HUMAN MUTATION Mutation in Brief #940 (2007) Online MUTATION IN BRIEF © 2006 WILEY-LISS, INC. Received 15 May 2006; accepted revised manuscript 16 August 2006. Sub-Populations Within the Major European and African Derived Haplogroups R1b3 and E3a Are Differentiated by Previously Phylogenetically Undefined Y-SNPs Lynn M. Sims 1 , Dennis Garvey 4 , and Jack Ballantyne 1-3* 1 Biomolecular Sciences, Graduate Program in Chemistry, University of Central Florida, Orlando, Florida; 2 Department of Chemistry, University of Central Florida, Orlando, Florida; 3 National Center for Forensic Science, Orlando, Florida; 4 Department of Physics, Gonzaga University, Spokane, Washington *Correspondence to: Jack Ballantyne, Ph.D., Department of Chemistry, University of Central Florida, Bldg #5, 4000 Central Boulevard, Orlando, FL 32816-2366; Tel.: 407-823-4440; Fax: 407-823-2252; E-mail: jballant@mail.ucf.edu Grant sponsor: National Institute of Justice (NIJ), Department of Justice; grant numbers: 1998-IJ-CX-K003 and 2005-Mu-MU-K044. Communicated by Michael Dean Single nucleotide polymorphisms on the Y chromosome (Y-SNPs) have been widely used in the study of human migration patterns and evolution. Potential forensic applications of Y- SNPs include their use in predicting the ethnogeographic origin of the donor of a crime scene sample, or exclusion of suspects of sexual assaults (the evidence of which often comprises male/female mixtures and may involve multiple perpetrators), paternity testing, and identification of non- and half-siblings. In this study, we used a population of 118 African- and 125 European-Americans to evaluate 12 previously phylogenetically undefined Y-SNPs for their ability to further differentiate individuals who belong to the major African (E3a)- and European (R1b3, I)-derived haplogroups. Ten of these markers define seven new sub- clades (equivalent to E3a7a, E3a8, E3a8a, E3a8a1, R1b3h, R1b3i, and R1b3i1 using the Y Chromosome Consortium nomenclature) within haplogroups E and R. Interestingly, during the course of this study we evaluated M222, a sub-R1b3 marker rarely used, and found that this sub-haplogroup in effect defines the Y-STR Irish Modal Haplotype (IMH). The new bi- allelic markers described here are expected to find application in human evolutionary studies and forensic genetics. © 2006 Wiley-Liss, Inc. KEY WORDS: Y-SNPs; Y-chromosome; E3a; R1b3; M222; IMH; forensic; ethnogeographic origins INTRODUCTION Single nucleotide polymorphisms (SNPs) are the smallest and most abundant type of human DNA polymorphisms (Brookes, 1999). SNPs have been extensively used in the study of human evolutionary and migratory patterns (Shastry, 2002) and are increasingly being used in genome-wide association studies (Syvanen, 2005). It is unclear the extent to which SNPs will augment STRs as the primary method of genotyping in forensic DOI: 10.1002/humu.9469