Exams

Exam format:

Open book/blog/notes. No collaboration.

30% fill-in-the-blank, very short answer, standard exam questions. Largely fact-based.

30% short answer (5-6 questions) that can be answered in 2-4 sentences. Somewhat more synthetic with limited options.

40% short essay (choose 4 of 6 questions) that will require both writing and illustration. Synthetic and multiple correct answers possible.

Time: 80 minutes.

Example questions:

Very short answer: What is the problem of long branch attraction? How is it solved?

Short answer: Draw one taxa-area curve for birds, and a second curve for bacteria, using the same set of well-labelled axes.

Short essay: Why sex? Provide two explanations: one “in with the good,” the other “out with the bad,” illustrating the relative advantage of sex using relevant figures.

Key topics

  • Define ecology, evolution, population biology
  • Discuss “Everything is everywhere, the environment selects”
  • Why is identifying amounts of diversity important?
  • Discuss the taxa-area relationship (the correlation between geography and genetic relatedness)
  • Identification and distinction of species using molecular techniques (benefits, applications, and limitations of each?): BOX-PCR, RAPD, 16S, MLST, targeted function cloning, whole genome sequencing, metagenomics.
  • Why is the identification and distinction of species important?
  • Why do species exist? What causes differentiation?
  • -“A jack of all trades is a master of none.” Discuss the relevance in a microbial evolution context.
  • -Define periodic selection; relevance in a microbial evolution context.
  • -Discuss Mayr’s biological species concept, and its importance (in eukaryotic and/or prokaryotic context).
  • Problems meeting requirements for prokaryotic use (low recombination rates…
  • Bacterial taxonomy (methods for determining; phenotype, DNA-DNA similarity, and 16S DNA gene)
  • Ecotype definition (why is this necessary?); problems and advantages of this definition.
  • How/why does MLST help distinguish ecotypes
  • Phylogenetics:

-Difference between rooted and unrooted trees
-Definition of an outgroup (use?)
-Methods for tree building
-Parsimony
-Distance matrix
-Maximum likelihood
-What are some problems associated with tree building? (long branch attraction, homoplasy, etc)
-Definition of phylogenomics; contrast w/ phylogenetics

  • Experimental evolution:
    • Experimental design examples (eg: chemostat, static culture)
    • What kinds of questions can be addressed using this method?
    • When is this method preferred? Disfavored?
    • Define fitness; how do you quantify it?
    • Outcomes: generalization vs. specialization; consequences of specialization
    • Methods for determining the consequences of adaptation
    • Direct vs. correlated effects of adaptation (pleiotropy; define)
    • Distinguish Mutation accumulation vs. antagonistic pleiotropy
    • Be able to describe the Lenski et al long term E. coli evolution experiment and other relevant experiments (carbon source utilization experiment; temperature niche experiment; loss of ribose catabolism)
    • What are Wrightian and Fisherian adaptive landscapes
    • What mechanisms of adaptation following experimental evolution have been identified? How have they been identified? (think insertion sequences; others)?)
  • The roles of mutation rate and population size in adaptation. Is the mutation rate optimal or minimal? How can you tell?
  • Phi-6 biology, evolution, and potential for cheating/cooperation.
  • What is prisoner’s dilemma? How is it similar to / different from frequency dependence?
  • Explain the biology of Myxococcus xanthus and why its strategies are susceptible to cheating, cooperation, antagonism, and parasitism