Microsatellite genotyping errors: detection approaches, common sources and consequences for paternal exclusion.

Area of Science:

• Genetics
• Population Genetics
• Conservation Biology

Background:

• Microsatellite genotyping errors are prevalent and can compromise downstream genetic analyses.
• Quantifying these errors and identifying their sources is crucial for reliable scientific conclusions.

Purpose of the Study:

• To explore error detection methods for microsatellite genotyping.
• To identify common sources of genotyping errors.
• To assess the consequences of genotyping errors on paternal exclusion analyses.

Main Methods:

• Genotyping of nearly 2000 Antarctic fur seals at nine microsatellite loci.
• Comparison of various error-rate estimation approaches, including blind repeat-genotyping and mother-offspring comparisons.
• Simulations to evaluate the impact of errors on paternity exclusion.

Main Results:

• Error rates ranged from 0.0013 to 0.0074 per single locus polymerase chain reaction (PCR).
• The most frequent errors (80%) stemmed from misinterpreting allele banding patterns, particularly confusing homozygotes with adjacent allele heterozygotes.
• Genotyping errors significantly impacted paternity exclusion, leading to false exclusions and altered reproductive skew estimates.

Conclusions:

• Microsatellite genotyping errors are ubiquitous and require careful management.
• Error rates are influenced by locus polymorphism and product size, suggesting areas for targeted error reduction.
• Researchers should routinely report error rates and assess the robustness of their analyses to potential genotyping errors.