1. Define homology and analogy. Can you provide some examples, in addition to those we discussed in class?
Homology - a character shared by 2 species that was present in a
common ancestor. Example: feathers in blue jays and hummingbirds
Analogy - a similar character that arose independently on different lineages
(i.e., a case of convergent evolution). Example: wings in birds, bats,
and butterflies.
2. Why is phylogenetics considered a more useful way to classify organisms than phenetics?
Phylogenetics seeks to reconstruct evolutionary relationships and is based on explicit consideration of common ancestry. Phenetics may result in grouping unrelated taxa based on superficial similarities.
For the Questions 3-7, consider the following phylogeny (for Group ABCD), which was derived from the following character matrix (presumed ancestors are indicated as E, F, and G):
| Taxon | a | b | c | d |
| X (outgroup) | 0 | 0 | 0 | 0 |
| A | 1 | 1 | 0 | 0 |
| B | 1 | 1 | 0 | 0 |
| C | 1 | 0 | 1 | 0 |
| D | 1 | 0 | 1 | 1 |
3. What are the presumed character states of ancestors E, F, and G?
E: a1, b1, c0, d0 (i.e., the derived state for char. a and b; ancestral
state for c and d)
F: a1, b0, c1, d0 (i.e., the derived state for char. a and c; ancestral
state for b and d)
G: a1, b0, c0, d0 (i.e., the derived state for char. a; ancestral state
for b, c, and d)
4. Which ancestral taxon is the closest shared relative of Species a) A
+ B; b) A + C; c) B + D; d) B, C + D?
a) E
b) G
c) G
d) G
5. Which character(s) was (were) not useful in constructing the tree? Why?
Character d was not useful because its derived state was present in only one species (D) and was therefore not shared by any taxa. Thus it provided no information about common ancestry. Try building the tree without Character d to convince yourself (You could also try rebuilding the tree without the other characters to demonstrate that they do provide useful information).
6. Give an example of a monophyletic group (i.e., name the species that comprise it).
A+B, C+D, and A,B,C+D are each examples of monophyletic groups.
7. The outgroup (X) also possesses a variety of character states that are shared with Species A, B, C, and D. Why weren't these states used in constructing the tree?
Character states that are present in all of the taxa do not provide any information to distinguish patterns of common ancestry. These traits represent ancestral homologies.
8. Using the following Character Matrix, construct the most parsimonious tree(s). In doing this, you'll probably generate a number of other trees - keep them - they'll be useful for discussing your final answer (i.e., hypothesis):
| Taxon | Characters and States | ||||
| a | b | c | d | e | |
| X (outgroup) | 0 | 0 | 0 | 0 | 0 |
| W | 1 | 1 | 1 | 1 | 1 |
| Y | 1 | 0 | 1 | 1 | 0 |
| Z | 1 | 1 | 1 | 0 | 1 |
In section, you went over 2 trees that were equally parsimonious (i.e., required the same number of evolutionary steps.
9. What is the Principle of Parisomony and why is it useful?
The simplest explanation (i.e., the one with the fewest transitions between character states) is assumed to be the most likely to have occurred. Without some criteria, we would be left with no means to evaluate the plausibility of different trees (there are many possible trees for even a simple character matrix). Of course, this does not guarantee that the most parsimonious tree is correct -- it is only a hypothesis -- more complicated scenarios might actually be correct (although we don't think this will be the case very often!.