Fig. 2

Global haplotype variation of the LCE3BC locus and allele frequency of the LCE3BC deletion in modern and ancient populations. a Simplified phylogenetic tree based on 5008 human haplotypes from the 1000 Genomes Project. We constructed the tree using the single nucleotide variants downstream of the deletion (also see Additional file 1: Figure S3). Haplotypes separated into two distinct haplogroups, which segregate into haplotypes that carry the deletion (deleted, red circle) and those that do not carry the deletion (non-deleted, blue circle). Frequency pie charts were superimposed to the tree for an overview of the distribution of the major haplotype groups across continental populations (Africans: [ACB, ASW, ESN, GWD, LWK, MSL, YRI], Asians: [BEB, CDX, CHB, CHS, GIH, ITU, JPT, KHV, PJL, STU] and Europeans: [CEU, FIN, GBR, IBS, TSI]). b Frequency distribution of the LCE3BC deletion in ancient human genomes. The x-axis indicates the date of the samples. The y-axis indicates the allele frequency of the deletion (as imputed by the frequency of tag single nucleotide variants rs6693105). The population acronyms are EN: Early Neolithic European; MN: Middle Neolithic European; BA: Bronze Age European. Each blue box indicates the ancient population and the length of the box spans the estimated age of the samples. The sample size of each population is indicated by the red number on the top or bottom of each box. c The geographic distribution of the LCE3BC deletion allele frequency. The red color indicates the frequency of the haplotypes in each population carrying the deletion, whereas white are haplotypes without the deletion