PHILOSOPHY AND THE TREE OF LIFE THE METAPHYSICS AND EPISTEMOLOGY OF PHYLOGENETIC SYSTEMATICS Joel D. Velasco PHILOSOPHY AND THE TREE OF LIFE: THE METAPHYSICS AND EPISTEMOLOGY OF PHYLOGENETIC SYSTEMATICS by Joel D. Velasco A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Philosophy) at the UNIVERSITY OF WISCONSIN-MADISON 2008 © Copyright by Joel Velasco 2008 All Rights Reserved i Abstract: This dissertation examines the foundations of phylogenetic systematics which involves both the construction of phylogenetic trees to represent evolutionary history and the use of those trees to study various aspects of that history. I begin by defending a genealogy-based view of biological taxonomy: the view that all taxa—the formal groups in our classification system—must be monophyletic, i.e., they must consist of an ancestor and all of its descendants. Furthermore, I argue that, contrary to current practice, these taxa should not be assigned ranks (such as genus, family, and order). I then proceed by applying these principles to the debate about species. I argue that non- genealogically based species concepts (such as the popular “biological species concept”) are unacceptable. Instead, a species concept must delimit species so that they form genealogically exclusive groups – groups of organisms more closely related to each other than to any organisms outside the group. With this in mind, I develop two distinct phylogenetic species concepts. Each treats a species as a genealogically exclusive group of organisms. The first determines genealogical relatedness in terms of recency of common ancestry; the second understands genealogy as a composite of gene histories. Finally, I argue that there can be no objective ranking criteria for species and therefore biologists can either keep the species rank, while acknowledging that which taxa are ranked as species is arbitrary, or alternatively, can simply get rid of the rank of species. Having carefully described what phylogenies represent, I move to the epistemological problem of inferring phylogenetic trees and argue that a Bayesian methodology is appropriate. I then focus on one common objection to Bayesian inference – “the problem of prior probabilities.” I argue that this problem has been misunderstood in some cases, which leads to the failure of a variety of objections in the literature. I then develop the beginnings of a solution to this problem within phylogenetics, describe just what has been achieved, and acknowledge what has yet to be accomplished. ii Acknowledgements Thanks to my committee members Elliott Sober, Malcolm Forster, Dan Hausman, Ken Sytsma, Bret Larget and unofficial member David Baum who read the entire manuscript. Elliott and David in particular provided detailed comments on multiple drafts of the entire dissertation making the final version far better than it would have otherwise been. Thanks also to Matt Barker, Marc Ereshefsky, Matt Haber, Joe LaPorte, and Greg Novack who read portions of the thesis in article form again leading to a far better final version. As of the completion of this dissertation (May, 2008), it incorporated text from three journal articles and a number of referees helped improve those articles and therefore this thesis. These include anonymous referees from the British Journal of the Philosophy of Science and Studies in the History and Philosophy of Science who have helped improve portions of Chapters 1 and 2. These include Mike Alfaro on behalf of Molecular Phylogenetics and Evolution, as well as Kim Sterelny and an anonymous referee from Biology and Philosophy who made very helpful suggestions for Chapter 5. iii Contents Abstract i Acknowledgements ii 1 Two Principles of Phylogenetic Systematics 1 The Tree of Life 1 Phylogenetic trees 8 Why paraphyletic groups are bad 17 Ranking 22 Are ranks even consistent? 29 Why sister groups must have the same rank 31 Rank as age 35 Why classification is not important 40 Back to the Tree of Life 44 2 The Need for a Phylogenetic Species Concept 46 Introduction 46 The Biological Species Concept 48 How the BSC distorts history 50 Responses to the paraphyly problem 55 The second kind of misrepresentation 58 Species and the Tree of Life 63 iv 3 Developing a Phylogenetic Species Concept 72 A Phylogenetic Species Concept 72 Monophyletic groups of organisms 76 Epistemological issues 77 The real problem with non-nested groups 80 From monophyly to exclusivity 82 From organism pedigrees to gene genealogies 89 Gene genealogies 92 Exclusivity as recentness of genetic coalescence 98 From 100% to less 100 Criticisms of the genealogical species concept 104 Organisms or genes? 