Biologists use tree diagrams to illustrate phylogenetic relationships among species. However, both novices and experts are prone to misinterpret this notational form. A difficulty with reasoning with cladograms is that intuitive narrative conceptions of evolution as a linear progression interfere with perceiving the hierarchical relationships that tree diagrams are intended to convey. We challenge the use of standard cladograms to teach phylogenetic reasoning and attempt to disentangle the effects of content beliefs, conceptual metaphors, and visual structure. We explain how and why students misinterpret cladograms and investigate the effects of alternative, more intuitive representations and approaches. Through clinical interviews with 24 undergraduate students. Study 1 describes students’ invented representations for depicting the concept of relatedness and investigates the impacts of recontextualizing their representational activities within non-evolutionary contexts. Study 2 examines the effects on students’ reasoning with the standard cladogram after they first invent a diagram of their own. Findings from our mixed quantitative and qualitative analyses display the range of representational resources that students bring to the task of reasoning about relatedness. They suggest potential value in building upon such representations when teaching novices to reason about phylogenies. We observed that the quality of students’ reasoning differed depending on whether students invented a representation, what kind they invented, and in what context. While some findings are promising, others reaffirm the powerful influence of Gestalt perceptual processes on students’ misinterpretations of these difficult, but critical scientific diagrams. We end by discussing implications for instructors and designers.