A global analysis of Y-chromosomal haplotype diversity for 23 STR loci.
Bottom Line: Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework.A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study.Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent.
Affiliation: Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany.Show MeSH
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Mentions: Multidimensional scaling (MDS) analysis was performed based upon linearized RST, separately for the five marker sets, considering either all 129 populations or the 68 populations of European residency and ancestry alone. When assessed for the PPY23 marker panel, Kruskal's stress value showed a clear ‘elbow’ with increasing dimensionality in both population sets, pinpointing an optimal trade-off between explained variation and dimensionality. For the worldwide analysis, two MDS components were optimal with PPY23 whereas four components were deemed optimal for the Europeans-only analysis. Both solutions explained the haplotypic variation well, with R2 = 95.1% in the worldwide analysis and R2 = 99.2% in the Europeans-only analysis. For comparability, MDS analyses for other marker panels were carried out with two or four dimensions, respectively. Haplotypic variation among populations within continental groups was lower than between continental groups (Fig. S3). For all five marker sets, the first MDS component clearly separated the African populations from the non-African populations (Fig. 6a, Fig. S4). Moreover, MDS also confirmed the previously reported East–West separation in the Y-STR haplotype variation  in the European analysis (Fig. 6b, Fig. S5). Higher MDS components were strongly dependent upon the respective marker set (Figs. S4–S6) and lacked comparably clear population patterns.
Affiliation: Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany.