&nbs p; ; Example Quiz
You may use any books, notes, or references, but you must work independently of other people, inside or outside of the course: you are on your honor to do so.
To keep the amount of writing under control, please confine the
answers
to the space provided (but write clearly and large enough to see!);
outlines
are fine. You of course may type the answer if you want, following the
same space constraint (no smaller than 10 pt. font). Include literature
citations (author and year are enough)
where you use them.
1.(9 points) Briefly describe each of the following morphometric
methods,
and their possible uses in
systematics:
a) Bivariate plot
b) Procrustes analysis
c) Thin-plate spline
2.(6 points) You have just overheard an argument about reconstructing
relationships between a phenetist,
cladist, and an evolutionary biologist. Briefly compare and contrast
each individual's position.
3. (5 points) How is it possible that branch lengths on a tree
produced
using UPGMA may not agree with
branch lengths calculated directly from the distance matrix?
4. (5 points) What is the difference between divisive and
agglomerative
clustering methods? Give one example
of each.
5.(20 points) What are the general attributes of a "good" taxonomic
character? Give: a) A list with a
few-sentence explanation of each criterion; b) An indication of
particular
problems faced by morphological and
DNA-sequence data for each criterion.
6. (5 points) You have constructed a tree using the parsimony
criterion
and a second tree using the largest
clique found in your data by compatibility analysis. Why might your
two trees have different topologies?
7. (10 points) Briefly define the following terms:
DNA hybridization
Step matrix
Manhattan distance
Retention index
transversion
character weighting
epistemology
The alternating sister group rule
Dollo parsimony
Median state rule
8. (20 points) Briefly contrast the following pairs of terms (Use diagrams if they help):
maximum likelihood vs. maximum parsimony
Strict consensus trees vs. majority-rule consensus trees
transformational vs. taxic homology
Lundberg rooting vs. outgroup rooting
decay index vs. bootstrap support
9. (10 points) Quantitative, continuous characters are an intially
attractive
set of potential characters that seem
often to contain phylogenetic signal. Discuss why they are so
difficult
to use. When can they be included in an
analysis? How?
10. (10 pts.) In which one of the following cases is the maximum
parsimony
method most likely to be
inconsistent (i.e., not converging on the correct tree as more data
are added). Why? What properties of data
make the problem worse?