Y-chromosomal microsatellite mutation rates: differences in mutation rate between and within loci

Area of Science:

• Population Genetics
• Forensic Genetics
• Human Evolutionary Genetics

Background:

• Accurate Y-chromosomal short tandem repeat (STR) mutation rates are crucial for paternity testing and tracing Y chromosome lineage origins.
• Existing data suggest considerable variability in mutation rates among Y-STR loci (interlocus) and within individual loci (intralocus).

Purpose of the Study:

• To investigate Y-STR mutation rate variability across nine specific Y-STR loci.
• To analyze the relationship between mutation rates, STR allele length, and paternal age.
• To determine if Y-STR mutation rates differ across major Y-chromosome haplogroups.

Main Methods:

• Analyzed 1,766 confirmed father-son pairs (15,894 meioses) for mutations at nine Y-STR loci.
• Genotyped five biallelic markers to define Y-chromosome haplogroups.
• Calculated mutation rates, noting gains and losses, and assessed correlations with allele length and paternal age.

Main Results:

• Observed 36 fragment length mutations, with a significant surplus of gains (24 gains vs. 12 losses).
• Mutation rate positively correlated with STR repeat length, showing excess losses in long alleles and gains in short alleles.
• Significant interlocus differences in mutation rates were found, ranging from zero to eight mutations per locus. No correlation with paternal age was observed.

Conclusions:

• Y-STR mutation rates exhibit significant locus-specific and allele-specific variation.
• Mutation rate differences are influenced by allele size and vary between haplogroups.
• Allele-specific mutation rate estimates are essential for accurate forensic and population genetic applications.