Pedigree-Based Estimation of Y-STR Mutation and Male Differentiation Rates: Application to Historical Remains Identification

TL;DR

This study uses family data to estimate Y-STR mutation rates and male differentiation rates, showing their usefulness in identifying historical remains.

Contribution

The study provides new insights into Y-STR mutation rates and differentiation rates using pedigree data for historical remains identification.

Findings

Mutation rates for 22 of 25 Y-STR loci matched published father–son values.

Differentiation rates reached 60.1% for male relatives, aiding in distinguishing unrelated individuals.

Excessive mutations over generations may obscure patrilineal relationships in distant comparisons.

Abstract

Background/Objectives: High differentiation rates provided by Y-chromosomal short tandem repeats (Y-STRs) are highly advantageous in most forensic and genealogical casework, as they enhance the ability to exclude close or moderately related individuals, refine an individual’s position within a pedigree, and uncover the population substructure in otherwise homogeneous groups. However, the impact for historical remains identification casework is underexplored. Methods: We present a pedigree analysis of 366 males from 183 pedigrees, separated by 4 to 16 meioses at 27 Y-STR loci, from the Yfiler Plus kit. The differentiation rate for a given degree of separation was defined as the proportion of pairs at that specific number of meioses showing at least one allelic difference, relative to the total number of such pairs. Results: Our pedigree-based locus-specific mutation rates were consistent with published father–son values for 22 of 25 loci, with 3 loci (DYS389II, DYS449, and DYS570) being significantly different (p < 0.05). These results were consistent with previous pedigree-based estimates, and the strong agreement between father–son and pedigree-based mutation rates supports the use of pedigrees as a reliable method for estimating mutation rates. The probability of differentiating male relatives reached 60.1%, which is similar to previous studies using the Yfiler Plus kit. Conclusions: This high male differentiation rate is advantageous for distinguishing unrelated individuals within the same population, reducing false inclusions. However, when comparing distantly related individuals, excessive mutations accumulated over many generations may obscure genuine patrilineal relationships, increasing the risk of false exclusions. Our findings are likely to be highly valuable for future interpretation of Y-STR haplotypes from patrilineal relatives across a wide range of applications, with significant relevance to historical remains identification casework.

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