Introduction to Phylogenetic Systematics.

I. 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 describing the order in the diversity of living things. Typically, systematists employ a taxonomic system 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 such as "evolutionary history," or "utility to humans."

    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:

    Animals
    ____________ |_____________
    Pets...............Vermin...............Livestock

    Generally, there is little ambiguity. Cows are livestock, cats are pets, cockroaches are vermin, etc. Nevertheless, the criteria that we use to classify animals according to this system are arbitrary and subjective. A reptile enthusiast might classify a boa constrictor as a pet, where a person who was terrified of snakes would call it vermin, and an entrepeneur who raises boas for the pet trade would view it as livestock. Ideally, we would like to have some non-arbitrary, natural organizing principle for a taxonomic system that natural scientists can use. Such a principle is provided by the pattern of evolution. In order to understand it, you must first understand the conventions for graphically displaying the pattern of evolution.

    II. 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.

    cladogram 1
    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.

    cladogram 1
    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.

    III. 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.

    cladogram 1
    Working from this cladogram, systematists have named the following taxonomic groups:

    cladogram 1
    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:

    cladogram 1
    Thus, the pattern of evolution provides:

  • A heirarchy 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.

    IV. 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.

    V. 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.

    It is also possible to refer 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.

    VI. Closeness of relationships: In phylogenetic systematics, how closely two taxa are related depends entirely on how recent their most recent common ancestor was.

    cladogram 1
    Who is more closely related to taxon B, A or C? To answer this, we must identify the most recent common ancestor of B and A, and of B and C. Having done this, we see that the last common ancestor of B and C lived more recently than the last common ancestor of B and A. Thus, we say that B is more closely related to C than to A.

    VII. Scoring a matrix:

    If God revealed the true cladogram to us and all that we, as systematists, had to do was read it and provide group names, our lives would be easy indeed. Instead, we must draw the cladograms ourselves, based on what we know about organisms.

    A simple example. We have three taxa whose phylogeny we would like to know: Willow trees, parrots, and cows. To start, we assume only that the three are related and have a common ancestor but that we don't know anything more about their relationship. When we draw a picture of this assumption, we see a polytomy, or branch point with more than two lineages growing from it. This means that we do not know the true relationship between the various descendant branches.

    cladogram 1
    We want to resolve this polytomy into one of three possible trees:

    cladogram 1
    We know that synapomorphies can be used to identify monophyletic groups. Our task, then, is to identify synapomorphies. An easy means of organizing information for this purpose is a matrix, or chart of taxa and characters. For now, we code each character as "yes" or "no".

    Character
    1. Cell membranes present
    2. Leaves present
    3. Paired limbs present
    A-Willow
    Y
    Y
    N
    B-Parrot
    Y
    N
    Y
    C-Cow
    Y
    N
    Y

    We can map these character state changes onto the three alternative trees to obtain three possible sequences of character changes.

    cladogram 1
    VIII. Parsimony:

    Now we must choose the one that seems the most reasonable. We don't just close our eyes and point. Instead we use the principle of parsimony to guide us.

    Applying simplicity to our choice of cladograms, we assume that the tree that requires the fewest character state changes is the most likely to be true. The changes are counted, and tree A is seen to have the fewest changes, so we are finally left with one cladogram which represents our best approximation of the phylogeny of willows, parrots, and cows.

    With large matrices, hand manipulation of the data is impossible. For these, phylogenetic analysis computer programs exist.

    IX. Outgroups:

    When we look at alternative character states such as "Paired limbs present" or "Paired limbes absent." We need to know which characters are ancestral or primitive and which are derived. This is because only shared derived characters tell us anything about organismal relationships. In the last example, you simply took our word for which characters were ancestral and which were derived. In real life, no one tells us this. Instead, we choose a taxon which we consider distantly related to the taxa whose phylogeny we want to know and let it be our standard. This standard taxon is called the outgroup. We assume that the character states that it shows are ancestral, and score the other taxa (the ingroup) by comparison with it.

    cladogram 1
    Imagine that we have landed on the planet of the potato heads, and want to perform a phylogenetic analysis of the different taxa that we have found. Natives tell us that taxon A is very distantly related to the others, so we choose it as our outgroup. We now score our matrix using the systematist's convention that "0"=ancestral and "1"=derived instead of with "yes" and "no" (which is systematists' baby-talk.):

