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20/12 GEOL 331 Phylogenetics

ww.geol.umd.edu/~tholtz/G331/lectures/331phylo.html

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 dedicte

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 intogroups or taxa (singular: taxon). Many different taxonomic systems are conceivable, but all have the following features:

A heirarchy of internested groupsAn organizational principle.

For example, in our lives, we have all employed the taxonomic system in which animals are classified according to the organizationalprinciple of their utility to humans. Generally, there is little ambiguity.

Livestock Pet Vermin

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Problem: The criteria that we use to classify animals according to this systemare arbitrary and subjective. For example, the green tree python Moreliaviridis: 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 raisesreptiles 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 firstand 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 onreproductive 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. Expendedsubsequently into the familiar kingdom, phylum, class, order, family, genus, species.

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A fantastic achievement, but late in his life, Linnaeus lamented that for all hiswork, he felt that he had never succeeded in identifying the true organisingprinciple of the diversity he had described. In retrospect, that principle was thebranching pattern of phylogeny produced by evolution, first proposed publicly acentury after the publication of the 10th edition.

The Linnaean System in the age of Darwin: The recognition that Linnaean taxawere products of shared common ancestry provoked refinements of the systemsuch that only groups that shared common ancestry were acknowledged. Thus,"Pachydermata" containing rhinos, elephants, and hippos, but not their commonancestor, 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 inwhich the Linnaean system was used and interpreted in an evolutionary sense, butwhere certain infelicities were tolerated.

Conflation of true extinctions and pseudoextinctions: Any serious attempt to assess lineage longevity (e.g. Van Valen's RedQueen) 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 groupsAlligatoridae, including modern alligators and caimans, and Ostreidae, containing modern oysters, have the rank of "family" in theLinnean system, suggesting that they are somehow biologically equivalent. Many measures of equivalence can be imagined.

Maybe the progenitors ofOstreidae andAlligatoridae 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 andAlligatoridae 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 establishingtaxonomic 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 evolutionby counting, say, families inevitably must confront the fact that they really are not counting equivalent units. Stephen Jay Gouldfamously fell for this in his influential book Wonderful Life.

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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 onebased on closeness of common ancestry. Alas, on a practical level, such an undertaking was impossible until the invention of digitalcomputers.

During the mid 20th century, two separate approaches developed seeking to use numerical algorithms to establish a rational basis for asystem of taxonomy:

Numerical taxonomy (Phenetics): Introduced by Robert Sokal and Peter Sneath in late 1950s. Attempted to base classification on


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similarity alone, regarding the tree of evolution as fundamentally unknowable. Pheneticists tend to use continuous numericalmeasurements in multivariate statistical analyses to identify groups based on similarity.

Phylogenetic Systematics (Cladistics): Introduced by Willi Hennig in 1950. Book Phylogenetic Systematics translated into Englishin 1966. Viewed evolution as the indespensible organising principle of biology and the basis for a taxonomic system. Cladists tendto use characters with discrete states and parsimony based analyses to reconstruct the Tree. From this, they take their taxonomicsystem.

By the mid 1970s, cladistics had eclipsed phenetics. By the 90s it was the dominant school of taxonomic thought. In North America, the1980s were the heady era of taxonomic revolution in which cladistic revolutionaries in institutions such as the University of California atBerkeley 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, birdwings, 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 inflying 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.

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The triumph of phylogenetic systematics sets the tone for contemporary academic discussions of phylogeny and systematics. This requiresthe 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 itthat 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 areknown as terminal taxa. The lines themselves represent evolving lineages.Branch points represent lineage splitting events. The point at the fork of eachsplit is called a node, and represents the latest common ancestor of thedescendants depicted above it. Time runs from oldest events at the bottom toyoungest ones at the top. Thus, in this example, the last common ancestor of A, Band 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, whereascladogram 3 is different.

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The phylogenetic taxonomic system: Taxonomic groups can be named and defined based on their descent from a common ancestor. Thecladogram 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, andindicated 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 thosedescended from more distant ones. For instance, "Tetrapoda", the common ancestor of land vertebrates and its descendants, is nestedwithin "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.

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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 descenfrom 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.

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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 wouldbe 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 fromancestral 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 treeof 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 derivedcharacter 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 wasinherited 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'tknow 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.

Character1. Large jaws present2. Small antennae present3. Spots present4. Stripes present

A0000

B1000

C1110

D1111

This matrix records whether the observed state for each taxon is ancestral or derived. How do we know? You may have noticed thawe 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 priorinformation, we can assume is more distantly related to beetles A, B, and C than any of them are to one another. Maybe we found itfossilized 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 inthe matrix.

Tree 1:

Tree 2:

Tree 3:

We now compare every possible evolutionary tree arrangement by mapping onto them the simplest possible distribution of eachcharacter state change.

principle of parsimony, which holds that the simplest solution is usually the best. For us, the simplest hypothesis is the one thatinvokes the fewest character state changes. That is tree 1, with only six changes. Is this the true tree? God only knows. The bestwe can say is that it is our best approximation based on current knowledge.

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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 evolvingones. (Note: Adjectiveal form is "homoplastic.")

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Of course, an alert observer would raise a serious question: Phylogenetic Systematics absolutely requires us to identify variation inhomologous structures, genes, or behaviors How do we know when character states are homologous? Cladists rely on three tests tofalsify 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 wingsof birds and insects.

Congruence: The hypothesis of homology can be falsified by showing, through a phylogenetic analysis, that the structures musthave had independent origins. Thus, the wings of birds and the wings of bats are non-homologous AS WINGS, becuase theyevolved 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 actualangel, 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, nomatter how similar they looked.

Feeling vulnerable? For more review see:

Cladistics reviewCladistics quiz

To Syllabus.

Last modified: 2 October 200 8

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