Simulated wood duck maternity analysis results from COLONY and CERVUS

Modern genetic parentage methods reveal that alternative reproductive strategies are common in both males and females. Under ideal conditions, genetic methods accurately connect the parents to offspring produced by extra-pair matings or conspecific brood parasitism. However, some breeding systems and sampling scenarios present significant complications for accurate parentage assignment. We used simulated genetic pedigrees to assess the reliability of parentage assignment for a series of challenging sampling regimes that reflect realistic conditions for many brood-parasitic birds: absence of genetic samples from sires, absence of samples from brood parasites, and female kin-structured populations. Using 18 microsatellite markers and empirical allele frequencies from two populations of a conspecific brood parasite, the wood duck (Aix sponsa), we simulated brood parasitism and determined maternity using two widely used programs, CERVUS and COLONY. Errors in assignment were generally modest for most sampling scenarios but differed by program: CERVUS suffered from false assignment of parasitic offspring, whereas COLONY sometimes failed to assign offspring to their known mothers. Reducing the number of markers (9 loci rather than 18) caused the assignment error to slightly worsen with COLONY but balloon with CERVUS. One potential error with important biological implications was rare in all cases—few nesting females were incorrectly excluded as the mother of their own offspring, an error that could falsely indicate brood parasitism. We consider the implications of our findings for both a retrospective assessment of previous studies as well as suggestions for the best practices for future studies. 

Methods
Please refer to the publication for detailed methods on the data collection and processing.