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.