Discussion on The Structure of Life
1/27/05

1.  Define phylogeny.



2. a. List some of the recently discovered dinosaur characteristics from
preserved fossils that have added to our understanding of dinosaur
phylogeny.



b. How long ago did the dinosaur era begin?  And how long did it last?

c. Did dinosaurs have multiple origins or a single common ancestor?

3. a. How long did it take for dinosaurs to reach global dominance?

b. Traditional explanations for the ascendancy of dinosaurs claimed they
were better competitors.  More recent explanations suggest that a global
physical perturbation was responsible.  Discuss how the physical pertubation
might have improved dinosaur fitness.




4. Sauropodomorphs (Long-necked Titans) were quite morphologically
variable, "united by only a few characters."  What were the characters?
Do you think that those characters are enough to establish common ancestry?



5. Figure 3B, in Sereno, shows a member of the Theropoda dinosaurs clade.
Give an example of a species alive today that is a member of that clade.  Does
the species from today resemble the theropod?



6. The radiation of land-based nonavian dinosaurs is described as sluggish, while
the avian radiation was somewhat faster.  By contrast, the mammalian radiation
was explosive.   The current view is that body size may have "played a major
role in shaping the dinosaur radiation."  Summarize how this would have worked.




7.  "The only sustained trend toward decreased body mass occured during the
evolution of birds."  At least among nonavian dinosaurs this suggests that large body size
was adaptive.   a. Do you think that large body size always confers higher fitness?  Why?



b. Figures 1 and 2 show a fantastic range of morphologies for dinosaurs.  How can you
explain the previous statement on body mass for such a wide range of creatures?




8. Some of the early branches on the tree of life have recently started to look like
a tangled mess (see Doolittle).  What process or mechanism is responsible for the
 confusion?




9.  Doolittle, "Molecular phylogeneticists will have failed to find the "true tree," not
because their methods are inadequate or because they have chosen the wrong genes,
but because the history of life cannot properly be represented as a tree."  Suggest a
better metaphore and explain why it is better.



10. Doolittle, "Many genes give believably different phylogenies for the same organisms,
almost certainly because they have been "laterally transferred." If instances of LGT can
no longer be dismissed as "exceptions that prove the rule," it must be admitted
(i) that it is not logical to equate gene phylogeny and organismal phylogeny and
(ii) that, unless organisms are construed as either less or more than the sum of their genes,
there is no unique organismal phylogeny.  Thus, there is a problem with the very conceptual
basis of phylogenetic classification."

a. What is the point of constructing a phylogeny?



b. Given this new view, is it still worthwhile to construct phylogenies?




11. Draw a sketch of a phylogeny containing five species alive today and all sharing
a common ancestor.  Somewhere in your sketch indicate a lateral gene transfer event.
You may find it helpful to use multiple colors.  Feel free to do this by hand, rather than
using a computer drawing program.