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 RST 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.

Evidence for Gradients of Human Genetic Diversity Within and Among Continents

“…Thus, studies in which individuals from Europe, sub-Saharan Africa, and Southeast Asia are used (e.g., Jorde et al 1997) might be an adequate description of the major components of the U.S. population (e.g., see Kayser et al 2003). However, it would be incorrect to conclude that such studies necessarily generalize to subdivisions of the human gene pool on a worldwide scale.…”

Apparent intrachromosomal exchange on the human Y chromosome explained by population history

“…For most of the samples, Y-STR data for the loci DYS19 (synonym DYS394), DYS389I, DYS389II, DYS390, DYS391, DYS392 and DYS393 were already available from our previous studies, 17,26,27 and for the remaining samples Y-STRs were analysed as described in detail on the website of the Y chromosome Haplotype Reference Database (YHRD) for US Populations (http:// www.ystr.org/usa). 23 Y-STR nomenclature is according to Kayser et al 15 except that DYS389II is considered without variation at DYS389I.…”

“…DNA sequencing of various length alleles of both loci was performed on ABI Prismt 377 DNA Sequencer (Applied Biosystems) using Big Dye chemistry (Applied Biosystems, Foster City, CA, USA) according to the recommendations of the manufacturer. For DYS385a, five different length alleles were sequenced (11,12,13,16,17), and for DYS385b eight alleles were sequenced (11,12,(14)(15)(16)(17)(18)20 Nei,37 was calculated using the software package Arlequin. 38 …”

“…15,18 The Y-STR system DYS385 shows one of the highest levels of polymorphism yet observed for Y-STRs, and hence it is often used in forensic 15,19 -23 and population history studies. 17,24,25 It has been previously assumed that DYS385 exists in two polymorphic copies on the Y chromosome, 15 although the lack of sequence information excluded separate analysis of the assumed two copies. 18 Consequently, no individual locus assignment has been possible, and so the two alleles have been treated as a combined allele class, resulting in a loss of information and potential misinterpretation of true ancestry.…”

Pediatric Stroke Belt

“…However, a recent study in the US found no evidence that geography had a significant impact on genetic variation within several different ethnic groups. 38 Geographic differences in cultural or environmental factors may therefore be of greater importance to the observed regional disparities in disease susceptibility.…”