    Character
    1. Eyes present
    2. Feet present
    3. Hat present
    4. Lips present
    A-Outgroup
    0
    0
    0
    0
    B
    0
    0
    1
    0
    C
    0
    0
    0
    1
    D
    0
    1
    0
    1

    The outgroup characters are assumed to be ancestral by definition, so everything in the outgroup column gets a 0. Others are scored based on the presence or absence of particular anatomical features, as compared with the outgroup. The resulting table shows us the distribution of ancestral and derived characters. In any matrix, we can identify the following different types of character states:

  • Plesiomorphies: Ancestral character states. E.G. Character 1, Eyes present.

  • Autapomorphies: Unique derived characters, I.e. characters that show their derived state only in a single terminal taxon. E.G. Character 2, Feet absent; and character 3, Hat present.

  • Synapomorphies: Shared derived character states. E.G. Character 4, lips present. Seen in terminal taxa C and D. Synapomorphies are the only characters that tell us anything about phylogenetic relationships.

    Using the information in the matrix, we can reconstruct the following cladogram: By definition, taxa B, C, and D are more closely related to one another than to the outgroup. Additionally, the only synapomorphy, character 4, shows that C and D share a more recent common ancestry with one another than either does with B.

    cladogram 1
    X. Homoplasy:

    For our final exercise, we will look at some real organisms: Bass, turtle, snake, and crocodile. We will choose a shark as the outgroup. We score the following matrix:

    Character
    1. Paired limbs present
    2. Supratemporal fenestra present
    3. Infratemporal fenestra present
    4. Breathes air
    OG-Shark
    0
    0
    0
    0
    A - Bass
    0
    0
    0
    0
    B - Turtle
    1
    0
    0
    1
    C - Snake
    0
    1
    1
    1
    D- Croc
    1
    1
    1
    1

    Now we have a problem. Characters 2 and 3 are synapomorphies of the snake and croc, while character 1 is a synapomorphy of the turtle and croc, but NOT of the snake. Thus, these characters seem to tell different stories about evolutionary history. This character discordance is called homoplasy (adj. is homoplastic). This may result from character reversals, convergent evolution, or any of a variety of other causes. We may not like it, but we have to deal with it. To do this this we again resort to simlicity. The matrix suggests two possible cladograms:

    cladogram 1
    To choose between them, we bite the bullet and count character state changes for both cladograms. What we see is that the second tree is considerably simpler, so we accept it. Our result suggests that snakes are descended from a recent common ancestor with crocs, and have secondarily lost their limbs.

    XI. Reservations:

    The cladistic technique is very good at unraveling the phylogenies of related lineages. Indeed, anything related by ancestry and descent; organisms, languages, etc. are fair game. It is based on a series of assumptions which must not be broken if the result is to have meaning:

  • The taxa being analyzed must be related through ancestry and descent.

  • The taxa must be related as a tree of branching lineages. The cladistic technique will not work out relationships inside a lineage of interbreeding organisms. (Try drawing a cladogram of your family and you'll see).

  • The characters that you choose to score in your matrix must be reasonable. Imagine the result if, in our first example (willow, etc) we had chosen the presence of the color green as a character. (assuming a green parrot).

  • Characters are must be heritable. Fur color might be a character, but a tattoo is not.

  • Your choice of outgroup must be well informed. What if we had chosen potatohead D as the outgroup in example 2?

    The worst part: If you violate one of these assumptions, you may never know. The cladistic technique simply assumes that you have done your homework properly.

    IX. Essential vocabulary: Know these terms. They are your friends.

    Systematics
    Taxon (plural taxa)
    Heirarchy
    Organizing principle
    Cladogram
    Node
    Terminal taxon
    Phylogeny
    Phylogenetic systematics (=cladistics)
    Monophyletic group
    Paraphyletic group
    Polyphyletic group
    Polytomy
    Matrix
    Outgroup
    Ingroup
    Homoplasy
    Derived
    Ancestral (=primitive)
    Synapomorphy
    Plesiomorphy

    Go to phylogenetic Systematics Exercise.