Representations are a critical way to communicate scientific knowledge. Systematists biologists are acknowledged as expert tree thinkers who can both read and build phylogenetic trees (e.g., cladograms) accurately. The purpose of this study was to identify the core skills essential to help college students overcome tree-thinking challenges. In this study, I used pre/posttests, interviews, weekly reflective journal entries, field notes from course observations, and student responses to coursework to learn how upper-level college biology students developed representational competence with phylogenetic trees. I identified essential core skills by investigating students' tree-thinking progression over the course of the semester. Three major patterns emerged from the data: (1) students became better tree readers than tree builders by the end of the plant systematics course; (2) core skills are essential for students to develop tree-thinking competence; and (3) tree reading skills developed before tree building skills. By diagnosing challenges students face with tree-thinking, identifying core skills necessary to overcome these challenges, and developing a starting point for a context-based framework for representational competence, this study adds to our understanding of critical elements necessary for designing effective instructional interventions and improving student learning with phylogenetic trees.Keywords Tree-thinking . Cladogram . Phylogenetic tree . Challenges . Core skills . Representations . EvolutionPeople use representations to explain how we make sense of things on a daily basis. Often biologists generate phylogenetic representations to express their understandings of the evolutionary relationships they are investigating (Matuk 2007). In systematic biology, biological information is organized using phylogenetics and "evolutionary trees serve not only as tools for biological researchers across disciplines but also as the main framework within which evidence for evolution is evaluated" (Baum et al. 2005). Evolutionary biologists interpret phylogenetic trees in accordance with how they illustrate evolutionary histories or inferred evolutionary relationships among a set of taxa (Baum and Offner 2008). Scientists compare phylogenetic representations in search of similar patterns to provide support for hypothesized relationships among taxa. They find similarities by comparing monophyletic groups, or clades, across representations. Being able to correctly interpret and compare phylogenetic trees is a critical component to developing tree-thinking.A second component of tree-thinking involves generating phylogenetic trees by isolating and interpreting informative data into evidence of evolutionary relationships. There are many different styles of representations an expert could generate if asked to draw a visual representation illustrating the relationships among taxa (e.g., Matuk 2007). In addition, scientifically accurate phylogenetic representations share the following features: relationships are gr...