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

Kaye N Ballantyne, Arwin Ralf, Rachid Aboukhalid, Niaz M Achakzai, Maria J Anjos, Qasim Ayub, Jože Balažic, Jack Ballantyne, David J Ballard, Burkhard Berger, Cecilia Bobillo, Mehdi Bouabdellah, Helen Burri, Tomas Capal, Stefano Caratti, Jorge Cárdenas, François Cartault, Elizeu F Carvalho, Monica Carvalho, Baowen Cheng, Michael D Coble, David Comas, Daniel Corach, Maria E D'Amato, Sean Davison, Peter de Knijff, Maria Corazon A De Ungria, Ronny Decorte, Tadeusz Dobosz, Berit M Dupuy, Samir Elmrghni, Mateusz Gliwiński, Sara C Gomes, Laurens Grol, Cordula Haas, Erin Hanson, Jürgen Henke, Lotte Henke, Fabiola Herrera-Rodríguez, Carolyn R Hill, Gunilla Holmlund, Katsuya Honda, Uta-Dorothee Immel, Shota Inokuchi, Mark A Jobling, Mahmoud Kaddura, Jong S Kim, Soon H Kim, Wook Kim, Turi E King, Eva Klausriegler, Daniel Kling, Lejla Kovačević, Leda Kovatsi, Paweł Krajewski, Sergey Kravchenko, Maarten H D Larmuseau, Eun Young Lee, Ruediger Lessig, Ludmila A Livshits, Damir Marjanović, Marek Minarik, Natsuko Mizuno, Helena Moreira, Niels Morling, Meeta Mukherjee, Patrick Munier, Javaregowda Nagaraju, Franz Neuhuber, Shengjie Nie, Premlaphat Nilasitsataporn, Takeki Nishi, Hye H Oh, Jill Olofsson, Valerio Onofri, Jukka U Palo, Horolma Pamjav, Walther Parson, Michal Petlach, Christopher Phillips, Rafal Ploski, Samayamantri P R Prasad, Dragan Primorac, Gludhug A Purnomo, Josephine Purps, Hector Rangel-Villalobos, Krzysztof Rębała, Budsaba Rerkamnuaychoke, Danel Rey Gonzalez, Carlo Robino, Lutz Roewer, Alexandra Rosa, Antti Sajantila, Andrea Sala, Jazelyn M Salvador, Paula Sanz, Cornelia Schmitt, Anil K Sharma, Dayse A Silva, Kyoung-Jin Shin, Titia Sijen, Miriam Sirker, Daniela Siváková, Vedrana Škaro, Carlos Solano-Matamoros, Luis Souto, Vlastimil Stenzl, Herawati Sudoyo, Denise Syndercombe-Court, Adriano Tagliabracci, Duncan Taylor, Andreas Tillmar, Iosif S Tsybovsky, Chris Tyler-Smith, Kristiaan J van der Gaag, Daniel Vanek, Antónia Völgyi, Denise Ward, Patricia Willemse, Eric PH Yap, Rita YY Yong, Irena Zupanič Pajnič, Manfred Kayser

Relevant for various areas of human genetics, Y-chromosomal short tandem repeats (Y-STRs) are commonly used for testing close paternal relationships among individuals and populations, and for male lineage identification. 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. Strikingly, >99% of the 12,272 unrelated males were completely individualized. Haplotype diversity was extremely high (global: 0.9999985, regional: 0.99836-0.9999988). Haplotype sharing between populations was almost absent except for six (0.05%) of the 12,156 haplotypes. Haplotype sharing within populations was generally rare (0.8% nonunique haplotypes), significantly lower in urban (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-son pairs. Relative to Yfiler, haplotype diversity was increased in 86% of the populations tested and overall 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.