The demographic history and mutational load of African hunter-gatherers and farmers

Abstract

The distribution of deleterious genetic variation across human populations is a key issue in evolutionary biology and medical genetics. However, the impact of different modes of subsistence on recent changes in population size, patterns of gene flow, and deleterious mutational load remains unclear. Here, we report high-coverage exome sequencing data from various populations of rainforest hunter-gatherers and farmers from central Africa. We find that the recent demographic histories of hunter-gatherers and farmers differed considerably, with population collapses for hunter-gatherers and expansions for farmers, accompanied by increased gene flow. We show that purifying selection against deleterious alleles is of similar efficiency across African populations, in contrast with Europeans where we detect weaker purifying selection. Furthermore, the per-individual mutation load of rainforest huntergatherers is similar to that of farmers, under both additive and recessive models. Our results indicate that differences in the cultural practices and demographic regimes of African populations have not resulted in large differences in mutational burden, and highlight the beneficial role of gene flow in reshaping the distribution of deleterious genetic variation across human populations.not peer-reviewed)

Inferring Genome-Wide Correlations of Mutation Fitness Effects between Populations

“…Experiments suggest that stressful environments can alter DFEs between populations ( Wang et al 2014 ). Previous population genetic studies also have found evidence for differences in marginal DFEs between populations of humans ( Boyko et al 2008 ; Lopez et al 2018 ) and also between populations of other primates ( Ma et al 2013 ; Castellano et al 2019 ; Tataru and Bataillon 2019 ). Although we assumed that the mean and the variance of mutation fitness effects did not differ between the two populations in our models for the joint DFE, those previous studies found only slight differences and our simulation study suggests that inferences of the DFE correlation are robust to relatively large differences in marginal DFEs ( fig.…”

Genomic inference of a human super bottleneck in Mid-Pleistocene transition

“…African populations have complex population structure (Hsieh et al, 2016;Lopez et al, 2018;Schlebusch and Jakobsson, 2018;Skoglund et al, 2017), and a complex population structure model is proposed for African and European populations (Lopez et al, 2018) (Figure S35). To address the effects of population structure, we simulated data for a western rainforest hunter-gatherer (wRHG) and a western farmer (wARG) population and estimated their demographic histories (Figure S35).…”

Searching for archaic contribution in Africa

“…Recent studies looking at African hunter-gatherer and farmer populations have explored how deleterious genetic variation amongst human populations is affected by changes in population size and gene flow (Lopez et al 2018). Specifically, hunter-gatherers are efficient in purifying selection despite having a recent population collapse (Simons et al 2014;Lopez et al 2018).…”

“…Recent studies looking at African hunter-gatherer and farmer populations have explored how deleterious genetic variation amongst human populations is affected by changes in population size and gene flow (Lopez et al 2018). Specifically, hunter-gatherers are efficient in purifying selection despite having a recent population collapse (Simons et al 2014;Lopez et al 2018). Long-term selection against archaic introgression in Africa has not been looked at although recent studies have shown that non-African populations demonstrate selection against introgression in regulatory regions more than in protein-coding regions (Petr et al 2019).…”