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# Exercise One – Fastener Phylogeny

## Construction of a phylogenetic tree

You now have sufficient background to attempt to reconstruct a phylogenetic tree for a group of fasteners. The information at your disposal consists of a box of various fasteners, a table for your data matrix (the characters in each of your taxa) and a table for your species by species distance matrix. To construct a phylogenetic tree based on shared derived characters, follow the following procedure:

• Select a set of derived characters using the fossil nail as the ancestor. Begin by first choosing binomial characters (those that can be scored "present" or "absent"). It will be important for your bookkeeping to assign all of your ancestral characters the "O" character state and all of your derived characters the "I" character state. In phylogenetics, characters do not need to be binary like this, but it greatly simplifies this exercise. The more characters the better! If you are not confident, begin with approximately 7. Remember, though, the more characters you measure, the more accurate your tree is likely to be, but the longer it will take to complete it.
• Fill in your data matrix.
• You now need to estimate the "evolutionary distance" between each species and the ancestor. Do this by adding the evolutionary "steps" necessary to give rise to all the derived characters of a species. These numbers are a measure of how far a given species has diverged from the ancestor and are sometimes called the divergence distances. If you defined all the derived character states as an "I", the evolutionary distance is simply the number of "I’s" for each species in the data matrix. Enter these values as a separate column in your data matrix

### The following steps are for constructing the tree

•  Find the species with the smallest evolutionary distance, i.e. the fewest number of steps from the original ancestor. Begin with a blank sheet of paper, and connect this first species to the ancestor (fossil nail) with a straight vertical line.
•  Find the species with the next smallest divergence distance from the original ancestor and connect it as a branch off the first line.
• Note that in placing the second species you automatically "create" a new ancestor whose characters must be taken into account. Indicate the character state changes between the original ancestor and the new ancestor with hatch marks on the line separating them (as shown in introduction). Name the newly created ancestors HTUI (hypothetical taxonomic unit 1) and enter its characters into the species x character matrix. The characters of HTU I are either 0 or 1. If the two species above the HTU have shared derived characters (both I's), then the HTU has that character (i.e. 1). If one has a zero and the other has a 1, then the HTU has the character zero (by parsimony).
•  Among the remaining species to be placed on the phylogeny, find the species with the next smallest divergence distance from the fossil. If more than one species has the same distance, deal with them one at a time.
•  Compare the new species with the species you have already placed on the tree, including any HTUS, and find the species on the tree that has the most shared derived characters with the species you want to place.
•  Place the new species on the tree by drawing a line originating below the species with which it shares the most shared derived characters (this may be one of your HTUS).
• This creates a new HTU. Enter it characters on the species x character matrix.
•  Repeat steps 7-1 1 until you have placed all the species.
• You now have a phylogenetic hypothesis for the evolution of fasteners.
• Can you identify the major lineages of fasteners, major innovations in the morphology of fasteners.
•  Does you tree suggest there have been reversals, convergence, or the loss of derived characters during faster evolution?
LINK TO PRINTABLE DATA SHEET (PDF)
LINK TO PRINTABLE DATA SHEET (WORD)