Marc W. Allard, 1 Ph.D.; Deborah Polanskey, 2 B.S.; Mark R. Wilson, 3 Ph.D.; Keith L. Monson, 4 Ph.D.; and Bruce Budowle, 5 Ph.D. Evaluation of Variation in Control Region Sequences for Hispanic Individuals in the SWGDAM mtDNA Data Set ABSTRACT: The Scientific Working Group on DNA Analysis Methods (SWGDAM) Hispanic data set was analyzed to determine the diversity, phylogeny, and relevant single nucleotide polymorphisms (SNPs) that describe haplogroup patterns for Hispanic Americans (N 5 686), and to assess the degree of admixture regarding mitochondrial DNA (mtDNA). The largest component of admixture based on mtDNA analysis derives from the four major haplogroups previously observed in Native American ancestry, including A (29.3%), B (15.7%), C (20.6%), and D (4.8%). European (17.8%) and African (11.8%) haplogroups also were observed within this data set. Hispanic SWGDAM samples from the southwest, compared with other SWGDAM Hispanic samples, were observed to have a greater percent of Native American haplogroups present (79.9%), and fewer African American haplogroups (4.5%). A total of 234 SNPs were observed in the data set, including 36 newly reported variable positions. These SWGDAM Hispanic data set SNPs ranged from having 1 to 31 changes (Length 5 L) on the phylogenetic tree, with site 16519 being the most variable. On average, there were 3.9 character changes for each variable position on the tree. The most variable sites (with 13 or more changes each listed from fastest to slowest) observed were 16519 (L 5 31), 16189 (L 5 23), 152 (L 5 23), 16311 (L 5 19), 146 (L 5 17), 195 (L 5 17), 16093 (L 5 15), 16362 (L 5 14), 16129 (L 5 13), 150 (L 5 13), and 153 (L 5 13). These sites are consistent with other reports on highly variable positions. A total of 27 SNPs were chosen to identify all clusters containing 1% (N 5 7) or more individuals in the SWGDAM Hispanic data set. The descriptive analyses revealed that the SWGDAM Hispanic data set is similar to published Native American and Hispanic data sets. KEYWORDS: forensic science, mitochondrial DNA, SWGDAM forensic mtDNA data set, haplogroup, control region, SNP, Hispanic The Hispanic population is a geopolitical group defined as de- scendants from Latin America or other Spanish cultures (1). These cultures are genetically heterogeneous population groups gener- ally comprised of a tri-hybrid structure of European, Native Amer- ican, and African contributions. Western Hispanics (e.g., Mexicans) are comprised predominantly of European and Native American ancestry and to a lesser extent African; while Eastern Hispanics (e.g., Puerto Ricans and Cubans) are comprised pre- dominantly of European and African ancestry and to a lesser ex- tent Native Americans (1–7). In U.S. Hispanics the largest contribution is from European genes. This ethno-history is sup- ported by analysis with polymorphic autosomal DNA markers. However, there are differences between nuclear autosomal and mitochondrial DNA (mtDNA) markers that can impact the esti- mate of component contributions in Hispanics. The mtDNA is inherited uniparentally through the maternal lineage. Therefore, because of directional mating, one would expect the tri-hybrid admixture structure to be different based on mtDNA than that es- timated using nuclear autosomal markers (6). Native American mtDNA is defined by four major haplogroups A, B, C, and D, and including the X haplogroup as well (8–43). These genetic subdivisions have been characterized by RFLP analysis (6,9–31) and sequences of the mtDNA control region (CR) (8,32–42). Several studies have suggested that the largest of the maternal admixture components in Hispanics is from Native American ancestry (6,8,28). Thus, any study of Hispanic popula- tions might expect to observe the four major haplogroups of Native Americans and to a lesser extent European and African mtDNA haplogroups. The Scientific Working Group on DNA Analysis Methods (SWGDAM) mtDNA database typically con- sists of sequence data on the hypervariable regions 1 (HV1) and 2 (HV2) of the CR of the human mtDNA genome (43–47). One of the population groups represented in the data set is Hispanics (N 5 686). The mtDNA genetic variation in the SWGDAM His- panic sample is described herein. The data support that the var- iation observed in the SWGDAM data set is comparable with other studies on Hispanics and that the major component of ad- mixture based on mtDNA analysis derives from Native American ancestry. Methods Subjects Approximately one third of the self-identified Hispanic indi- viduals in the SWGDAM data set (N 5 686) come from the south- western (N 5 245, Texas or New Mexico) United States, with the remainder coming from Connecticut (N 5 148), Illinois (N 5 5), or from an unknown location (N 5 288). Data Availability All sequence designations are based on comparisons with the revised Cambridge Reference Sequence (rCRS) (48,49). The 1 Department of Biological Sciences, George Washington University, Wash- ington, DC 20052. 2 Federal Bureau of Investigation, DNA Unit 2, Quantico, VA 22135. 3 Federal Bureau of Investigation, Chem-Bio Sciences Unit, FBI Laboratory, Quantico, VA 22135. 4 Federal Bureau of Investigation Academy, Counterterrorism and Forensic Science Research Unit, FBI Laboratory, Quantico, VA 22135. 5 Federal Bureau of Investigation, Laboratory Division, Quantico, VA 22135. Received 22 Jan. 2005; and in revised form 18 July 2005 and 4 Aug. 2005; accepted 31 Dec. 2005; published 21 April 2006. Copyright r 2006 by American Academy of Forensic Sciences 566 J Forensic Sci, May 2006, Vol. 51, No. 3 doi:10.1111/j.1556-4029.2006.00136.x Available online at: www.blackwell-synergy.com