III.  Cladistics - Specifics

A.  Characters
    Cladograms are based on shared derived characters.  A derived or advanced character is called an apomorphy. A primitive character is called a plesiomorphy. If a character is derived, it is assumed to be a "step up" from the primitive, plesiomorphic condition. Plesiomorphies arose before the taxon evolved, whereas apomorphies evolved with the taxon. Advanced characters shared by taxa are called synapomorphies, while shared primitive characteristics are symplesiomorphies.

B.  Homologous characters
    These are features shared by common ancestry, equivalent in an evolutionary sense.  For example, various types of mammal forelimbs are homologous characters.  In contrast, bird wings vs. insect wings are analogous characters and not equivalent.  A cladogram (or evolutionary classification, for that matter) based on analogous traits clearly would be flawed.  A cladogram must be based on comparing homologous characters.  This is easier said than done, especially considering the problem of convergent evolution.  For example, if we used succulence to develop a cladogram, we might erroneously group certain members of the Euphorbiaceae with the Cactaceae.  And, consider underground structures of plants.  Rhizomes, corms, tubers, and runners are all stems and therefore, homologous structures.  However, the potato and a sweet potato are not homologous since one is a stem (=potato) and the other a root (sweet potato).

C. Cladogram
    Assume that you have three taxa. How many possible cladistic relationships exist between them? Four (see your text or in class). As the number of taxa increases, so does the number of possible cladograms [for example with 4 taxa there are 26 possible cladograms, with 5 taxa there are 125, and with 7 taxa there are a whopping 7 trillion possible cladograms!]. So, how do you determine which one is "best"?  In practice, this is somewhat complex, but in theory it's relatively simple.  Let's use some "fun" examples:

IV.  Chain Letters & Telephone - Models for Cladistics

A.  The Game of Telephone
    Did you ever play "telephone?"   Recall that in this game that there is a chain of people and that the person at the beginning of the chain whispers a message to next individual who secretly whispers it to the next and so on all the way down the line.  By the end of the line the message is usually garbled in a humorous way.  This game provides a model for how cladistics works by imagining that the path of people is not straight but branched, much like the branching pattern by which taxa evolve.  Thus, in our new game we would have branches where individuals at the nodes would relay the same message to two different individuals and so on.  Can we reconstruct the pathway of individuals if we just know what the end message is?  You bet - and that's exactly what cladistics does.  Taxa are like the message at the end of the chain and we can reconstruct the branches by comparing the taxa to the presumed original message (or likely ancestor of the group).  Click here for an example/exercise of "the cladistic telephone."

B.  Chain Letters
    Chain letters are another good model for cladistics.  Over time, chain letters change or "evolve" and cladistic methodology can be used to track the most likely changes.  In an article in Scientific American, Bennett et al (June 2003) argue that changes in these chain letters can be analyzed much like changes in the nucleotide sequence of DNA. Using a series of 33 versions of a chain letter they had collected, they were able to demonstrate the probably path of changes.  Check out the article.

C.  Conclusions:  Note that in both cases, the original "message" changed (mutated) as it was passed from individual to individual.  These changes are analgous to the apomorphies, advanced derived features, that evolve in various taxa.  Just like the changes in chain letter and game of telephone can be used to reconstruct the history of message passage, so too can the apomorphies be used to reconstruct phylogenetic history. 

V.  How to do a Cladistic Analysis

A.  Cladogram Construction.

1. Select characters and character states for study.  Use as many as possible, including morphological, anatomical, chemical, DNA nucleotide sequences, amino acid sequences, etc.  Note that some characters are more conserved (e.g., floral features) than others and that these provide the best features to use.
   
2. Determine the polarity of the character states. 
       In other words, identify the characters that are primitive (plesiomorphy) and those that are derived (apomorphy). This can be done in a number of ways such as:  (a) studying development - early phases of development have been thought to reflect primitive features.  For example, since petal primordia are initially separate, distinct petals are likely the plesiomorphic state and connate petals the apomorphy (distinct → connate); (b) examining character associations - if A → B, then the most primitive members of B should appear more like A;  (c) determining if there is a "common ground plan" - characters in common to a group suggests that the feature is more primitive; (d) analyzing character distribution (e.g., betalains vs. anthocyanins - example in class); and (e) studying fossils. 
    
3. Select an outgroup.  An "outgroup," which is a group that is clearly not part of the group under consideration and presumably more primitive is typically chosen.  The outgroup is used as a reference for comparative purposes. If a character is present in the outgroup and the in-group (the taxa that are being classified), then it is probably a plesiomorphy. Characters present in just the in-group are likely to be apomorphies that evolved with the taxa in the in-group.
    
4. Score the taxa for each character - use a data matrix
   
5. Run a computer analysis. 
       There are many excellent programs including PAUP (David Swofford, Illinois Natural History Survey), PHYLIP (Joe Felsenstein, University of Washington), Hennig86, and MacClade (Sinauer). 
    
6. Analyzing the cladogram
       The computer program will generate one, or perhaps many, cladograms that fit the data. The "best" tree is selected based on:  (a) Parsimony Principle - the simplest (requires the fewest evolutionary changes with the fewest number of homoplasies - see below) one is the best. This idea is based on Occam's Razor (13th Century Philosopher; given two explanations, the simplest one is usually correct); (b) minimum distance methods (not discussed here); or (c) maximum likelihood methods (not discussed). 
    
7. Selecting the best tree (consensus & monophyletic)
        After the analysis, there may be several trees left with the same number of homoplasies, so the best one, called the "consensus tree" must be picked by other means.  Cladograms should have only monophyletic groups - include all the descendents of a common ancestors (in other words, all the ancestors of a particular node).  Cladograms should not include paraphyletic groups (includes some, but not all the descendents of a node) or polyphyletic groups (includes descendents from different nodes). 
   
       A strict consensus tree will have only monophyletic groups while a majority rule tree might only require more than 50% monophyletic groups.  Bootstrapping is a technique to determine how good a cladogram is.

B. Exercise
    Click here for an exercise creating/analyzing a cladogram.

VI. Disadvantages of Cladistics
    The final cladogram may include examples of homoplasy - a situation where unexpected characters occur in a taxon. These may result from convergent evolution (unrelated taxa evolve similar features because of similar selection pressures) and parallel evolution (taxa that diverged from a common ancestor evolve in a similar manner). Problems can arise from the wrong outgroup being selected or reversal of characters to the plesiomorphic state.  Other problems include:

1. Plants are phenotypically plastic so it makes it hard to determine character states and whether advanced or derived;
   
2. Determining which characters to use can be problematic
   
3. Parallel and convergent evolution
   
4. Creates naming problems since sister groups should have the same taxonomic rank

VII.  Advantages of cladistics
    Reproducibility and objectivity!