Microbial Population Biology

Open access blog network of courses focused on the population biology of bacteria and viruses

1. Syllabus 2010 and Assignments

Basic Structure

  1. Blogging and discussion of readings (40% )
  2. Two exams (30%)
  3. Research paper (30%)
  4. General Participation (max 10% extra credit)

General Subjects

The overall flow of the class is as follows:

syllabus-flow-chart.jpg

Micropopbio Central Questions:

  1. True or False: “Everything is everywhere; the environment selects.”
  2. What is a microbial species and why might they exist?
  3. How important is horizontal gene transfer (HGT) in microbial evolution?
  4. How do we construct the best models of evolutionary relationships among organisms?
  5. What are the effects of chance, history, and adaptation on microbial evolution?
  6. How do bacteria elude the “competitive exclusion principle” and shape their own niches?
  7. In a given environment, how does immigration affect microbial diversity and diversification?
  8. What are the consequences of adaptation to a constant environment?
  9. Is the mutation rate minimal or optimal?
  10. Why sex?
  11. Why cooperate? Why cheat?
  12. Why are some pathogens so virulent, and others so mild?
  13. What are the optimal life-history strategies for pathogens under various transmission regimes?
  14. What happens when the life history of a symbiont (parasites or commensals) becomes increasingly dependent on a host organism?
  15. What fraction of human microbial commensals is stuck with us, and what fraction is just hitching a ride?
  16. How stable is the structure of microbial communities, in general?
  17. What rules govern the assemblage of microbial communities, and are they the same as for macroscopic eukaryotes?
  18. How many prokaryotic species are there really out there?

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Course schedule

Class #

Date

 General topic Specific topic Reading Lab topic

1

1/26

 Intro: the big picture No lab

2

1/28

 Microbial diversity Is everything everywhere? Hughes-Martiny et al, Nat Rev Micro

3

2/2

 Microbial diversity Species-area relationships, island biogeography

Microbial biogeography of thermophilic Archaea: Whitaker et al Science 2003
4

2/4

 Defining bacterial species Cohan and Perry, Current Biology

5

2/9

 Defining bacterial species Classification criteria Why do species exist?

http://www.biomedcentral.com/1741-7007/3/6

6

2/11

 No class

7

2/16

 Defining bacterial species Horizontal genetic transfer, phylogenomics ochman-et-al-pnas-hgt-and-species-concept

supplemental:

http://dx.doi.org/10.1371/journal.pbio.0030130

 Population structure (computer lab)

mlst-lab-2009

Blogging assignment: commentary on colleagues and reflection

8

2/18

 Adaptation Experimental evolution As a reference, see a chapter of mine, paying attention to the first few sections

9

2/23

 Adaptation Rewinding life’s tape Travisano et al. 1995, How chance and history affect evolution

10

2/25

 Adaptation Limits to adaptation: mutation supply Being a mutator while infecting a mouse

11

3/2

 Speciation Adaptive radiation Pseudomonas adaptive radiation Build your own adaptive radiation

12

3/4

 Speciation Niche subdivision Burkholderia biofilm diversity

13

3/9

 Speciation The paradox of the plankton Build your own adaptive radiation (take II)

3/11

 Exam 1

3/17

 Spring Break

3/19

 Spring Break

14

3/23

 Evolution of community complexity i. Immigration and diversity

ii. Effects of recombination

 Fukami et al, immigration history and diversity Build your own adaptive radiation (take III). Grant proposal workshop.

14

3/25

 Why sex? Testing Fisher-Muller Tim Cooper, PLOS

17

3/30

 Cooperation and cheating Prisoner’s Dilemma and Game theory Turner and Chao PD in an RNA virus

 Continue labs on own.

18

4/1

 Cooperation and cheating Quorum sensing, group behavior

Myxococcus xanthus behavioral evolution

 The background:

http://www.pnas.org/content/95/21/12376

19

4/6

 Cooperation and cheating Mechanisms of myxo evolution Resequencing to find adaptive mutations that alter behavior:

velicer-pnas-px.pdf

 Choose 1 of the following:

1. velicer-et-al-nature-2000.pdf

2. velicer-and-yu-2003-nature.pdf

3. velicer-plos-2005.pdf

4. velicer-nature-2006.pdf

20

4/8

 Evolution of virulence Why are some parasites mild and others severe?

21

4/13

 Evolution of virulence Specific examples Please find an article from the literature that addresses this question in some way, uses “population thinking” and specifically addresses how/why virulence evolves.

22

4/15

 Host associated communities Human microbiota The Human Microbiome Project

Supplemental: the role of microbes in obesity

 Science Friday program or any article from a PubMed search on “Gordon JI”

(you choose)

23

4/20

 Host associated communities Animal microbiota and transplants From mouse to zebrafish and vice versa Supp methods for this paper

24

4/22

 Rules of community assembly Sargasso Sea:

Global Ocean Survey: http://collections.plos.org/plosbiology/gos-2007.php

25

4/27

 Exam 2

26

4/29

 Practical micropopbio Bioprospecting

27

5/4

 Grant proposals

28

5/6

 Grant proposals