The Pattern of Evolution - Phylogenetic Systematics Review

John Merck

Follow along with exercise

The Phylogenetic System of Taxonomy: Any system of taxonomy, scientific or folk, has:

The organizing principle of modern biology is evolution (descent with modification). Ultimately, evolution implies that all taxa - units of diversity (sing. taxon) descend from a single common ancestor. The history of these lineages is their phylogeny. This supplies the organizational principle used by modern systematists. A taxonomic system based on it is hierarchical because groups that are descended from very recent common ancestors are be nested within groups descended from distant common ancestors.

Graphic representation of a the tree
of evolution of three taxa, A, B, and C.
The Cladogram: A stick-figure representation of our hypothesis of the tree of evolution.


  • 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.

    Hypotheses of Phylogeny

    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

    Note: Just as we have disphonious cladobabble describing different types of taxonomic groups, we have it for characters, too:

    Note that when we discuss types of characters, it is essential that we agree on the frame of reference. The opposable thumb is a synapomorphy of primates, but a plesiomorphy of hominids.

    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.

    What does this method yield:

    Potatohead Exercise: The take home concept is that the hypothesis of phylogeny that our technique generates is falsifiable. We can falsify it by adding new information or changing basic assumptions like outgroup choice.

    Feeling vulnerable? For more review see:

    What Phylogenies Tell Us

    Hypotheses of the pattern of evolution: Duh. But it does not stop here. For all that the pattern of evolution is a worthwhile thing to know, it is not an end in itself. Reconstructing Missing Information: A robust phylogeny can enable us to develop hypotheses about the state of characters in extinct organisms for which we have no direct evidence.

    Reconstructing missing data using the Extant Phylogenetic Bracket: Phylogeny reconstruction algorithms like T.N.T. also reconstruct optimum character states at reconstructed tree nodes. From these reconstructions, hpothetical states for taxa with missing data can be reconstructed as well. In 1999, Larry Witmer coined useful vocabulary to describe how unknown character states for fossil taxa are reconstructed with respect to extant taxa called the extant phylogenetic bracket (EPB). This is the bracket formed on either side of the taxon with the missing information by extant taxa in which the character state is known. Using it, we can make three types of inference, listed in order of decreasing confidence. Consider the distribution of a soft-tissue character - the four-chambered heart - among three fossil reptiles:

    Phylogenies meet the Rock Record

    Phylogenies and Biostratigraphy: Traditional biostratigraphers - Geologists who use the fossil record to date sedimentary rock units tend to be literal-minded souls who think that either fossils of a taxon are e present at a particular time, or they aren't. What if a group of organisms is known only from relatively rare specimens. I we reconstruct a robust phylogeny, it might help us identify ghost lineages intervals of time in which a lineage ought to have been present but for which no fossils have been found. This:

    Ghost Lineages and minimum divergence ages: When we know that two taxa are sister taxa (descendants of the same recent common ancestor), we in essence know that they originated at the same point in geologic time - the time of their last common ancestor and the speciation event that gave rise to them. Say we know one of these taxa from 100 million year old rocks, and the other from 90 million year old rocks. Even without seeing a fossil, we know that the second group must have representatives dating back at least to 100 million years, simply from its sister-taxon relationship with the other. 100 million years is the minimum divergence age of the monophyletic group formed by the two total groups. A lineage whose existence can be inferred from the cladogram, but which is not known from actual fossils is called a ghost lineage. The examination of ghost lineages should allow biostratigraphers to refine their models of the stratigraphic ages of organisms.

    Stratigraphic congruence:. How do we identify ghost lineages and measure their prevalence in a cladogram? All other things being equal, we expect the terminal taxa that branch off of a cladogram first to appear first in the fossil record. When this is true, the cladogram is said to be stratigraphically congruent. Often, when there are long ghost lineages, cladograms are not stratigraphically congruent. This could mean:

  • Node-based definitions: Until now, all of the groups we have considered have been defined using the formula "The most recent common ancestor of A and B and all of its descendants." Doodadichthyes, for example is the most recent common ancestor of Whatsitichthyes and Thingamabobichthyes and all of its descendants. To identify this on a cladogram, one need only point to the node representing the common ancestor, which is its first ever member. Everything that sprouts from that node is a member of the group.

    Crown-group definitions: A special case of the node based definitions in which the anchor taxa are living. Thus:


  • Total-group definitions: are defined using the formula "All organisms more closely related to A than to B." So, Panthingamabobichthyes is defined as all organisms more closely related to Thingamabobichthyes than to Whatsitichthyes. The first member of this group would have been at the base of the stem leading to A. In this example, Panthingamabobichthyes begins during the first generation after the splitting of the lineage represented by the last common ancestor of Doodadichthyes.