- Lab 6 Systematics
This lab is based upon the following reference:
Brooks, D., D. A. McClennan, J. P. Carney, M. D. Dennison, and C. A. Goldman. 1995. Phylogenetic Systematics. Pages 239-258 in Tested studies for laboratory teaching, vol. 15 (C. A. Goldman, ed.). Proceedings of the 15th workshop/Conference of the Association for Biology Laboratory Education (ABLE), 390pp.

Introduction - A biochemical examination of all life on earth reveals a shared chemistry, indicating that life had a single origin. This is one aspect of the theory that supports biology as a science, the theory of evolution. If all life had a single origin, then all life is genetically related at some level. Our hierarchical scheme of classification, based upon that of Linnaeus, attempts to show relatedness among taxa, or groups of organisms. Thus, species that are in the same family are more closely related to one another than to species in any other family, much as you are more closely related to other members of your family than to members of another family. How do biologists determine the taxon to which a species belongs, or how do they determine whether organisms belong to a distinct species?

Many schemes have been tried over the centuries, culminating in the currently used process of phylogenetic systematics. Systematists attempt to infer the evolutionary relationships among taxa based on shared and distinct characteristics of those taxa. The result is an evolutionary hypothesis known as a phylogeny. A phylogeny is depicted as an evolutionary tree, with different taxa occupying different branches. If 2 taxa are on the same branch, they are more closely related than either is to a taxon on another branch. We place them on the same branch because they share characters.

If a character is shared among taxa because it was present in a common ancestor of those taxa, then we say that character is homologous among those taxa. Taxa may share a characteristic even though they have no common ancestor with that trait. An example would be wings on birds and bats. This is an example of convergence, not of homology. In this case, flight was developed independently in the 2 taxa.

Part one - Learning the lingo Systematists have been noted for developing their very own language, or at least what seems their own language from the point of view of other biologists. You'll need to know some of their terms to complete this exercise.

Character - An observable trait of an organism, can be anatomical, behavioral, etc.

Character state - Different manifestation of a character. Different eye colors are different character states.

Apomorphy - A new, derived character state that appears in a taxon but was not in its ancestral taxon. Loss of a character can also be an apomorphy.

Synapomorphy - A derived character state shared among 2 or more taxa. These are used to establish evolutionary relationships among those taxa.

Plesiomorphy - An ancestral character state. This may change to become an apomorphy.

Monophyletic - A monophyletic taxon contains all the descendant taxa of a particular ancestral taxon.

Paraphyletic - A paraphyletic taxon contains only part of the descendants of an ancestral taxon, and is thus not a natural grouping.

Outgroup - A taxon thought to have the character states of an ancestral taxon to the taxa you are considering. The outgroup will be used to determine which of the character states in your taxa are apomorphic.

Convergence - Independent evolution of characters

Parsimony - The simplest method of doing things. Systematics is ruled by parsimony based on the assumption that few evolutionary events are more likely to occur than lots of them.

Derived - Derived characters are character states new to taxa. These are different from the ancestral character state. A derived character is an apomorphy for that taxon.

Part 2, Examples of Phylogenies

	You are interested in determining the relationships of a particular taxon, all of which share character 1
	The relationships you are most interested in are among taxa A - E, which are distinguished from taxon X by character 2. Taxon X is your outgroup, the taxon most like the ancester to A - E.
	Character 3 is synapomorphous for taxa D and E.
	Character 4 divides taxa B and C from A.
	Character 5 appears to have independently evolved twice, separating taxa C and E as unique taxa. The other way to map character 5 would be to assume that all the other taxa lost that character. Assuming convergence is more parsimonious.

1. Divide into groups of 3
2. Collect all the materials necessary. These materials are anatomical diagrams and prepared skeletal material of the amniotes. Your instructor will explain what amniotes are and some of the adaptations of amniotes for a terrestrial existence.
3. Use the following table to develop a list of character states for 10 characters as listed below:

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Now, recode this table as follows:

• Code 2 condyles as 0, 1 condyle as 1
• Code 5 digits as 0, 4 as 1, and 0 as 2
• Code no gizzard as 0, gizzard as 1
• Code bladder as 0, no bladder as 1
• Code urea as 0, uric acid as 1
• Code ectothermy as 0, endothermy as 1
• Code extra-embryonic membranes as 1, none as 0
• Code a hemi-penis as 1, single penis as 0
• Code a fused quadrate as 0, an unfused quadrate as 1
• Code no temporal holes as 0, one as 1, and two as 2

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On the back of one of these pages, use your coded characters to build a phylogeny of the amniotes. Amphibians will be your outgroup. One character is convergent. Make a tick mark on your phylogeny for each character/state and write the character/state next to it. For example, Fen(1) or Fen(2).

Once you have completed your phylogeny, compare it with that of the instructor to determine if yours is correct. If it is not, rework it.

1. Based on your tree, describe the major features of evolution for dry land existence in vertebrates.
2. Based on your tree, classify the amniotes into larger taxa. For example, lizards and snakes are more closely related to one another than to other amniotes. What about the rest of the amniotes? Group them into ever-larger taxa.
3. If the class Reptilia includes lizards, snakes, crocodiles and alligators, is it monophyletic or paraphyletic? Should it include another group?
4. Phylogenies are hypotheses of evolutionary relationships. How might you further test your hypothesis?