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GEOL 331 Phylogenetics

GEOL 331 Principles of Paleontology

Fall Semester 2008 Phylogenetic Systematics
Evolution as Pattern The goal of systematics: The diversity of living things presents us with a seemingly infinite variety. The science of systematics is dedicted to identifying and ordering the diversity of living things. : The ordering of this diversity. Since prehistory, systematists have employed taxonomic systems in which organisms are classified into groups or taxa (singular: taxon). Many different taxonomic systems are conceivable, but all have the following features: A heirarchy of internested groups An organizational principle. For example, in our lives, we have all employed the taxonomic system in which animals are classified according to the organizational principle of their utility to humans. Generally, there is little ambiguity.

Livestock

Pet

Vermin

More Problem: The criteria that we use to classify animals according to this system are arbitrary and subjective. For example, the green tree python Morelia viridis: A reptile enthusiast might classify this as a pet, where a person who was terrified of snakes would call it vermin, and an entrepeneur who raises reptiles for the pet trade would view it as livestock.

The Linnaean System: The first attempt to organize the diversity of life in an explicit and non-arbitrary manner was made by Carl
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Linnaeus (a.k.a. Carolus Linnaeus and, after his ennoblement, Carl von Linn.) Linnaeus was a Swedish botanist who may be the first and last person in history to publish on every known organism. His Systema Naturae is the basis for the Linnaean system of taxonomy. Its first edition was in 1735, but the tenth is regarded as the most authoritative, published in 1758. Its major features: Systematized and popularized the use of the binomial nomenclature first proposed by the Bauhin brothers in 1596. Organisms grouped according to physical similarity of key features. Linnaeus had pioneered the classification of plants based on reproductive structures, which he considered the least ambiguous, and applied this concept to animals, as well. By this means, whales were moved from fish to mammals, and humans were placed among the primates. Groups formed an internested hierarchy. A groups position in the hierarchy was expressed as its taxonomic rank. Expended subsequently into the familiar kingdom, phylum, class, order, family, genus, species. More A fantastic achievement, but late in his life, Linnaeus lamented that for all his work, he felt that he had never succeeded in identifying the true organising principle of the diversity he had described. In retrospect, that principle was the branching pattern of phylogeny produced by evolution, first proposed publicly a century after the publication of the 10th edition. The Linnaean System in the age of Darwin: The recognition that Linnaean taxa were products of shared common ancestry provoked refinements of the system such that only groups that shared common ancestry were acknowledged. Thus, "Pachydermata" containing rhinos, elephants, and hippos, but not their common ancestor, was out. Beyond that, before the age of digital computers and electronic media, not much else was really practical. The result was an awkward century in which the Linnaean system was used and interpreted in an evolutionary sense, but where certain infelicities were tolerated. Conflation of true extinctions and pseudoextinctions: Any serious attempt to assess lineage longevity (e.g. Van Valen's Red Queen) or identify mass extinction events absolutely needed to factor pseudoextinctions out, but this was usually impractical. The biological unreality of taxonomic ranks: Cosider this example: How are alligators like oysters? - Both the groups Alligatoridae, including modern alligators and caimans, and Ostreidae, containing modern oysters, have the rank of "family" in the Linnean system, suggesting that they are somehow biologically equivalent. Many measures of equivalence can be imagined. Maybe the progenitors of Ostreidae and Alligatoridae lived at the same time in the geologic past. Maybe the two groups include the same number of species. Maybe they encompass the same degree of morphological divergence. But alas... Ostreidae: appears in Late Triassic (about 210 mya). Alligatoridae: appears in Paleocene (about 60 mya). There are considerably more ostreid species (39 fossil) than alligatorid (26 fossil). Ostreidae and Alligatoridae are so different that an objective standard of morphological similarity can't be envisioned. So what, exactly, does it mean to say that oysters and alligators are related at the "family" level? Can it be that establishing taxonomic rank is, "more of an art than a science," involving the interpolation of new groups into the preexisting system? That's OK if you only intend to use the system for information retrieval, but academics who attempt to measure patterns of evolution by counting, say, families inevitably must confront the fact that they really are not counting equivalent units. Stephen Jay Gould famously fell for this in his influential book Wonderful Life. More The History of Phylogenetic Systematics (Cladistics) Ideally, we would like to have some non-arbitrary, natural organizing principle for a taxonomic system that natural scientists can use. Indeed, Darwin, in the Origin noted that the Linnean system of taxonomy, based on general similarity, ought to be superceded by one based on closeness of common ancestry. Alas, on a practical level, such an undertaking was impossible until the invention of digital computers. During the mid 20th century, two separate approaches developed seeking to use numerical algorithms to establish a rational basis for a system of taxonomy: Numerical taxonomy (Phenetics): Introduced by Robert Sokal and Peter Sneath in late 1950s. Attempted to base classification on
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GEOL 331 Phylogenetics

