In the previous chapter, we covered techniques for reasoning about evolution in terms of trees of descent. The algorithms we covered for tree-building, UPGMA and neighbor-joining, assumed that we were comparing fully aligned sections of sequences.
In this section, we present additional models for using phylogenetic trees in different contexts. Here we clarify the differences between species and gene trees. We then cover a framework called reconciliation which lets us effectively combine the two by mapping gene trees onto species trees. This mapping gives us a means of inferring gene duplication and loss events.
We will also present a phylogenetic perspective for reasoning about population genetics. Since population genetics deals with relatively recent mutation events, we offer the Wright-Fisher model as a tool for representing changes in whole populations. Unfortunately, when dealing with real-world data, we usually are only able to sequence genes from the current living descendants of a group. As a remedy to this shortcoming, we cover the Coalescent model, which you can think of as a time-reversed Wright-Fisher analog.
By using coalescence, we gain a new means for estimating divergence times and population sizes across multiple species. At the end of the chapter, we touch briefly on the challenges of using trees to model recombination events and summarize recent work in the field along with frontiers open for exploration.