1. What do we mean by "concerted evolution"? What empirical evidence do we have that it is an important element of the evolutionary process?
   
   
2. Describe briefly how gene families originate.
   
   
3. Which arguments best support the notion that the best characters to use to infer phylogenetic relationships are neutral characters (make sure you define clearly what a neutral character is).
   
   
4. What is the evidence that nucleotide sequence variation within the antigen recognition site of the human MHC gene has been driven by natural selection?
   
   
5. How might the haplodiploid gender determination system of the Hymenoptera predispose them toward the evolution of sociality?
   
   
6. In phylogenetic inference, what do we mean by "compatibility"?
   
   
7. Discuss the value of each of the following characters for use in phylogenetic inference: identity of nucleic acids at third positions in a codon triplet, nucleic acid sequences in eukaryotic introns, surface proteins in viruses, numbers of flower parts in angiosperms, presence of alkaloids in leaf tissues of angiosperms, diversity of hemoglobin types within an individual organism in tetrapods, presence or absence of specific recombination factors in bacteria, relative limb length (limb length relative to body size) in tetrapods
   
   
8. If you're in an adventurous mood, tackle this question with the aid of the PAUP program in the computer lab. A series of taxa, which are actually sports, have the following sets of character   states in which a signifies "presence" and a "-" signifies absence of the character. The ancestral "outgroup" has the "-" character state for all of these traits, which are, in order,

1. One or more balls are used in the sport.
2. Participants drink gin during the game.
3. Participants use a wooden object to strike one or more balls.
4. Participants run at least some of the time.
5. Participants may kick ball.
6. Participants may throw one or more balls into the air.
7. Participants must wear white clothing.
8. Sport has important literary meaning.
   

9. Describe the hypotheses that have been developed to explain why females choose among  male phenotypes; be careful to explain in which of these female choice is under direct selection.What is the evidence that horizontal gene transfers have occurred (outside of plasmid transfer among bacterial cells)?
   
   
10. It appears that there are cases in which kin selection can generate not cooperation but conflict. Describe one such situation and explain how kin selection is maintaining the patterns of behavior that are exhibited. (Hint: Did you read p. 620 in the textbook?)
    
    
11. Can you apply the notion of "co-option" to examples of different types of male ornamentation  in different species?
    
    
12. What is "codon bias," and why might it exist?
    
    
13. What is Hamilton's principle?
    
    
14. Which processes appear to govern the evolution of copy number in highly repetitive DNA sequences?
    
    
15. Describe how the inability to find any characteristics that distinguish lineages that survived the Permian extinction from those that did not survive can be viewed as a real challenge to Lyell's assertion that "the fitter species are more likely to survive these periods of change than the others." Now, having answered that question, can you reconcile the results of the Cretaceous-Tertiary extinctions in marine systems with Lyell's assertion? How about trying to reconcile the great diapsid extinctions?
    
    
16. Rates of morphological change measured over short time periods may be very high, as we saw in house sparrows, for example. Yet when the rate of sustained change is measured over a very long period, the net rate appears to be much lower. How might this paradox be resolved?
    
    
17. Distinguish the "introns-early" theory from the "introns-late" theory for genome evolution. Which empirical patterns support each idea?
    
    
18. The Australian fauna has many distinctive features. Two of them are the extraordinary abundance of marsupial mammals and elapid snakes (elapids are relatives of cobras). These groups are the majority of mammal and snake species respectively. By contrast, the mammal and snake faunas of Eurasia and North America are dominated by eutherian mammals and colubrid snakes. Can you offer a coherent hypothesis for these two distinctive features of the Australian fauna, based on everything you know?
    
    
19. How many times has the autotrophic lifestyle evolved? Which evidence supports your answer?
    
    
20. Is concerted evolution more likely in a family of genes in which each copy has many intervening sequences? Why or why not? How about less likely? Why or why not?
    
    
21. It has been hypothesized that the rate of molecular evolution exhibits a clock-like constancy, but the clock appears to tick at different rates for different genes. The protein clock appears to correspond to absolute time, whereas silent substitutions and pseudogenes appear to accumulate mutations in accordance with generation time. What specific evolutionary forces could account for the differences observed in the two molecular clocks?
    
    
22. What do we mean by an alternative male strategy?
    
    
23. Consider two fish species. Males of species A swim about after females, investigate females they find for olfactory cues as to their receptivity and fertility, and, for some females, exhibit an elaborate courtship display in an attempt to elicit female cooperation in mating. Males of species B swim about rather randomly and when they encounter a female, attempt to inseminate her without any prior attempt at eliciting cooperation. In which species are males more likely to be "choosy"?
    
