Figure 2. NE1 haplotypes share ancestry with Neandertals.

(A) The principal component analysis (PCA) of the SNP haplotypes from CEU, CHB/JPT and YRI populations indicates population substructure between African and Eurasian populations, as well as within Eurasians. Please note the separation of NE1 and NonNE1 haplogroup. (B) Nucleotide diversity (π) within populations is depicted. For most of the genomic segments, π is higher within the YRI population (blue line) when compared to Eurasian populations (red line). However, there is an increase of π for Eurasian populations at the NE1 locus, surrounding the CNVR 8163.1 deletion. (C) The evaluation of 12 SNPs (that separate NE1 and nonNE1 haplogroups) in the CEU sample, NA12891, as well as Denisovan, Neandertal and chimpanzee consensus haplotypes. (D) Normalized read-depth of the Neandertal and Denisovan sequences across the NE1 locus. Please note the drop of the sequence read-depth to 0 for the region corresponding to the human CNVR8163.1 deletion.