A comprehensive mutation study in wide deep-rooted R1 b Serbian pedigree: mutation rates and male relative differentiation capacity of 36 Y-STR markers

Abstract

Haplotyping of Y-chromosomal short tandem repeats (Y-STRs) reflects the paternal lineage, although, the father-son pair profiles may differ due to the germline mutations. In order to discriminate between closely related males in criminal cases, as well as for the correct application of Y-STRs in the paternity/kinship analysis and determination of the most recent common ancestor in the familial searching or genealogy research, the assessment of mutation rates of routinely used Y-STRs is of a great importance. We genotyped 120 males belonging to one wide deep-rooted pedigree separated by 1-20 meiosis. The haplotypes of analyzed males distributed over 12 different families (according to their surnames), with 113 originating from one ancestor, and the remaining 7 from the second, closely related to the previous one, belong to the Rlb haplogroup. The analysis was performed using Powerplex (R) Y23 kit, Yfiler (TM) plus kit and 13 rapidly mutating (RM13) Y-STRs. In 20,855 allele transmissions, 175 mutations (61% repeat losses and 39% gains) and one gene conversion event were found at 25 out of 36 markers. The medians of locus-specific mutation rates estimated using the Bayesian approach ranged from 1.42 x 10 (-3) (95% credible interval (CI): 0.05 x 10(-3)- 7.56 x 10(-3)) for loci with no observed mutations to 130.91 x 10(-3) (95% CI: 102.91 x 10(-3) - 162.78 x 10(-3)) for DYF399S1, with a median rate across all 36 markers of 10.06 x 10(-3) (95% CI: 8.65 x 10(-3)- 11.61 x 10(-3)). In 6349 male relative pairs, the 36 Y-STR set distinguished 98.4% relative pairs by at least one mutation, compared to 95.9%, 65.5% and 57.4% for RM13, Yfiler (TM) plus, and Powerplex (R) Y23 set, respectively. The extra-pair paternity rate was estimated at 11.9 x 10(-3) (95% CI: 4.4 x 10(-3)- 25.8 x 10(-3)) fitting within the range reported for some European populations. A significant positive correlation was observed between fathers' ages at the time of the Y chromosome transmission and mutability rates (R-2 = 0.9495, p = 0.0256), with more significant results when analyzing RM markers (R-2 = 0.9827, p = 0.0087).