Short tandem-repeat polymorphism/Alu haplotype variation at the PLAT locus: Implications for modern human origins

Two dinucleotide short tandem-repeat polymorphisms (STRPs) and a polymorphi c Alu element spanning a 22-kb region of the FLAT locus on chromosome 8p12- q11.2 were typed in 1,287-1,420 individuals originating from 30 geographica lly diverse human populations, as well as in 29 great apes. These data were analyzed as haplotypes consisting of each of the dinucleotide repeats and the flanking Alu insertion/deletion polymorphism. The global pattern of STR P/Alu haplotype variation and linkage disequilibrium (LD) is informative fo r the reconstruction of human evolutionary history. Sub-Saharan African pop ulations have high levels of haplotype diversity within and between populat ions, relative to non-Africans, and have highly divergent patterns of LD. N on-African populations have both a subset of the haplotype diversity presen t in Africa and a distinct pattern of LD. The pattern of haplotype variatio n and LD observed at the FLAT locus suggests a recent common ancestry of no n-African populations, from a small population originating in eastern Afric a. These data indicate that, throughout much of modern human history, sub-S aharan Africa has maintained both a large effective population size and a h igh level of population substructure. Additionally, Papua New Guinean and M icronesian populations have rare haplotypes observed otherwise only in Afri can populations, suggesting ancient gene flow from Africa into Papua New Gu inea, as well as gene flow between Melanesian and Micronesian populations.