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

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Lorente-Galdos , B , Lao , O , Serra-Vidal , G , Santpere , G , Kuderna , L F K , Arauna , L R , Fadhlaoui-Zid , K , Pimenoff , V N , Soodyall , H , Zalloua , P , Marques-Bonet , T & Comas , D 2019 , ' 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 ' , Genome Biology , vol. 20 , no. 1 , 77 . https://doi.org/10.1186/s13059-019-1684-5

Title: 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
Author: Lorente-Galdos, Belen; Lao, Oscar; Serra-Vidal, Gerard; Santpere, Gabriel; Kuderna, Lukas F. K.; Arauna, Lara R.; Fadhlaoui-Zid, Karima; Pimenoff, Ville N.; Soodyall, Himla; Zalloua, Pierre; Marques-Bonet, Tomas; Comas, David
Contributor: University of Helsinki, Archaeology
Date: 2019-04-26
Language: eng
Number of pages: 15
Belongs to series: Genome Biology
ISSN: 1474-760X
URI: http://hdl.handle.net/10138/307925
Abstract: BackgroundPopulation 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.ResultsHere, 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 (similar to 4.0% in Khoisan, similar to 4.3% in Mbuti Pygmies, and similar to 5.8% in Mandenka) from an early divergent and currently extinct ghost modern human lineage.ConclusionThe 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.
Subject: 1184 Genetics, developmental biology, physiology
Human population genetics
Genome diversity
Whole-genome sequences
Africa
Archaic introgression
PYGMY HUNTER-GATHERERS
EVOLUTIONARY HISTORY
DEMOGRAPHIC HISTORY
MUTATION-RATE
JEBEL IRHOUD
Y-CHROMOSOME
ADMIXTURE
ADAPTATION
DNA
NEANDERTHAL
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