Texas Population Substructure and Its Impact on Estimating the Rarity of Y STR Haplotypes from DNA Evidence*

Abstract

Three sampled populations of unrelated males--African American, Caucasian, and Hispanic, all from Texas-were typed for 16 Y short tandem repeat (STR) markers using the AmpFlSTR Yfiler kit. These samples also were typed previously for the 13 core CODIS autosomal STR loci. Most of the 16 marker haplotypes (2478 out of 2551 distinct haplotypes) were observed only once in the data sets. Haplotype diversities were 99.88%, 99.89%, and 99.87% for the African American, Caucasian, and Hispanic sample populations, respectively. F(ST) values were very small when a haplotype comprised 10-16 markers. This suggests that inclusion of substructure correction is not required. However, haplotypes consisting of fewer loci may require the inclusion of F(ST) corrections. The testing of independence of autosomal and Y STRs supports the proposition that the frequencies of autosomal and Y STR profiles can be combined using the product rule.

The Y-STR Genetic Diversity of an Idaho Basque Population, with Comparison to European Basques and US Caucasians

“…There was no significant difference between the Idaho and (Budowle et al 2009). Both Basque populations were significantly differentiated from all other populations we compared.…”

Y-STR loci diversity in native Alaskan populations

“…Bias correction (i.e., multiplication of this expression by a factor of N(N−1) −1 ) was not done because of the possibility that when each haplotype is observed once in a database of size N, bias-corrected estimate of PD would equal 1. F ST was estimated following Weir and Cockerham [8], using haplotype data according to the logic described previously [9][10][11][12]. The coefficient of gene differentiation (G ST ) was estimated by the method described by Nei [13].…”

Pedigree likelihood ratio for lineage markers

“…usually 0.05 [38, 39] 4 The "surveying" methods [40,41] 5 p ¼ x n þ q 1 À x n À Á [15,16], where θ is the measure of population substructure 6 Upper bound of 95% binomial confidence interval [16];…”

“…Generally, a DNA profile comprised of both mtDNA and Y haplotypes will be shared once in about every 1,000,000 individuals using current typing strategies. Although biologically independent of autosomal markers, Walsh et al [17] and Budowle et al [15] statistically tested for dependence and found that for the forensic markers on the Y chromosome and mtDNA haplotypes there were no detectable departures from independence with the forensically selected autosomal STR loci. Therefore, the likelihood ratios calculated for autosomal markers, Y-STR haplotypes, and mtDNA sequences can be directly multiplied together.…”

“…The genetic markers carried on these lineage chromosomes can be useful for kinship analysis to provide additional support or to exclude relationships particularly for complex kinships, for more distant relationships, and for database searches (with very limited family member candidates) [1][2][3][4][5][6][7][8][9][10][11][12][13][14]. The discrimination power of current multiplex Y-STR systems used for identification, although dependent on the size of the population sample, can reach 0.999 with 10 Y-STRs and 0.9999 with 16 YSTRs [15,16]. Haplotypes of the hypervariable regions I and II (HVI and HVII, respectively) of the mtDNA genome yield a similar discrimination power which is dependent on the length of sequence used and also on the size of the reference population database [13].…”