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In the early 1990s, geneticists faced a crisis: the workhorse method of linkage analysis, revolutionized by the production of chromosomal maps of DNA markers over the course of the preceding decade, might be incapable of locating genetic causes of more common traits and conditions. For an emerging community of statisticians and statistical geneticists, loosely united by the new flagship journal Genetic Epidemiology, this crisis prompted difficult questions about the nature of genetic investigation and the causal role of genetic factors. Did the non-replication of linkage findings demand more complex models of inheritance, more refined definitions of diseases or phenotypes, or a new paradigm for thinking about and studying the architecture of genetic causation? Using a combination of citation network analysis and oral history interviews with key figures, this paper traces how the linkage crisis fractured the fledgling discipline of genetic epidemiology, giving rise to divergent epistemic networks characterized by distinct research questions, collaborations, and strategies for interrogating genetic causality. These divisions would inform the later criticism of genetic association studies in the early 2000s, feeding an acrimonious debate about the future and potential futility of complex disease genetics. The eventual success of the association approach, I suggest, reflects its constitution as a tractable problem space for a diverse network of expertise, even as it has also demanded a redefinition of genetic causation.