Parentage analysis with incomplete sampling of candidate parents and offspring

Many breeding systems include 'multiple mating' in which males or females mate with multiple partners. We identify two forms of multiple mating: 'single-sex', where the next-generation individuals (NGIs) are the product of multiple mating by one sex; and 'two-sex', where the NGIs are the product of multiple mating by both sexes. For both mating systems we develop models that estimate the proportion of NGIs that is fathered (paternity) or mothered (maternity) by the putative parents. The models only require genetic data from the parent or parents in question and the sample of NGIs, as well as an estimate of population allele frequencies. The models provide unbiased estimates, can accommodate loci with many alleles and are robust to violations of their assumptions. They allow researchers to address intractable problems such as the parentage of seeds found on the ground, juvenile fish in a stream, and nestlings in a communal breeding bird. We demonstrate the models using genetic data from a nest of the bluegill sunfish Lepomis macrochirus, where the NGIs may be from multiple females that have spawned with multiple males from different life histories (cuckolder and parental).