Life on a Tree

In this chapter we consider the set of family relationships that resulted from Darwin’s process of species subdividing into new species over evolutionary time. We call this problem that of finding the tree of life and note that the tree diagrams we will use to represent it have some tricky properties we need to be aware of. We next recognize that the number of possible evolutionary trees for https://www.w3.org/1998/Math/MathML" display="inline"> n species grows so rapidly that we cannot possibly consider all such trees when the number of species is even moderately large. We then give a short sketch of using a maximum parsimony approach to identifying a good evolutionary tree and comment on some of the weaknesses of this approach. Building on the work in Chapters 11 and 12 , we create a differential equation model of the probabilities of various sequence changes happening in an alignment over evolutionary time. We find this model is one of the rare cases where an analytic solution exists. We introduce the maximum likelihood approach to tree inference, using a coin-flipping example for intuition. We perform an example maximum likelihood analysis to convince ourselves that whales and dolphins are not fish.