Male-specific Y-chromosome (chrY) polymorphisms are interesting components of the DNA for population genetics. While single nucleotide polymorphisms (Y-SNPs) indicate distant evolutionary ancestry, short tandem repeats (Y-STRs) are able to identify close familial kinships. Detailed chrY analysis provides thus both biogeographical background information as paternal lineage identification. The rapid advancement of high-throughput massive parallel sequencing (MPS) technology in the past decade has revolutionized genetic research. Using MPS, single-base information of both Y-SNPs as Y-STRs can be analyzed in a single assay typing multiple samples at once. In this study, we present the first extensive chrY-specific targeted resequencing panel, the ‘CSYseq’, which simultaneously identifies slow mutating Y-SNPs as evolution markers and rapid mutating Y-STRs as patrilineage markers. The panel was validated by paired-end sequencing of 130 males, distributed over 65 deep-rooted pedigrees covering 1,279 generations. The CSYseq successfully targets 15,611 Y-SNPs including 9,014 phylogenetic informative Y-SNPs to identify 1,443 human evolutionary Y-subhaplogroup lineages worldwide. In addition, the CSYseq properly targets 202 Y-STRs, including 81 slow, 68 moderate, 27 fast and 26 rapid mutating Y-STRs to individualize close paternal relatives. The targeted chrY markers cover a high average number of reads (Y-SNP = 717, Y-STR = 150), easy interpretation, powerful discrimination capacity and chrY specificity. The CSYseq is interesting for research on different time scales: to identify evolutionary ancestry, to find distant family and to discriminate closely related males. Therefore, this panel serves as a unique tool valuable for a wide range of genetic-genealogical applications in interdisciplinary research within evolutionary, population, molecular, medical and forensic genetics.

The Y‐chromosome is a valuable kinship indicator in family history and forensic research. To reconstruct genealogies, the time to the most recent common ancestor (tMRCA) between paternal relatives can be estimated through Y‐STR analysis. Existing models are the stepwise mutation model (SMM, only one‐step Y‐STR changes) and the infinite allele model (IAM, new allele per Y‐STR change). In this study, these mutation models and all existing tMRCA calculators were validated through a genetic‐genealogy database containing 1,120 biologically related genealogical pairs confirmed by 46 Y‐STRs with known tMRCA (18,109 generations). Consistent under‐ and overestimation and broad confidence intervals were observed, leading to dubious tMRCA estimates. This is because they do not include individual mutation rates or multi‐step changes and ignore hidden multiple, back, or parallel modifications. To improve tMRCA estimation, we developed a user‐friendly calculator, the “YMrCA”, including all previously mentioned mutation characteristics. After extensive validation, we observed that the YMrCA calculator demonstrated a promising performance. The YMrCA yields a significantly higher tMRCA success rate (96%; +20%) and a lower tMRCA error (7; −3) compared to the mutation models and all online tMRCA calculators. Therefore, YMrCA offers the next step towards more objective tMRCA estimation for DNA kinship research.

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