Neanderthal and Denisova genetic affinities with contemporary humans: introgression versus common ancestral polymorphisms

Gene. 2013 Nov 1;530(1):83-94. doi: 10.1016/j.gene.2013.06.005. Epub 2013 Jul 19.


Analyses of the genetic relationships among modern humans, Neanderthals and Denisovans have suggested that 1-4% of the non-Sub-Saharan African gene pool may be Neanderthal derived, while 6-8% of the Melanesian gene pool may be the product of admixture between the Denisovans and the direct ancestors of Melanesians. In the present study, we analyzed single nucleotide polymorphism (SNP) diversity among a worldwide collection of contemporary human populations with respect to the genetic constitution of these two archaic hominins and Pan troglodytes (chimpanzee). We partitioned SNPs into subsets, including those that are derived in both archaic lineages, those that are ancestral in both archaic lineages and those that are only derived in one archaic lineage. By doing this, we have conducted separate examinations of subsets of mutations with higher probabilities of divergent phylogenetic origins. While previous investigations have excluded SNPs from common ancestors in principal component analyses, we included common ancestral SNPs in our analyses to visualize the relative placement of the Neanderthal and Denisova among human populations. To assess the genetic similarities among the various hominin lineages, we performed genetic structure analyses to provide a comparison of genetic patterns found within contemporary human genomes that may have archaic or common ancestral roots. Our results indicate that 3.6% of the Neanderthal genome is shared with roughly 65.4% of the average European gene pool, which clinally diminishes with distance from Europe. Our results suggest that Neanderthal genetic associations with contemporary non-Sub-Saharan African populations, as well as the genetic affinities observed between Denisovans and Melanesians most likely result from the retention of ancient mutations in these populations.

Keywords: 1st principal component; 2nd principal component; 3rd principal component; Archaic; DNA; Denisova; Human evolution; NaDa; NaDd; NdDa; NdDd; Neandertal; Neanderthal; Neanderthal ancestral and Denisova ancestral; Neanderthal ancestral and Denisova derived; Neanderthal derived and Denisova ancestral; Neanderthal derived and Denisova derived; PC1; PC2; PC3; PCA; PCAs; Phylogenetics; SNP; SNPs; UCSC; University of California, Santa Cruz; deoxyribonucleic acid; hg18; human genome (18th assembly by the University of California, Santa Cruz); kya; principal component analyses; principal component analysis; single nucleotide polymorphism; single nucleotide polymorphisms; thousand years ago.

MeSH terms

  • Africa South of the Sahara
  • Animals
  • DNA, Mitochondrial / genetics
  • Europe
  • Fossils
  • Genetic Drift
  • Genetics, Population
  • Genome, Human
  • Humans
  • Neanderthals / genetics*
  • Pan troglodytes / genetics
  • Phylogeny*
  • Polymorphism, Genetic*


  • DNA, Mitochondrial