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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 - PubMed

  • ️Tue Jan 01 2019

Comparative Study

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

Belen Lorente-Galdos et al. Genome Biol. 2019.

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.

Keywords: Africa; Archaic introgression; Genome diversity; Human population genetics; Whole-genome sequences.

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Conflict of interest statement

Ethics approval and consent to participate

This study was approved by the institutional review board of the CEIC-IMAS (2013/5429/I).

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

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Figures

Fig. 1
Fig. 1

Samples, genetic diversity, and runs of homozygosity. a Geographical, linguistic and life-style distribution of African individuals analyzed. b On the top, pairwise differences per kbp between individuals. Each line corresponds to the genetic differences of a specific individual to the rest of the samples. The line color corresponds to the label color of the individual in the x axis. The value given for the same individual is counted considering differences between its two chromosomes. On the bottom, total length of runs of homozygosity per individual. In blue, smaller lengths (from 0.5 to 1 Mbp); in green, intermedium lengths (from 1 to 1.5 Mbp) and in orange, the largest windows (bigger than 1.5 Mbp), the latter are a sign of inbreeding at population or individual level

Fig. 2
Fig. 2

Principal component analysis (PCA) and ADMIXTURE. a First two components of a PCA, percentage of explained variance shown in axis; African samples are grouped in four major genetic ancestries, representative samples of each ancestry are shown with a circle colored with its correspondent main genetic ancestry estimated in b, North Africans and African samples not circled might be heavily admixed according to b; b ADMIXTURE plot for the 25 samples in our dataset; the seven ancestries are named according to individuals that have almost exclusively a given ancestry. The plot for the remaining 705 samples is shown in Additional file 1: Figure S6.3

Fig. 3
Fig. 3

PSMC analyses on eight populations. Ne and time have been scaled with a mutation rate of 2.5 × 10−8 and a generation time of 25 years

Fig. 4
Fig. 4

Tested demographic models. Left figures: topology of the demographic models for ABC-DL analyses considering East Asian (EAs), European (Eu), western sub-Saharan (WAf), Mbuti Pygmy (Mbt), and Khoisan (Kho) anatomically modern humans, Altai Neanderthal (N), Neanderthal-like population (NI) with introgressed DNA present in Eurasian populations, Denisova (D), Denisovan-like population (NI) with introgressed DNA present in East Asian populations, an archaic ghost population (Xe) that has left their footprint into Denisovan genome, a putative African extinct basal branch population (XAf), and a second putative archaic ghost population Neanderthal-like (Xn). In all models, recent migrations described in the text are allowed, but not shown in the figure to ease visualization. The posterior probability obtained with our ABC-DL approach is shown for each model; right figure: fitted B model

Comment in

  • The long walk to African genomics.

    Tucci S, Akey JM. Tucci S, et al. Genome Biol. 2019 Jun 27;20(1):130. doi: 10.1186/s13059-019-1740-1. Genome Biol. 2019. PMID: 31248437 Free PMC article. No abstract available.

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