups, the genetic diversity of 20 Khoe-San groups fitted an isolation-by-distance model. Even though isolation-by-distance explained most genetic affinities between the different autochthonous groups, additional signals of contact between Khoe-San groups could be detected. For instance, we found stronger genetic affinities, than what would be explained by isolation-by-distance gene flow, between the two geographically separated Khoe-San groups, who speak branches of the Kx'a-language family (ǂHoan and Ju). We also scanned the genome-wide data for signals of adaptive gene flow from farmers/herders into Khoe-San groups and identified a number of genomic regions potentially introduced by the arrival of the new groups. This study provides a comprehensive picture of affinities among Khoe-San groups, prior to the arrival of recent migrants, and found that these affinities are primarily determined by the geographic landscape.
| S-EPMC6735883 | biostudies-literature
Project description:Genotype data from 50 Khoe-San individuals from Xade and 1 individual from Ghanzi in Botswana. The data was typed in Illumina Omni2.5-Octo BeadChip.
2019-04-26 | E-MTAB-7813 | biostudies-arrayexpress
Project description:The genetic structure of the indigenous hunter-gatherer peoples of Southern Africa, the oldest known lineage of modern man, holds an important key to understanding humanity's early history. Previously sequenced human genomes have been limited to recently diverged populations. Here we present the first complete genome sequences of an indigenous hunter-gatherer from the Kalahari Desert and of a Bantu from Southern Africa, as well as protein-coding regions from an additional three hunter-gatherers from disparate regions of the Kalahari. We characterize the extent of whole-genome and exome diversity among the five men, reporting 1.3 million novel DNA differences genome-wide, and 13,146 novel amino-acid variants. These data allow genetic relationships among Southern African foragers and neighboring agriculturalists to be traced more accurately than was previously possible. Adding the described variants to current databases will facilitate inclusion of Southern Africans in medical research efforts.
2010-02-18 | GSE19048 | GEO
Project description:The genetic structure of the indigenous hunter-gatherer peoples of Southern Africa, the oldest known lineage of modern man, holds an important key to understanding humanity's early history. Previously sequenced human genomes have been limited to recently diverged populations. Here we present the first complete genome sequences of an indigenous hunter-gatherer from the Kalahari Desert and of a Bantu from Southern Africa, as well as protein-coding regions from an additional three hunter-gatherers from disparate regions of the Kalahari. We characterize the extent of whole-genome and exome diversity among the five men, reporting 1.3 million novel DNA differences genome-wide, and 13,146 novel amino-acid variants. These data allow genetic relationships among Southern African foragers and neighboring agriculturalists to be traced more accurately than was previously possible. Adding the described variants to current databases will facilitate inclusion of Southern Africans in medical research efforts. Copy number differences between NA18507 and KB1 were predicted from the depth of whole-genome shotgun sequence reads. These predictions were then validated using array-CGH using a a genome-wide design as well as a custom design targeted at specific regions of copy number difference
2010-02-17 | E-GEOD-19048 | biostudies-arrayexpress
Project description:Genetic Insights into Italy's Epigravettian Hunter-Gatherers
| PRJEB90269 | ENA
Project description:We examine from whom children learn in mobile hunter-gatherers, a way of life that characterized much of human history. Recent studies on the modes of transmission in hunter-gatherers are reviewed before presenting an analysis of five modes of transmission described by Cavalli-Sforza and Feldman [L. L. Cavalli-Sforza, M. W. Feldman, Cultural Transmission and Evolution: A Quantitative Approach (1981)] but not previously evaluated in hunter-gatherer research. We also present two modes of group transmission, conformist transmission, and concerted transmission, seldom mentioned in hunter-gatherer social learning research, and propose a unique mode of group transmission called cumulative transmission. The analysis of the additional modes of transmission indicated that cultural evolutionary signatures of vertical transmission, such as the conservation of cultural traits, have been underestimated because previous studies have seldom considered remote generations or distinguished intrafamilial from extrafamilial horizontal and oblique transmission. However, field data also indicate that hunter-gatherer children interacted with and learned from many nongenetically related individuals; about half of children's and adolescents' horizontal and oblique social learning came from nongenetically related individuals. Intimate living conditions of hunter-gatherers provide opportunities for group transmission, and ethnographic evidence presented demonstrates that at least three types of group transmission exist. All three forms of group transmission theoretically contribute to the conservation of culture, homogeneity of intracultural diversity, and high intercultural diversity. Analysis of additional modes of oblique and horizontal transmission and discussion of previous and unique modes of group transmission demonstrate the various mechanisms by which hunter-gatherer children learn and how cultures are conserved and contribute to cumulative culture.
