This problem set will familiarize you with various aspects of phylogeny reconstruction. The exercises will help you draw cladograms, define character states, recognize homoplasies and most parsimonious (shortest) trees, and infer states of common ancestors. Although you will not be graded on this problem set, it will provide indispensable practice for exams. Answer keys for these problems will be put on reserve in the Biology Library.

1. Assume that this cladogram depicts the correct branching pattern for the five species. The states for eight characters are shown for each species. Assume unprimed states are plesiomorphic, that primed ones are apomorphic, and that double-primed states can evolve either from the plesiomorphic or a single-primed state. Assuming parsimony, infer (1) the branch (internodal segment) on the tree where each apomorphic state evolved and label it with a tick mark, and (2) infer the set of character states defining each labelled node (i.e., I, II, & III) and the common ancestor. In this instance, the common ancestor for the cladogram need not show the plesiomorphic state for all characters.

2. Each X on the next page represents one of five species (not necessarily in numerical order). Draw the most parsimonious cladogram based on the character state distribution in the table, and label the species. Single and double-primed states are different apomorphic states, and unprimed ones are plesiomorphic. Assume that there is no homoplasy and that each apomorphic state evolved from a plesiomorphic (unprimed) state. Draw labelled tick marks on the branches of your tree to indicate where apomorphic states evolved. Also label the inferred states of the common ancestor, which need not be unprimed.

 Species Character States

1 A' B' C D E' F G

2 A' B C D' E' F G'

3 A B" C' D E F' G

4 A' B C D' E' F G'

5 A B C' D E F' G

.XCommon Ancestor

 Species Character States

1 A' B C' D E

2 A B' C D E'

3 A B C' D' E

4 A B C' D' E

5 A B C D E'

.X Common Ancestor

 Species Character States

1 A B' C D' E F G'

2 A' B C' D' E F G

3 A B C D' E F' G'

4 A' B C D' E F G

5 A B C' D E F' G

.X Common Ancestor

3. You are given five species, their character states, and the true cladogram. Place a labelled tick mark on the branch where each character state changes (it will either become more derived or apparently revert to a plesiomorphic state), and infer which states the common ancestor has. Do any of the characters show homoplasy? If so, circle where on the tree their homoplastic apomorphies evolve. How many steps long is this tree. (A step = a character state change = a tick mark)?

4. Below are the character states for four species and an "outgroup." Assume that the outgroup shows the plesiomorphic states, that reversions to the plesiomorphic state may occur, and that any state can evolve from any other. On a separate sheet draw as many different cladograms as you can think of with the states for the common ancestor inferred for each. Can you come up with one most parsimonious tree, or are there several equally short (i.e., with fewest steps) trees? Any cladogram might show homoplasy.

Species Character States

1 A" B C

2 A' B C'

3 A' B" C'

4 A" B" C

Outgroup A B C

5. Three possible cladograms are presented depicting relationships between four species. The common ancestor is shown for each. Place tick marks on each cladogram to indicate where apomorphic character states evolved. Circle instances of homoplasy, and indicate which of the three trees is most parsimonious by counting its number of state changes. Assume that there are no reversions from apomorphic to plesiomorphic states, and that both single and double primes must evolve directly from the plesiomorphic (unprimed) state only.

6. A matrix of character states for five species and their inferred common ancestor are shown. Assume that each apomorphic character state is derived directly from a plesiomorphic state. Draw the most parsimonious cladogram on the right and label the species at the top.

Species Character States

1 A B' C' D E F

2 A B' C D E' F

3 A B C D E F'

4 A B C D' E F

5 A' B C D E F

Ancestor A B C D E F

7. A matrix of character states for four species and their inferred common ancestor are shown. Assume that apomorphic character states are derived from the plesiomorphic state, but that reversals can occur. Draw the most parsimonious cladogram on the right and label the species at the top.

Species Character States

1 A B C D' E' F

2 A B' C D' E' F'

3 A' B C' D' E' F'

4 A' B C' D E' F'

Ancestor A B C D E F

8. Each X below represents one of four species. Draw the most parsimonious cladogram based on the character state distribution in the table, and label the X with the appropriate species. Single and double-primed states are different apomorphic states, and unprimed ones are plesiomorphic.

Species Character States X X X X

1 A B' C D' E' F G' H

2 A B C' D' E' F' G' H

3 A B C D' E F G H'

4 A' B C' D' E' F' G' H'

X Ancestor

Which characters, if any, appear to have homoplasies? ___________________

Which characters have autapomorphies, and in which species do those aut apomorphies occur? ____________________

Which characters are totally uninformative concerning relationships of species within this clade?

____________________

How many monophyletic groups are there in this cladogram? _______________

Which character state(s) are homoplasies? _______________

Which character state is an autapomorphy for Species 4? ______________

For what species is B' a synapomorphy? _______________

For what species is D' a synapomorphy? _______________

How many steps long is the tree? _______________

9. Using the character matrix below, write the cladogram for the species listed. Indicate where on the cladogram apomorphic states evolved using tick marks labeled with the character state. Remember that the species will not necessarily be listed in numerical order across the top of the cladogram. Plesiomorphic states are unprimed. Double-primed character states may or may not evolve directly from the unprimed plesiomorphic state.

Species Character States

1 A' B C' D' E F G' H"

2 A B' C D E' F G H'

3 A' B C' D' E F G' H"

4 A B C' D E F' G' H'

5 A B' C D E' F" G H'

X X X X X

X Ancestor (Character states = A B C D E F G H)

Which character state (if any) is a homoplasy? _______________

How many symplesiomorphies do species 1 and species 3 share? _____________

How many synapomorphies do species 3 and 4 share? ______________