112 4 Species as a Rank 114 Species as a Rank 114 Species as basal taxa 119 Species as individuals 123 Category vs. taxon 127 Sidestepping more metaphysics 129 An ambiguous debate 135 Species as evolutionary units 140 Species as a grade 142 v Getting rid of Species 147 Phylogenetics without species 150 5 Inferring Phylogenetic Trees 155 1 Introduction 155 2 Bayesian phylogenetics 157 Priors on clades 164 Possible Priors and the Principle of Indifference 172 The Yule Process 174 The Base-Rate Fallacy 181 References 185 1 ONE TWO PRINCIPLES OF PHYLOGENETIC SYSTEMATICS 1. The Tree of Life It was, of course, Darwin who revolutionized our understanding of the diversity of life with his On the Origin of Species (Darwin 1859). It is in the Origin that we first see the importance of genealogy on a grand scale where Darwin convincingly argues that common ancestry explains both the striking similarities between different species and the groups within groups hierarchy of traits. As he says, “All the foregoing rules and aids and difficulties in classification are explained, if I do not greatly deceive myself, on the view that the natural system is founded on descent with modification; that the characters which naturalists consider as showing true affinity between any two or more species, are those which have been inherited from a common parent, and, in so far, all true classification is genealogical; that community of descent is the hidden bond which naturalists have been unconsciously seeking, and not some unknown plan of creation, or the enunciation of general propositions, and the mere putting together and separating objects more or less alike” (420). Earlier, Darwin had introduced the metaphor of the Tree of Life which connects all life through genealogy. 2 “The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth….…The green and budding twigs may represent existing species; and those produced during former years may represent the long succession of extinct species….….the great Tree of Life…covers the earth with ever-branching and beautiful ramifications.” (129-30.) To help us understand the Tree, Darwin gives us a figure – the only figure in the entire Origin – which he then repeatedly refers back to (116). Figure 1.1 Darwin's "Tree-Thinking". The only figure in On the Origin of Species, it represents "decent with modification". 3 Key to understanding the diagram is that this represents real genealogical history – and not simply a subordination of groups within groups such as the diagrams previously given by Linnaeus, among others. It is also important that Darwin did not label the Tree more specifically than he did – for example, by saying that this is how various groups of mammals are related to each other. Rather, the idea is that this same pattern is seen throughout all life. In addition, the Tree is not meant to be just a depiction of how species are related but rather, how taxa are related. A "taxon", (plural "taxa") refers to any formally named group, such as Homo sapiens, in our system of biological classification. Darwin refers to this same diagram in discussing the relationship of higher taxa like genera (123) (where "higher taxa" simply means any taxa more inclusive than a species) and subspecific groups like varieties (117) as well as species (120). In this manner, the figure is rather like a fractal – the same pattern emerges when we “zoom in” or “zoom out” on some particular aspect of the Tree. Although Darwin believed that genealogy was important for classification, he did not believe that it was sufficient for providing a full classification. But for now, ignore classification and focus just on the concept of genealogy and the Tree of Life. This idea of the Tree which connects all life was prevalent in the literature for the next 100 years, but mainly served as a metaphor for evolution or even for progress. Famously, Ernst Haeckel depicted various versions of the Tree in many different works. One of his more famous figures is first seen in his 1874 work Antrhopogenie. Figure 1.2 is from the 1876 translation of this work into English called The Evolution of Man. 4 Figure 1.2 A depiction of the Tree of Life from Ernst Haeckel (1874 and 1876) Plate XV. Although there is certainly some branching depicting common ancestry, the diagram is clearly still influenced by ladder thinking. Notice that humans stand at the top of the Tree while more “primitive” forms are at the base giving the impression that mammals, primates, and humans actually arose from these more primitive groups. However, these 5 primitive groups are not direct ancestors. Rather, they are currently existing groups! Instead of the groups sharing an ancestor/descendant relationship, currently existing groups must share common ancestry – that is, they are all the descendants of some common ancestor. The tree is obviously anthropocentric as well with humans at the top. This smacks of a kind of progressivism – certainly popular historically (Ruse 2005) but which is unpopular today. Not only is it progressively leading to humans at the top, but there is clearly a “main” line of evolution and then various branches split off from the main line.