• male philopatry;
  • microsatellite genotyping;
  • Monte Carlo simulation;
  • paternal exclusion probabilities;
  • paternity

The statistical power of single-locus paternity analyses has previously been assessed by calculating an expected exclusion probability (E), the probability of excluding a randomly chosen nonfather. This E-statistic assumes that putative sires are a random selection of individuals from a panmictic study population. In species that display male natal philopatry, closely related individuals may be the principal competitors for paternity. In such structured populations, the E statistic will overestimate exclusion probability because males competing for paternity are more closely related than males chosen randomly from the population. A suite of loci thought to be sufficient for a panmictic population may frequently incorrectly assign paternity to close relatives of true sires. This study provides equations for calculating the expected probability of excluding a close male relative of the genetic sire (Erel) for any genotyping system that uses codominant markers. We also describe the use of Monte Carlo modelling to estimate exclusion probabilities when multiple male relatives compete for paternity. We show that the utility of a set of codominant markers will depend on the breeding behaviour and social system of the species in question.