similarity alone, regarding the tree of evolution as fundamentally unknowable. Pheneticists tend to use continuous numerical measurements in multivariate statistical analyses to identify groups based on similarity. Phylogenetic Systematics (Cladistics): Introduced by Willi Hennig in 1950. Book Phylogenetic Systematics translated into English in 1966. Viewed evolution as the indespensible organising principle of biology and the basis for a taxonomic system. Cladists tend to use characters with discrete states and parsimony based analyses to reconstruct the Tree. From this, they take their taxonomic system. By the mid 1970s, cladistics had eclipsed phenetics. By the 90s it was the dominant school of taxonomic thought. In North America, the 1980s were the heady era of taxonomic revolution in which cladistic revolutionaries in institutions such as the University of California at Berkeley and the American Museum of Natural History shaped the future of systematics. A revealing document from this era is: Kevin DeQueiroz, 1988. Systematics and the Darwinian Revolution. Philosophy of Science, 55: 238-259. DeQueiroz 1988 key concepts: Homology vs. Analogy Homology: Derivation of structures in different individuals from the same evolutionary precursor. E.G. Human arms, bird wings, whale flippers - all derived from the ancestral tetrapod forelimb. Analogy: Similarity of function without any necessary common derivation. E.G. Dragonfly wings and bird wings - used in flying but with no common derivation. Class vs. Individual Class: A group consisting of entities defined by their characteristics. (E.G. "electrons," "tax-collectors") System (or "individual"): A group consisting of entities defined by their historical origin and fate. Classification vs. System Classification: Taxonomy based on a hierarchy of classes. Systematics: Taxonomy based on a hierarchy of individuals related by an organizing principle. More The triumph of phylogenetic systematics sets the tone for contemporary academic discussions of phylogeny and systematics. This requires the well-informed reader to master graphic conventions and some rather clunky technical terms. You can do it. Cladograms: Throughout evolutionary history, lineages of interbreeding organisms have evolved through time and occasionally split into separate, reproductively isolated lineages. The result is an evolutionary "tree" with many branches. We represent this tree, or portions of it that we want to talk about, using stick-figure trees called cladograms. In this cladogram, the organisms A, B, and C at the ends of the branches are known as terminal taxa. The lines themselves represent evolving lineages. Branch points represent lineage splitting events. The point at the fork of each split is called a node, and represents the latest common ancestor of the descendants depicted above it. Time runs from oldest events at the bottom to youngest ones at the top. Thus, in this example, the last common ancestor of A, B, and C occurred earlier in time than the last common ancestor of B anc C.

Note that in a cladogram, it does not matter whether things apear on the left or right. What counts is the sequence of branching events (i.e. which ones appear on top or on the bottom). In the figure above, cladograms 1 and 2 depict exactly the same relationships, whereas cladogram 3 is different. More The phylogenetic taxonomic system: Taxonomic groups can be named and defined based on their descent from a common ancestor. The cladogram below shows the real relationships between several major vertebrate groups.

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Working from this cladogram, systematists have named the following taxonomic groups:

In this drawing, we have drawn circles around the groups that could be defined by the relationships shown on this cladogram, and indicated their names. Ordinarily, one would simply write the group names next to the node of the last common ancestor:

Thus, the pattern of evolution provides: A hierarchy of internested groups, with those descended from more recent common ancestors being nested within those descended from more distant ones. For instance, "Tetrapoda", the common ancestor of land vertebrates and its descendants, is nested within "Choanata", the common ancestor of vertebrates with choanae and all of its descendants. An organizing principle, the branching pattern of evolution itself. Presto! It's a proper taxonomic system. More

