Figure 4

Phylogenetic trees of STRUCTURE analyses and Haplotype Sharing Analyses (HSAs). The phylogenetic trees re-constructed based on two types of genetic distance methods, which are A) Cavalli DC and B) Nei’s DA. The clade of MIT consists of Malays, Indonesians and Thais, PM is Proto-Malays, CN is Chinese, NG is Semang, IN is Indians and YRI is Yoruba. The phylogenetic trees based on haplotype sharing distance from 100 kb bins of HSAs were showed by; C) PMY is private haplotypes found only in Malays samples of peninsula; PM is private haplotypes found only in Proto-Malays samples; NG is private haplotypes found only in Semang samples; Shared haplotypes is found in all PMY, PM and NG samples. D) NMY is private haplotypes found only in northern Malay samples; CN is private haplotypes found only in Chinese samples; IN is private haplotypes found only in Indians samples; Shared haplotypes is found in all NMY, CN and IN samples; YRI is the African haplotypes that were used as outgroup.