©Baum and Smith 1/19/09. Draft. Do not circulate. Page 1 Tree thinking and its importance in modern biology Tree thinking is the ability to interpret phylogenetic trees and apply them to describing and analyzing evolutionary phenomena. Tree thinkers visualize evolution as a branching process and use phylogenetic trees as tools to organize knowledge of biological diversity. Although, the idea that biological evolution can be represented as a branching tree goes back at least 150 years to Charles Darwin, the deeper implications of phylogenetic trees have really only emerged in the last few decades. In this introductory chapter we give a brief historical overview of the development of tree thinking and then discuss why it has become such an important skill for a biologically literate person in the 21st Century. Before Charles Darwin Jean Baptiste Lamarck (1744-1829), naturalist and Professor of Worms and Insects in Paris, is often credited with offering the first scientific theory of evolution. He proposed that simple life is constantly emerging from non-living matter by a process of spontaneous generation. From a modern perspective, the idea that life could emerge without any progenitors is hard to grasp, but spontaneous generation was a widespread view until it was discredited by the elegant experimentation of Louis Pasteur (1822-1895). Lamarck’s idea was that, after emerging from inanimate matter, life forms had an internal drive towards improvement causing them to evolve upwards on the Scala Naturae, the “ladder of life.” The ladder of life was a long-standing concept, tracing back to Aristotle. The idea is that living beings are organized in an ascending series, with simple organisms such as plants, sponges, and worms lower down the ladder than more complicated organisms like lizards, dogs, and humans. The ladder of life is prominent in popular culture, perhaps because it naturally resonates with how people think. Ask yourself: which of the following two orderings makes most “sense”: fish-newt-lizard-mouse-human or fish-human-lizard-mouse-newt. Probably you said the first. Actually, as described in later chapters, tree thinking implies that neither linear ordering is biologically meaningful Lamarck’s view implied that each living form had an independent origin at a different time in the past. It also implied that the longer a lineage had existed, the higher it would have progressed up the ladder of life. A human, the most advanced, would be descended from the most ancient lineage, whereas a slime mold would be the product of a more recent spontaneous generation. This view can be summarized graphically (credit Sam Donovan). “Advancement” primitive advanced Time past present©Baum and Smith 1/19/09. Draft. Do not circulate. Page 2 Lamarck not only proposed that evolution happened, but proposed a theory for how it happened, namely the inheritance of acquired characteristics through the use and disuse of parts. Indeed, the term Lamarckianism as contrasted with Darwinism, generally refers to this theory of how evolution happens. This is somewhat ironic since Charles Darwin and his contemporaries generally accepted the inheritance of acquired characteristics as a valid mechanism of evolution. Rather, the more important contrast between Lamarck and Darwin is: separate ancestry and a ladder metaphor (Lamarck) versus common ancestry and a tree metaphor (Darwin) It is not entirely clear why, but sometime between Lamarck’s era and that of Charles Darwin discourse concerning evolution switched from one involving multiple origins to one involving shared ancestry. This can be seen, for example, in Zoonomia, the lengthy primarily medical treatise published in 1803 by Charles Darwin’s grandfather, Erasmus Darwin (1731-1802). …would it be too bold to imagine, that in the great length of time, since the earth began to exist, perhaps millions of ages before the commencement of the history of mankind, would it be too bold to imagine, that all warm-blooded animals have arisen from one living filament…. In proposing that all warm-blooded animals arose from one ancestral “filament,” Erasmus implies some kind of evolutionary branching process that allows one ancestor to eventually yield multiple, very different descendants. Not long after the publication of Zoonomia, the great English geologist Sir Charles Lyell (1797-1875) provided what may be the first piece of formal tree thinking. In the course of describing (and discrediting) Lamarck’s ideas on evolution, he replaced a theory of separate ancestry and a ladder of life, with a theory of common ancestry and branching (“ramification”): “We know that individuals which are mere varieties of the same species, would, if their pedigree could be traced back far enough, terminate in a single stock; so according to the train of reasoning before described, the species of a genus, and even the genera of a great family, must have had a common point of departure. What then was the single stem from which so many varieties have ramified?” Lyell is pointing out that a valid evolutionary theory would imply that very different living forms, if traced back from offspring to parent to grandparent, etc., would ultimately converge on one common ancestor. But, the idea that there could be some organism that was a direct ancestor of both a worm and a human was just too hard to accept. Given the challenge that common ancestry posed to imagination and to religious doctrine, Lyell felt that firm evidence for this contention was needed. However, the evidence was flimsy, leading Lyell to reject common ancestry and, with it, evolution. However, his protégé, Charles Darwin, ultimately assembled the evidence that Lyell needed to become convinced of evolution.©Baum and Smith 1/19/09. Draft. Do not circulate. Page 3 Charles Darwin’s role in the development of tree thinking Charles Darwin (1809-1882), English naturalist and founder of modern evolutionary biology, was heavily influenced by the work of Lyell (and presumably also by Erasmus Darwin). Therefore, it is not surprising that when he pondered the origins of biological diversity Darwin was drawn to the tree metaphor rather than the ladder of life. His sketch of 1837, reproduced here, is generally identified as corresponding to a key moment in the development of Charles Darwin’s evolutionary views. The metaphor he developed is