PHILOSOPHY AND THE TREE OF LIFE - Joel Velasco

[Pages:217]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

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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 nongenealogically 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.

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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.

Contents

Abstract Acknowledgements

1 Two Principles of Phylogenetic Systematics The Tree of Life Phylogenetic trees Why paraphyletic groups are bad Ranking Are ranks even consistent? Why sister groups must have the same rank Rank as age Why classification is not important Back to the Tree of Life

2 The Need for a Phylogenetic Species Concept Introduction The Biological Species Concept How the BSC distorts history Responses to the paraphyly problem The second kind of misrepresentation Species and the Tree of Life

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1 1 8 17 22 29 31 35 40 44

46 46 48 50 55 58 63

3 Developing a Phylogenetic Species Concept A Phylogenetic Species Concept Monophyletic groups of organisms Epistemological issues The real problem with non-nested groups From monophyly to exclusivity From organism pedigrees to gene genealogies Gene genealogies Exclusivity as recentness of genetic coalescence From 100% to less Criticisms of the genealogical species concept Organisms or genes?

4 Species as a Rank Species as a Rank Species as basal taxa Species as individuals Category vs. taxon Sidestepping more metaphysics An ambiguous debate Species as evolutionary units Species as a grade

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72 72 76 77 80 82 89 92 98 100 104 112

114 114 119 123 127 129 135 140 142

Getting rid of Species Phylogenetics without species

5 Inferring Phylogenetic Trees 1 Introduction 2 Bayesian phylogenetics Priors on clades Possible Priors and the Principle of Indifference The Yule Process The Base-Rate Fallacy

References

v 147 150

155 155 157 164 172 174 181

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