In the introduction to Chapter 7, I mentioned that squamates had lost their limbs repeatedly over their evolutionary history. This is a pattern that has been known for decades, but analyses have been limited by the lack of a large, well-supported species-level phylogenetic tree of squamates (but see Brandley et al. 2008). Only in the past few years have phylogenetic trees been produced at a scale broad enough to take a comprehensive look at this question [e.g. Bergmann and Irschick (2012); Pyron et al. (2013); see Figure 8.1]. Such efforts to reconstruct this section of the tree of life provide exciting potential to revisit old questions with new data.
Plotting the pattern of limbed and limbless species on the tree leads to interesting questions about the tempo and mode of this trait in squamates. For example, are there multiple gains as well as losses of limbs? Do gains and losses happen at the same rate, or (as we might expect) are gains more rare than losses? We can test hypothesis such as these using the the Mk and extended-Mk models (see chapter 7). In this chapter we will fit these models to phylogenetic comparative data.