Terms to know: phylogeny, systematics, cladistics, homology, homoplasy, reversal, convergent evolution, parsimony, character, character state, primitive character state, derived character state, ingroup, outgroup, outgroup comparison, treelength, consistency index, phylogenetically informative

Questions:

1. Cladistics is based on the prinicple that derived character states can be phylogenetically informative, but primitive character states can not.  Clearly explain why this principle is true.
2. There are two reasons that two different species could have the same character state for some character.  What are they?  Which is expected to be more common? Why?
3. You are interested in studying the phylogenetic relationships among four mammal species: dogs, monkeys, rabbits, and deer.  Dogs and monkeys both have the primitive character state of having canine teeth; rabbits and deer have the derived character state of not having canine teeth.  Which character state, presence or absence of canine teeth, provides evidence for phylogenetic relationships within this group? Clearly explain why (to do this you must fully explain why one kind of character state, primitive or derived, provides evidence for phylogeny and why the other kind does not.  As part of this be sure to explain why it is that different species having the same characteristic can provide evidence for phylogeny at all.)
4. To determine the phylogenetic relationships between three species of plant, A, B, and C, you compare their characteristics to those of a species you know to be more distantly related to them than they are to each other, outgroup species O.  Based on the following descriptions of characters and character states, answer the questions given, then fill in the blanks below (if possible, given your answers to the questions in parts a and b) and then draw the tree that is best supported by the characters presented.
1. One of the characters listed below is not useful because it is impossible to determine which state is primitive and which is derived. Which character? Why?
2. One of the characters listed below is not useful because, while one can determine the derived state, it does not indicate relationships.  Which character?  Why does the derived state not indicate relationships?

	leaf shape	bark	leaf color
Species O (outgroup)	lobed	unstreaked	light green
Species A	lobed	streaked	dark green
Species B	simple	streaked	dark green
Species C	lobed	unstreaked	dark green
Derived Character State (if it can be determined; if not, leave blank):	__________	____________	____________
Species with the derived character state:	__________	____________	____________

5. For the following species, assume you have determined which character state is primitive and which derived through outgroup comparison.  A 0 indicates primitive states.  For each character, indicate the species that share the derived state.  Are all characters potentially phylogenetically informative? Draw the best supported tree.  On the tree, indicate where each derived character state for each phylogenetically informative character evolved with a "tick" mark. What is the treelength of this tree ?  What is the consistency index of this tree?  Do all traits support this tree?  If not, in which trait is there convergent evolution?

	Character 1	Character 2	Character 3	Character 4
Species A	1	1	0	1
Species B	0	1	0	0
Species C	1	0	1	1
Species D	1	0	1	1

6. For the following dataset, first determine the primitive and derived states for each character (character states are denoted by upper case letters) by outgroup comparison.  Are all characters potentially phylogenetically informative? Draw the most parsimonious (best supported) tree. On the tree, indicate where each derived character state apparently evolved for each phylogenetically informative characgter with a tick mark. Do all traits support this tree?  If not, in which trait is there convergent evolution?  What is the tree length of this tree?  What is the consistency index of this tree?

	Character 1	Character 2	Character 3
Outgroup	A	K	W
Species I	A	K	Z
Species II	B	L	W
Species III	B	L	Z

7. For the following information, determine primitive and derived states for each character by outgroup comparison.  Are all characters potentially phylogenetically informative?  Draw the best supported tree.  For potentially phylogenetically informative characters, mark the tree with "tick" (hatch) marks to indicate character evolution; label each mark with the character number it represents.  Calculate the treelength and consistency index for the tree and note which characters show homology and which show convergent evolution.

	Shell Present?	Hair present?	Metabolism	Amniotic Egg present?	Body color
Salamander (outgroup)	no	no	ectothermic	no	tan
Turtle	yes	no	ectothermic	yes	green
Armadillo	yes	yes	endothermic	yes	tan
Mouse	no	yes	endothermic	yes	tan
Crocodile	no	no	ectothermic	yes	green