Reconstructing Phylogeny

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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.

A brief review of where the diversity comes from: The splitting of interbreeding lineages to form daughter lineages that are free to accumulate their own evolutionary novelties

: 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:

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.


Problem: The criteria that we use to classify animals according to this system are arbitrary and subjective. For example:

A reptile enthusiast might classify a green tree python 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 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 Indeed, Darwin, in the Origin noted that the Linnean system of taxonomy, based on general similarity, ought to be superceded by one based on closeness of common ancestry.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:

    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:

    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.

    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.

    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:

    Presto! It's a proper taxonomic system.


  • 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.

    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.

    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.

    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.

    IV. What does this method yield:

    Feeling vulnerable? For more review see: