1.1: Introduction
Evolution is happening all around us. In many cases – lately, due to technological advances in molecular biology – scientists can now describe the evolutionary process in exquisite detail. For example, we know exactly which genes change in frequency from one generation to the next as mice and lizards evolve a white color to match the pale sands of their novel habitats (Rosenblum et al. 2010) . We understand the genetics, development, and biomechanical processes that link changes in a Galapagos finches’ diet to the shape of their bill (Abzhanov et al. 2004) . And, in some cases, we can watch as one species splits to become two (for example, Rolshausen et al. 2009) .
Detailed studies of evolution over short time-scales have been incredibly fruitful and important for our understanding of biology. But evolutionary biologists have always wanted more than this. Evolution strikes a chord in society because it aims to tell us how we, along with all the other living things that we know about, came to be. This story stretches back some 4 billion years in time. It includes all of the drama that one could possibly want – sex, death, great blooms of life and global catastrophes. It has had “winners” and “losers,” groups that wildly diversified, others that expanded then crashed to extinction, as well as species that have hung on in basically the same form for hundreds of millions of years.
There is, perhaps, no more evocative symbol of this grand view of evolution over deep time than the tree of life (Figure 1.1; Rosindell and Harmon 2012) . This branching phylogenetic tree connects all living things through a series of splitting events to a single common ancestor. Recent research has dramatically increased our knowledge of the shape and form of this tree. The tree of life is a rich treasure-trove of information, telling us how species are related to one another, which groups are exceptionally diverse or depauperate, and how life has evolved, formed new species, and spread over the globe. Our knowledge of the tree of life, still incomplete but advancing every day, promises to transform our understanding of evolution at the grandest scale (Baum and Smith 2012) .
Knowing the evolutionary processes that operate over the course of a few generations, even in great detail, does not automatically give insight into why the tree of life is shaped the way that it is. At the same time, it seems reasonable to hypothesize that the same processes that we can observe now - natural selection, genetic drift, migration, sexual selection, and so on - have been occurring for the last four billion years or so along the branches of the tree. A major challenge for evolutionary biology, then, comes in connecting our knowledge of the mechanisms of evolution with broad-scale patterns seen in the tree of life. This “tree thinking” is what we will explore here.
In this book, I describe methods to connect evolutionary processes to broad-scale patterns in the tree of life. I focus mainly – but not exclusively – on phylogenetic comparative methods. Comparative methods combine biology, mathematics, and computer science to learn about a wide variety of topics in evolution using phylogenetic trees and other associated data (see Harvey and Pagel 1991 for an early review) . For example, we can find out which processes must have been common, and which rare, across clades in the tree of life; whether evolution has proceeded differently in some lineages compared to others; and whether the evolutionary potential that we see playing out in real time is sufficient to explain the diversity of life on earth, or whether we might need additional processes that may come into play only very rarely or over very long timescales, like adaptive radiation or species selection.
This introductory chapter has three sections. First, I lay out the background and context for this book, highlighting the role that I hope it will play for readers. Second, I include some background material on phylogenies - both what they are, and how they are constructed. This is necessary information that leads into the methods presented in the remainder of the chapters of the book; interested readers can also read Felsenstein (Felsenstein 2004) , which includes much more detail. Finally, I briefly outline the book’s remaining chapters.