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Advances in genetic and genomic technologies have become widely available and have potential to provide novel insights into fish biology and fisheries science. In the present overview, we explore cases for which genomic analyses have proven instrumental in the rejection of hypotheses that have been well-motivated based on phenotypic and ecological properties of individuals and populations. We focus on study systems for which information derived using genomic tools contradicts conclusions drawn from traditional fisheries science methodologies and assumptions. We further illustrate the non-intuitive interplay of genomics and ecology in Atlantic salmon (Salmo salar L.) owing to the recently detected genetic architecture of age at maturity in this species. To this end, we explore a salmon management strategy applied in Québec, Canada and find that management measures aimed at protecting large, old individuals can lead to unexpected and undesired outcomes. Finally, we envisage ways in which genomic tools could be used more effectively in contemporary fisheries research and how their application could illuminate the ecological and evolutionary drivers of species and ecosystem dynamics.

When phenotypes fail to illuminate underlying genetic processes in fish and fisheries science