Character coding

Jeffrey Wilson

University of Michigan

Upper level undergraduate/graduate student course Methods in Paleontology.

Students should understand basic underpinnings of phylogenetic analysis, and they should have some background on how characters are constructed.

The activity was designed as a take-home assignment but could easily be done in class. It follows a series of lectures on the philosophy underlying systematics, characters, and operational taxonomic units. This is one of a series of exercises.

I would like students to develop a definition of what a character is.

I would like them to appreciate that there are different ways of coding characters, and that these ways have effects on phylogenetic analysis.

I would like students to be able to visualize coding strategies – i.e., schools of thought on how morphology should be coded.

How do assumptions influence outcomes (in this case of a phylogenetic analysis)?

I would like students to develop the identify the assumptions implicit in phylogenetic analysis.

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.

Students turn in answers to this assignment, and I check it against my own response to the same questions.