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As science instruction moves from lectures that emphasize lists of facts to more student-centered approaches that emphasize knowledge generation and justification, it is clear that assessments must also change. The assessment instruments developed for a nine-week high school course on evolution engaged students in activities that mirrored the practices of evolutionary biology. Students used the model to explain phenomena through a set of writing assignments documenting their evolving ideas and allowing them to see how their ideas changed. By the end of the nine-week course, students made important gains in their understandings of variation, selection, and heritability.