a, A haplotype network based on the number of pairwise differences between 43 unique haplotypes defined from the 20 most differentiated SNPs between Tibetans and the 14 populations from the 1000 Genomes Project. The R software package pegas (ref. 22) was used to generate the figure. The haplotype distances are from pairwise differences. Each pie chart represents one unique haplotype and the size of the pie chart is proportional to log 2 (number of chromosomes with that haplotype). The sections in the pie provide the breakdown of the haplotypes amongst populations. The width of the edges is proportional to the number of pairwise differences between the joined haplotypes; the thinnest edge width represents a difference of one mutation. The number 57 next to a Tibetan haplotype is the number of Tibetan chromosomes with that haplotype. Similarly, the number 1,912 is the number of chromosomes (across several populations) with that haplotype. b, The number of pairwise differences between the Denisovan haplotype and the 43 unique haplotypes defined from the 20 most differentiated SNPs between Tibetans and the 14 populations from the 1000 Genomes Project (same haplotypes as in a). Each bar is a unique haplotype, and they are sorted in increasing order of pairwise differences. The colours within each bar represent the proportion of chromosomes with that haplotype broken down by populations. The numbers on top of each bar represent the total number of chromosomes within the 1000 Genomes data set and Tibetans that have the haplotype. Note this is the same data set used to create the haplotype network in panel a. Supplementary Tables 5 and 6 contain the 43 haplotypes and the frequencies within each of the populations.