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GEOL 331 Phylogenetics

Definitions: Phylogeny: The branching evolutionary pattern of ancestry and descent. Phylogenetic systematics: The science of reconstructing phylogeny and developing a taxonomic system based upon it. Monophyletic groups: In phylogenetic systematics, taxonomic groups are defined strictly in terms of the non-arbitrary criterion of descent from a common ancestor. Such taxa are called monophyletic groups. *Memorize* this definition: A monophyletic group is an ancestor and ALL of its descendants. Note: You may be familiar with two types of non-monophyletic groups: Paraphyletic groups: An ancestor and some but not all of its descendants. Polyphyletic groups: A group of organisms which fails to include at least some of their common ancestors. Note carefully: Only monophyletic groups are based exclusively on natural, non-arbitrary criteria. When we define a paraphyletic group, we must arbitrarily decide which descendants to exclude. In the case of polyphyletic groups, we must decide which ancestors to leave out. More

Phylogeny reconstruction using parsimony

If God were to hand us the true phylogeny, and our only task were to read it and construct taxonomic system accordingly, our lives would be easy. Instead, we must somehow reconstruct phylogeny by making observations and testing hypotheses. This is where the "modification" side of "descent with modification" comes in. As lineages evolve, the characters of their members change. I.e. they go from ancestral to derived states. Sometimes we refer to cladograms as "trees." It helps to think of them that way. Imagine marker dye injected into branch. In the tree of evolution, the derived character states play the role of the marker dye. There is a particular type of derived character state that we are particularly interested in. Synapomorphy = A shared derived character I.e. an evolutionary novelty inherited from a common ancestor by different lineages. Synapomorphies allow us to identify monophyletic groups, because if a character is shared by two lineages, we assume that it was inherited from their most recent common ancestor Let's see how this works in a simple cladistic analysis of some imaginary beetles. We assume that they are related somehow, but we don't know if B shares a more recent common ancestor with C or A, or if C and D are more closely related to one another than to B.

The first thing we do is notice how they are different. One has long antennae while the others have short ones. One has plain wing covers while the others have spotted ones. One has stripes Two have stalked eyes while the third does not. We compile this information in a table called a taxon-character matrix. Character 1. Large jaws present 2. Small antennae present 3. Spots present 4. Stripes present A 0 0 0 0 B 1 0 0 0 C 1 1 1 0 D 1 1 1 1

This matrix records whether the observed state for each taxon is ancestral or derived. How do we know? You may have noticed that we we haven't had much to say about A. In this analysis, A is the outgroup taxon. This is a beetle that, on the basis of some prior information, we can assume is more distantly related to beetles A, B, and C than any of them are to one another. Maybe we found it fossilized in amber. The outgroup is our standard for what is derived and what isn't, in that anything we see in it, we assume to be
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the ancestral state. Incidentally, because it has smaller mandibles than the others, I've included a "large mandible" characteristic in the matrix. Tree 1:

Tree 2:

Tree 3:

We now compare every possible evolutionary tree arrangement by mapping onto them the simplest possible distribution of each character state change. principle of parsimony, which holds that the simplest solution is usually the best. For us, the simplest hypothesis is the one that invokes the fewest character state changes. That is tree 1, with only six changes. Is this the true tree? God only knows. The best we can say is that it is our best approximation based on current knowledge. More What does this method yield: Most reasonable hypothesis of phylogeny based on available data, not necessarily truth. Model of character evolution: We can identify likely points of character state change, and distinguish examples of homoplasy (discordant character evolution such as convergent evolution or reversals) from mutually consistent and unidirectionally evolving ones. (Note: Adjectiveal form is "homoplastic.") More Of course, an alert observer would raise a serious question: Phylogenetic Systematics absolutely requires us to identify variation in homologous structures, genes, or behaviors How do we know when character states are homologous? Cladists rely on three tests to falsify hypotheses of homology:
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Similarity: The homologies of two structures can be doubted if it can be shown that they are significantly dissimilar. E.g. the wings of birds and insects. Congruence: The hypothesis of homology can be falsified by showing, through a phylogenetic analysis, that the structures must have had independent origins. Thus, the wings of birds and the wings of bats are non-homologous AS WINGS, becuase they evolved from a precursor, the tetrapod forelimb, that was not used for flight. Conjunction: If two potentially homologous structures are both found in the same organism, they can't be direct homologues. E.g. We consider human arms and bird wings to be homologous as tetrapod forelimbs, but that homology could be rejected if an actual angel, having both, were to be scientifically described. BTW, I have listed these tests in order of increasing strength. We would, for instance, reject the homology of the angel arm and wing, no matter how similar they looked. Feeling vulnerable? For more review see: Cladistics review Cladistics quiz To Syllabus.
Last modified: 2 October 2008

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