    
24. Summarize the evidence that the entity we call a "pseudogene" really ought to be interpreted as a gene that was once active and has been silenced through the evolutionary process?
    
    
25. Define the following cladistic groups: monophyletic, paraphyletic, and polyphyletic.
    
    
26. Distinguish homoplasies from homologies. Distinguish shared ancestral homologies from shared derived homologies.
    
    
27. If one considers sexual selection and its operation, one might wonder why selection hasn't favored a mutant that produces a strongly female-biased sex ratio; such a mutant would not risk making offspring that don't obtain mates (i.e. male losers) and would, in addition, be making the gender that makes the babies, if you get my meaning. Something is obviously wrong with this argument because most populations have even or, at most, only slightly biased sex ratios. What's wrong with this argument?
    
    
28. Not so fast; indeed there are populations with characteristically female-biased sex ratios. Which factors might have favored this outcome anyway despite what you said in answering the last question?
    
    
29. You are at a swank soirée regaling some of your fellow guests with a lucid discussion of how gametic disequilibrium is generated by finite population size when a casual listener says "Isn't it true that disequilibrium would also be generated quickly by sexual selection?" Answer this person and offer a lucid explanation of why you answered as you did.
    
    
30. We discussed the pros and cons of female choice on the basis of "good genes." There is another idea we might call the "bad genes" hypothesis, that females choose among males who provide no direct benefit in order to minimize the chance that their offspring will carry deleterious mutations that have arisen recently. Think carefully: is this idea more plausible than the "good genes" idea? If not, why not? If so, why? (Hint: think about mutation accumulation and population size).
    
    
31. What is the purpose of an outgroup taxon in building a phylogeny using parsimony analysis? If you had no outgroup taxon, how might you go about determining how to "root" your phylogenetic tree?
    
    
32. Describe what we mean by the "cost" of a character state change in phylogenetic reconstruction and how these "costs" are employed.
    
    
33. Distinguish "top-heavy" from "bottom-heavy" lineages and discuss the significance of these descriptions of lineages.
    
    
34. Do the rates of origination or extinction vary systematically within lineages as they age? Explain the significance of this pattern (or the lack thereof if).

35. How might you infer how long ago a particular pseudogene became such (i.e. when was it silenced?)
    
    
36. What is the evidence that the components of vertebrate hemoglobin arose via gene duplication?
    
    
37. Distinguish the following varieties of parsimony: Fitch, Wagner, Dollo.
    
    
38. Consider the following set of taxa and characters ("ancestral rocker" is the outgroup for the others):

Trait

Taxon               Hair       Outfits              Choreography        Woodwinds    Syncopation

Ancestral         Greasy    Coordinated        Present                Present            Present
rocker

Garage band    Greasy     Singular              Absent                Absent            Absent

English             Dry         Coordinated         Absent               Absent           Present
"beat"

Doo-wop         Greasy     Coordinated         Present              Absent           Present

Surfer               Dry         Coordinated          Absent               Absent          Absent
dudes

Grateful            Dry         Singular                 Absent               Absent         Absent
Dead

Which are the phylogenetically informative characters?

1. Any well-defined clade (i.e. the in-group) should have a "group autapomorphy"; does this one?

2. How many possible unrooted trees might there be for our clade?

3. How many possible rooted ones?

4. Is there enough information here to construct a phylogeny for the clade? If so, offer your best tree. If not, why not?

39. While enduring the 10-hour FSU graduation ceremony, you hear someone behind you say, "Yes, there is a way to predict the time period when one should find the first fossil evidence for a taxon." Explain how one might go about offering such a prediction.

40. In the early part of the course we discussed homologies that were analogies, although highly modified (e.g. limbs in vertebrates), and the critical importance of homologies that were not analogies (e.g. gill arches and jaws, certain gill arches and bones of the mammalian ear). Prove that you are a broadly trained biologist and a disciplined thinker by recounting one molecular example of each of these phenomena (e.g. two genes that are homologous and broadly analogous and two genes that are homologous but not analogous). For the latter type (homologous but not analogous), describe the evidence that establishes the homology.

41. What is the evidence that male investment in secondary sex characters is driven by mate acquisition and not a force related to offspring fitness?

42. Why do the genders appear to maximize different components of the mating process as they attempt to maximize fitness?