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. 2019 Dec 5;105(6):1254-1261.
doi: 10.1016/j.ajhg.2019.11.005.

Identification of African-Specific Admixture between Modern and Archaic Humans

Jeffrey D Wall  1 , Aakrosh Ratan  2 , Eric Stawiski  3 ; GenomeAsia 100K Consortium
Collaborators, Affiliations

Identification of African-Specific Admixture between Modern and Archaic Humans

Jeffrey D Wall et al. Am J Hum Genet. .

Abstract

Recent work has demonstrated that two archaic human groups (Neanderthals and Denisovans) interbred with modern humans and contributed to the contemporary human gene pool. These findings relied on the availability of high-coverage genomes from both Neanderthals and Denisovans. Here we search for evidence of archaic admixture from a worldwide panel of 1,667 individuals using an approach that does not require the presence of an archaic human reference genome. We find no evidence for archaic admixture in the Andaman Islands, as previously claimed, or on the island of Flores, where Homo floresiensis fossils have been found. However, we do find evidence for at least one archaic admixture event in sub-Saharan Africa, with the strongest signal in Khoesan and Pygmy individuals from Southern and Central Africa. The locations of these putative archaic admixture tracts are weighted against functional regions of the genome, consistent with the long-term effects of purifying selection against introgressed genetic material.

Keywords: Denisovan; GenomeAsia project; Neanderthal; archaic humans; ghost admixture.

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Conflict of interest statement

E.S. was previously a full-time employee of Genentech, Inc. and is currently a full-time employee of MedGenome, Inc. J.D.W. is a consultant for Genentech, Inc., and MedGenome, Inc.

Figures

Figure 1
Figure 1
Boxplot Showing the Distribution of the Number of Putative Ghost Haplotypes (PGHs) per Individual for Different Continental Groups Eur refers to 75 European samples, EA to 315 East Asian samples, and Mel to 66 Melanesian samples. The whiskers are defined as 1.5 times the interquartile range. (A) PGHs identified assuming the Denisovan genome was unknown. (B) PGHs identified assuming the Denisovan genome was known.
Figure 2
Figure 2
Heatmap Showing the Average Number of PGHs Stratified by Country of Origin Countries with no samples are shaded light gray. The raw PGH counts on which this figure is based are provided in Table S2.
Figure 3
Figure 3
Percent Overlap of PGHs Relative to Expectations, Stratified by the Strength of Purifying Selection Quintile 1 is the fifth of the genome with the strongest purifying selection, while quintile 5 has the weakest. (A) Results for 2,319 PGHs in blue and results for a highly conservative thinned version of the data in red. (B) Results using increasingly less stringent definitions for PGHs. See Material and Methods for details.
See this image and copyright information in PMC

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