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Read the following paper (abbreviated hereafter as MF2015)…

Maddison, W. P., and R. G. FitzJohn. 2015. The unsolved challenge to phylogenetic correlation tests for categorical characters. Systematic Biology 64:127–136.

and briefly answer the following questions:

  1. What is pseudoreplication (as the term is used in this paper)?

  2. Describe the simulation experiment (p. 130) used to claim that Pagel’s (1994) test of character correlation is susceptible to pseudoreplication.

  3. If you were Mark Pagel, how would you conduct this simulation experiment if your goal was to show that the test for character dependence is not flawed. Hint: start by identifying ways in which the simulation done by MF2015 violates the assumptions of Pagel’s independence model.

  4. Explain why (according to MF2015) panels a and b in Figure 1 should be identified by comparative methods as evidence of significant evolutionary correlation and panels c and d should not.