This paper gives an example of how to address the challenge of designing a learning progression that describes student thinking, with the necessary specificity to align instructional opportunities and assessment tools. We describe the Conceptual Underpinnings of Evolution project and the iterative process of developing a novel learning progression theory, while critically testing that theory using structured interview data analyzed with Rasch models. We investigate elementary students' capacities for reasoning in biology, specifically focusing on microevolution as a strategic core idea for students between the ages of seven and nine. The learning progression theory informed the design of two instructional modules which aimed to build on students' intuitions. The modules provided opportunities for students to engage in scientific practices framed to develop more adequate explanations about how organisms may change over time, in accordance with environmental changes. Aligning the learning progression, instructional activities, and structured interview assessment was critical for meeting two of our underlying assumptions: that students' reasoning capacities rely on instructional opportunities; and that students' assessment scores must be interpretable in terms of learning progression levels. We share both initial and late-stage versions of the learning progression and describe how item-level information and Rasch analyses helped both to specify the learning progression levels and to define the two underlying dimensions.