Y chromosome STR haplotypes and the genetic structure of U.S. populations of African, European, and Hispanic ancestry

Abstract

To investigate geographic structure within U.S. ethnic populations, we analyzed 1705 haplotypes on the basis of 9 short tandem repeat (STR) loci on the Y-chromosome from 9-11 groups each of African-Americans, European-Americans, and Hispanics. There were no significant differences in the distribution of Y-STR haplotypes among African-American groups, whereas European-American and Hispanic groups did exhibit significant geographic heterogeneity. However, the significant heterogeneity resulted from one sample; removal of that sample in each case eliminated the significant heterogeneity. Multidimensional scaling analysis of R(ST) values indicated that African-American groups formed a distinct cluster, whereas there was some intermingling of European-American and Hispanic groups. MtDNA data exist for many of these same groups; estimates of the European-American genetic contribution to the African-American gene pool were 27.5%-33.6% for the Y-STR haplotypes and 9%-15.4% for the mtDNA types. The lack of significant geographic heterogeneity among Y-STR and mtDNA haplotypes in U.S ethnic groups means that forensic DNA databases do not need to be constructed for separate geographic regions of the U.S. Moreover, absence of significant geographic heterogeneity for these two loci means that regional variation in disease susceptibility within ethnic groups is more likely to reflect cultural/environmental factors, rather than any underlying genetic heterogeneity.

Figure 1.

Map showing sample localities included in this study. (1) Acadian (Lousiana); (2) California; (3) Connecticut; (4) Florida; (5) Illinois; (6) Indiana; (7) Lousiana; (8) Maryland; (9) Missouri; (10) New York City; (11) Oregon; (12) Pennsylvania; (13) Texas; (14) Vermont; (15) Virginia; (16) Washington.

Figure 2.

MDS plot based on R_ST values for Y-STR haplotypes for U.S. groups. Codes are from Table 1. (▴) African-Americans; (•) European-Americans; (▪) Hispanics.

Figure 3.

MDS plot based on R_ST values for Y-STR haplotypes, comparing global populations with the U.S. groups. Data for non-U.S. populations, West Africans (WAF), Cameroons (CAM) from this study; Germans (GER), Poles (POL), native South Americans (NSA), Chinese (CHI), Javanese (JAV), and Papua New Guineans from coastal (PNC) and highland (PNH) regions from Kayser et al. (1997, 2000a,b, 2001); Italians (ITA) from Caglia et al. (1997); Hungarians (HUN) and Baranya-Romanies (ROM) from Füredi et al. (1999); South Africans (SAF), Mbuti Pygmies (PYG), Mali (MAL), Ethiopians (ETH), San (SAN), Cambodians (CBD), native Americans (NAM), and Pakistani (PAK) from Seielstad et al. (1999); Spaniards (SPA) from M. Kayser (unpubl.); and Asian-Americans (ASA) from M. Prinz (unpubl.). (▵) Africans; (▴) African-Americans; (○) Europeans; (•) European-Americans; (□) Asian ancestry (including native Americans); (▪) Hispanics.

Figure 4.

MDS plot on the basis of F_ST values for mtDNA SSO-types for U.S. groups. (▴) African-Americans (AA); (•) European-Americans (EA); (▪) Hispanics (HA).

Figure 5.

Plot of R_ST values for Y-STR haplotypes vs. F_ST values for mtDNA SSO-types, for U.S. groups. (AA) African-American; (EA) European-American; (HA) Hispanic.