Whole-genome sequence analysis of a Pan African set of samples reveals archaic gene flow from an extinct basal population of modern humans into sub-Saharan populations

Abstract

Background Population demography and gene flow among African groups, as well as the putative archaic introgression of ancient hominins, have been poorly explored at the genome level. Results Here, we examine 15 African populations covering all major continental linguistic groups, ecosystems, and lifestyles within Africa through analysis of whole-genome sequence data of 21 individuals sequenced at deep coverage. We observe a remarkable correlation among genetic diversity and geographic distance, with the hunter-gatherer groups being more genetically differentiated and having larger effective population sizes throughout most modern-human history. Admixture signals are found between neighbor populations from both hunter-gatherer and agriculturalists groups, whereas North African individuals are closely related to Eurasian populations. Regarding archaic gene flow, we test six complex demographic models that consider recent admixture as well as archaic introgression. We identify the fingerprint of an archaic introgression event in the sub-Saharan populations included in the models (~ 4.0% in Khoisan, ~ 4.3% in Mbuti Pygmies, and ~ 5.8% in Mandenka) from an early divergent and currently extinct ghost modern human lineage. Conclusion The present study represents an in-depth genomic analysis of a Pan African set of individuals, which emphasizes their complex relationships and demographic history at population level. Electronic supplementary material The online version of this article (10.1186/s13059-019-1684-5) contains supplementary material, which is available to authorized users.

Archaic hominin introgression into modern human genomes

“…We estimated that this introgression happened roughly 100,000 years before present and that the source hominin population diverged from anatomically modern humans about two million years before present. Other studies using sophisticated genome‐wide approaches, found concordant evidence of such haplotypes across the genome (Durvasula & Sankararaman, ; Lorente‐Galdos et al, ). A recent model‐based approach suggests that a population‐specific introgression(s) may have happened as recently as 30,000 years before present affecting ancestors extant African populations (Hsieh et al, ).…”

“…It has been widely accepted that several hominin species have lived in Africa contemporaneously with anatomically modern humans (e.g., Homo naledi [Dirks et al, ]). Indeed, small but significant deviations from expected linkage disequilibrium and demographic trends invoke introgression from archaic hominin(s) in Africa (Durvasula & Sankararaman, ; Hammer et al, ; Hsieh et al, ; Lorente‐Galdos et al, ; Xu et al, ). A relative consensus of the admittedly small number of studies is that the source of this introgression is a now‐extinct hominin population that diverged from the modern human lineage between 0.5 and 2 million years before present.…”

Genome-wide analyses disclose the distinctive HLA architecture and the pharmacogenetic landscape of the Somali population

“…Numerous genetic variants associated with drug response and disease susceptibility have been identified in the past in different populations. Unfortunately, African populations are underrepresented in these studies despite most of the human genetic variation being present in Africa [1][2][3][4][5]9 . In this context, we have created a genome-wide and publicly accessible Somali dataset using Axiom PMRA SNP array.…”

Deep learning for population size history inference: design, comparison and combination with approximate Bayesian computation

“…the use of artificial neural networks (ANN), has only very recently been used to tackle population genetics questions. First, multilayer perceptron (MLP) were used to process large sets of summary statistics and to predict jointly selective sweeps and simple demographic changes (Sheehan and Song, 2016), or to disentangle between multiple scenarios of archaic introgression thanks to an additional ABC step (Lorente-Galdos et al, 2019, Mondal et al, 2019). A second type of ANN, convolutional neural networks (CNN), were then applied to summary statistics computed over 5Kb genomic regions in order to predict selective sweeps (Xue et al, 2019).…”