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Character coding has been called the bete noire of phylogenetic analysis. As you may have seen from class, the definition of "character" is squishy and varies between authors. Although there isn't agreement on exactly what a character is, it is possible to predict how certain character definitions and coding strategies affect phylogenetic analysis. This activity focuses on character coding, specifically about how different coding strategies can affect analysis. In this exercise we will try to look at different coding strategies by considering the simple shapes below. (1) What is a character, and what qualities do characters have? (2) Given the 'morphology' depicted above, what features vary? (3) Given the variation you identified, come up with as many character codings as you can; i.e., different ways that this variation can be coded into characters. (4) For each of the coding strategies you come up with in question 3, identify its assumptions, limitations, and strengths. (5) Identify your preferred coding strategy and defend your choice. Students asked to define what a character is and to discuss what they 'require', and then to come up with an exhaustive list of coding strategies for the sample morphology. They are then asked to list assumptions/limitations of each strategy.
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