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. 2017 Oct 5;101(4):578-589.
doi: 10.1016/j.ajhg.2017.09.010.

The Contribution of Neanderthals to Phenotypic Variation in Modern Humans

Michael Dannemann  1 , Janet Kelso  2
Affiliations

The Contribution of Neanderthals to Phenotypic Variation in Modern Humans

Michael Dannemann et al. Am J Hum Genet. .

Abstract

Assessing the genetic contribution of Neanderthals to non-disease phenotypes in modern humans has been difficult because of the absence of large cohorts for which common phenotype information is available. Using baseline phenotypes collected for 112,000 individuals by the UK Biobank, we can now elaborate on previous findings that identified associations between signatures of positive selection on Neanderthal DNA and various modern human traits but not any specific phenotypic consequences. Here, we show that Neanderthal DNA affects skin tone and hair color, height, sleeping patterns, mood, and smoking status in present-day Europeans. Interestingly, multiple Neanderthal alleles at different loci contribute to skin and hair color in present-day Europeans, and these Neanderthal alleles contribute to both lighter and darker skin tones and hair color, suggesting that Neanderthals themselves were most likely variable in these traits.

Keywords: Neanderthal; UK Biobank; introgression phenotype.

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Figures

Figure 1
Figure 1
Archaic Haplotypes Associated with Skin and Hair Phenotypes (A–D) Neanderthal allele frequency in percentage (x axis) and the number of individuals in the UK Biobank cohort for four aSNPs that show strong associations with skin and hair phenotypes (y axis): chr9: 16,904,635 (rs62543578) associated with skin color (A), chr9: 16,804,167 (rs10962612) associated with ease of skin tanning (B) and incidence of childhood sunburn (C) (illustrated are the average numbers of childhood sunburns for individuals with the three genotypes), and chr16: 89,947,203 (rs62052168) associated with hair color (D). (E and F) The genomic locations of introgressed haplotypes for the aSNPs showing significant associations in (A)–(D). Gray vertical lines denote the extent of the inferred archaic haplotypes on chromosomes 9 (E) and 16 (F). At the top, we show all aSNPs that are within the inferred archaic haplotypes and are present in any 1000 Genomes individual. The associated tag SNPs directly genotyped by the UK Biobank are marked in red, and other aSNPs within the archaic haplotypes and genotyped in the UK Biobank are marked in orange. The associated tag aSNPs represented in (A)–(D) are marked on the x axis.
Figure 2
Figure 2
Archaic Haplotype Associated with Chronotype (A) The Neanderthal allele frequency in percentage (x axis) and the number of individuals in the UK Biobank cohort for the four reported chronotype phenotypes (y axis; from top to bottom: definitely an evening person, more an evening than a morning person, more a morning than an evening person, definitely a morning person) for the archaic tag SNP with the strongest association with chronotype (position chr2: 239,316,043 [rs75804782] near ASB1). (B) Worldwide frequency of the archaic allele (C, blue) and the modern human allele (T, orange) in the Simons Genome Diversity Panel populations. (C) The association p values (y axis; in the form of −log10(p)) with chronotype for all archaic and non-archaic SNPs (squares) genotyped by the UK Biobank study in the region of the inferred archaic haplotype at chr2: 239,316,043–239,470,654. The tag SNP at chr2: 239,316,043 (rs75804782) is shown in red, other aSNPs are shown in orange, and non-archaic SNPs are shown in black. The genome-wide significance cutoff of p = 1.0 × 10−8 and the extent of the inferred archaic haplotype are illustrated with dashed horizontal and vertical gray lines, respectively. At the top, we show all aSNPs that are within the inferred archaic haplotype and are present in any 1000 Genomes individual. The directly genotyped SNPs from the UK Biobank are illustrated as red (the archaic tag SNP) and orange bars. One archaic allele that leads to a missense mutation in ASB1 is marked as a green bar. (D) The cumulative density distribution of p values (zoom in for p < 0.01, x axis log scale) for associations between archaic alleles and chronotype (red line) and the 95% confidence interval region for 1,000 cumulative density distributions of associations between non-archaic alleles matched to the Neanderthal allele frequency and chronotype (gray shading).
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