| S-EPMC11621818 | biostudies-literature
Project description:It has long been claimed that certain configurations of facial movements are universally recognized as emotional expressions because they evolved to signal emotional information in situations that posed fitness challenges for our hunting and gathering hominin ancestors. Experiments from the last decade have called this particular evolutionary hypothesis into doubt by studying emotion perception in a wider sample of small-scale societies with discovery-based research methods. We replicate these newer findings in the Hadza of Northern Tanzania; the Hadza are semi-nomadic hunters and gatherers who live in tight-knit social units and collect wild foods for a large portion of their diet, making them a particularly relevant population for testing evolutionary hypotheses about emotion. Across two studies, we found little evidence of universal emotion perception. Rather, our findings are consistent with the hypothesis that people infer emotional meaning in facial movements using emotion knowledge embrained by cultural learning.
| S-EPMC7051983 | biostudies-literature
Project description:This paper explores childhood social learning among Aka and Bofi hunter-gatherers in Central Africa. Existing literature suggests that hunter-gatherer social learning is primarily vertical (parent-to-child) and that teaching is rare. We use behavioural observations, open-ended and semi-structured interviews, and informal and anecdotal observations to examine the modes (e.g. vertical versus horizontal/oblique) and processes (e.g. teaching versus observation and imitation) of cultural transmission. Cultural and demographic contexts of social learning associated with the modes and processes of cultural transmission are described. Hunter-gatherer social learning occurred early, was relatively rapid, primarily vertical under age 5 and oblique and horizontal between the ages of 6 and 12. Pedagogy and other forms of teaching existed as early as 12 months of age, but were relatively infrequent by comparison to other processes of social learning such as observation and imitation.
| S-EPMC3049106 | biostudies-other
Project description:Recent studies of the evolution of religion have revealed the cognitive underpinnings of belief in supernatural agents, the role of ritual in promoting cooperation, and the contribution of morally punishing high gods to the growth and stabilization of human society. The universality of religion across human society points to a deep evolutionary past. However, specific traits of nascent religiosity, and the sequence in which they emerged, have remained unknown. Here we reconstruct the evolution of religious beliefs and behaviors in early modern humans using a global sample of hunter-gatherers and seven traits describing hunter-gatherer religiosity: animism, belief in an afterlife, shamanism, ancestor worship, high gods, and worship of ancestors or high gods who are active in human affairs. We reconstruct ancestral character states using a time-calibrated supertree based on published phylogenetic trees and linguistic classification and then test for correlated evolution between the characters and for the direction of cultural change. Results indicate that the oldest trait of religion, present in the most recent common ancestor of present-day hunter-gatherers, was animism, in agreement with long-standing beliefs about the fundamental role of this trait. Belief in an afterlife emerged, followed by shamanism and ancestor worship. Ancestor spirits or high gods who are active in human affairs were absent in early humans, suggesting a deep history for the egalitarian nature of hunter-gatherer societies. There is a significant positive relationship between most characters investigated, but the trait "high gods" stands apart, suggesting that belief in a single creator deity can emerge in a society regardless of other aspects of its religion.
| S-EPMC4958132 | biostudies-literature
Project description:Human gut microbiota directly influences health and provides an extra means of adaptive potential to different lifestyles. To explore variation in gut microbiota and to understand how these bacteria may have co-evolved with humans, here we investigate the phylogenetic diversity and metabolite production of the gut microbiota from a community of human hunter-gatherers, the Hadza of Tanzania. We show that the Hadza have higher levels of microbial richness and biodiversity than Italian urban controls. Further comparisons with two rural farming African groups illustrate other features unique to Hadza that can be linked to a foraging lifestyle. These include absence of Bifidobacterium and differences in microbial composition between the sexes that probably reflect sexual division of labour. Furthermore, enrichment in Prevotella, Treponema and unclassified Bacteroidetes, as well as a peculiar arrangement of Clostridiales taxa, may enhance the Hadza's ability to digest and extract valuable nutrition from fibrous plant foods.
| S-EPMC3996546 | biostudies-literature