Pleiotropy is the well-established phenomenon of a single gene affecting multiple traits. It has long played a central role in theoretical, experimental, and clinical research in genetics, development, molecular biology, evolution, and medicine. In recent years, genomic techniques have brought data to bear on fundamental questions about the nature and extent of pleiotropy. However, these efforts are plagued by conceptual difficulties derived from disparate meanings and interpretations of pleiotropy. Here, we describe distinct uses of the pleiotropy concept and explain the pitfalls associated with applying empirical data to them. We conclude that, for any question about the nature or extent of pleiotropy, the appropriate answer is always 'What do you mean?'.
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