Toward Male Individualization with Rapidly Mutating Y-Chromosomal Short Tandem Repeats

Relevant for various areas of human genetics, Y-chromosomal short tandem repeats (Y-STRs) are com- monly used for testing close paternal relationships among individuals and populations, and for male lineage iden- tification. However, even the widely used 17-loci Yfiler set cannot resolve individuals and populations completely. Here, 52 centers generated quality-controlled data of 13 rapidly mutating (RM) Y-STRs in 14,644 related and unrelated males from 111 worldwide populations. Strik- ingly, >99% of the 12,272 unrelated males were com- pletely individualized. Haplotype diversity was extremely high (global: 0.9999985, regional: 0.99836\u20130.9999988). Haplotype sharing between populations was almost ab- sent except for six (0.05%) of the 12,156 haplotypes. Haplotype sharing within populations was generally rare (0.8% nonunique haplotypes), significantly lower in ur- ban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). Analysis of molecular variance revealed 99.98% of variation within populations, 0.018% among populations within groups, and 0.002% among groups. Of the 2,372 newly and 156 previously typed male relative pairs,29% were differentiated including 27% of the 2,378 father\u2013son pairs. Relative to Yfiler, haplotype diversity was increased in 86% of the populations tested and over- all male relative differentiation was raised by 23.5%. Our study demonstrates the value of RM Y-STRs in identifying and separating unrelated and related males and provides a reference database