Molecular pedigree analysis in natural populations of fishes: approaches, applications, and practical considerations

Molecular markers can provide information on the family structure of natural fish populations through molecular pedigree analysis. This information, which is otherwise difficult to obtain, can give important insights into the expression and evolution of phenotypic traits. We review the literature to provide examples of how molecular pedigree analysis has been used extensively to examine patterns of distribution, dispersal, and social behaviour in fishes and how it provides a tool for the estimation of quantitative genetic parameters. Although multiple methodologies can be used to examine family structure, the efficacy of any molecular pedigree analysis is generally dependent on prior consideration of interrelated statistical and biological factors. Statistical issues stem from the choice of molecular marker type and marker set used, in addition to sampling strategy. We discuss these considerations and additionally emphasize the utility of supplemental nongenetic data for increasing the efficacy of pedigree analysis. We advocate that, where possible, a priori knowledge of the study system's biology should be used to inform study design and further highlight the need for additional empirical testing of methodologies.