Microbial Population Biology

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: Name two properties of bacteria that support “everything is everywhere, the environment selects.”

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 should bacteria evolve increased mutation rates? Why not? Provide two specific arguments or scenarios for both the pro and con.

Key topics from past years

• 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

• 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)
  • Be able to describe the Lenski et al long term E. coli evolution experiment and other relatedd experiments
  • 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?
• How do you explain the “paradox of the plankton?”  Does Gause’s law apply to bacteria?

Exam 2

• 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