Evolution in Action (OEB 100)

1. Evolution in Action (OEB 100) Instructor: Christopher MarxTeaching fellow: Dipti Nayak Weekly meeting: NW B127Time: Mondays 4 – 5:30 pmLaboratory: NW 152Time: 24/7/365 open accessWebsite: http://isites.harvard.edu/k77185 Please let me out of here: my barnacles and pigeons need me! OEB 100 – 11.01.24

2. Integration of systems-level physiology and evolution genotype Molecular, cell & developmental biology, biochem. physiology phenotype environment

3. Integration of systems-level physiology and evolution Evolutionary biology, ecology genotype genotype genotype mutation selection & drift phenotype phenotype phenotype ecological interactions environment

4. Integration of systems-level physiology and evolution “Biology” genotype genotype genotype mutation Use adaptation of laboratory populations of microbes as a forum to explore how biological systems evolve. physiology selection & drift phenotype phenotype phenotype ecological interactions The “functional synthesis” (Dean & Thornton, 2007) environment

5. Could tackle all levels through various aspects of the project… genotype genotype genotype Sequence genomes; parallelism?;mutational trajectories? Global gene expression? Competition assays; tradeoffs & recovery of past abilities? phenotype phenotype phenotype Adaptive diversification? Assay external medium conditions

6. Model system: Methylobacterium • M. extorquens is a plant epiphyte • Model for C1 growth (~50 years): • C1 compounds oxidized to formaldehyde • Oxidation of formaldehyde to CO2 • Assimilation of C1 units into biomass • Requires ~100 genes for C1 growth • C1 genes acquired via HGT • Limited growth on multi-C compounds • Genomes now available for 8 species including the one we’ll study (M. extorquens PA1) CH3-R HCHO CO2 biomass

7. t=1 t=2 t=……. Evolved isolates Ancestor Experimental evolution You’ll use 48-well plates in an automated, robotic system 1/64 dilution every 2 days (initially 4 days), Nfinal = ~2x109 Selection largely for growth rate Living fossil record

8. Fitness assayed via competitions Competition Flow Cytometry Evolved Fluor. ancestor Evolved Fluor. ancestor T0 T0 fluorescence Competitive growth T1 T1 fluorescence (Lee et al., 2009. Evolution)

9. Project: Using evolution to study bacterial resistancegrowth on the toxic chemical formaldehyde Methylobacterium

10. Formaldehyde is a key metabolic intermediate…. Living Cell Formaldehyde (1mM) But the cells cannot grow on it….

11. Evolution to Grow on Formaldehyde… ..We now have 4 populations that can grow on 30 mM formaldehyde

12. Sub-Projects • Generic increase in stress Response? • Has the ability to grow on Formaldehyde conferred a generic ability to withstand stress better? • Students will subject the evolved and ancestral isolates to several stresses such as : • High/Low Temperature • Antibiotics • Detergents • UV exposure • …… • Genetic mechanisms underlying stress response will be analyzed.

13. Coexistence of different genotypes? • Genotype 1 : Can withstand high concentrations of Formaldehyde which leads to penalty in growth at lower concentrations. • Genotype 2 : Cannot withstand high concentrations of Formaldehyde and grows faster at lower concentrations.

14. Tradeoffs between substrates? • How has the ability to grow on formaldehyde affected growth on other compounds? • We know that isolates from one population cannot grow on most carbon compounds it previously could. So there are MASSIVE tradeoffs? • What are they? • Can evolving these populations in an • alternate environment help these isolates • recover? (Lee et.al. Evolution 2009)

15. Genomics and Genetics • Pyrosequencing evolved strains to determine genetic loci that have undergone mutations. • Examining these loci in replicate populations to check for parallel mutational events. • Reconstructing mutations in the ancestral background to determine the order of mutational events and the phenotypic change caused by • individual mutations. • Conducting Microarray/RNA sequencing to understand patterns of global gene expression in evolved and ancestral strains.

16. Formaldehyde-Induced Mutagenesis? • Mutations arise spontaneously (one in ~300 cells), but at rates that can be affected by mutations (in DNA repair) or by the environment. • From genome resequencing we’ll know if there was an elevated mutation rate. • If so we can determine if formaldehyde specifically induces a higher mutation rate in the original strain, or whether the evolved strain has lowered (or increased) this rate.

17. From first time in 2009…

18. Last spring…

19. Undergraduate Diversity at the Evolution meetings 2011 We are pleased to announce a NSF-funded program for bringing talented and diverse undergraduates to the Evolution meetings this June 17-21 in Norman, Oklahoma.  For the ninth year in a row we will fly a cohort of 25 undergraduates from throughout the US and Puerto Rico to present a poster at the meetings, receive mentoring from graduate students, postdocs and faculty, and participate in the Diversity Social as well as a career-oriented 'Undergraduate Futures in Evolutionary Biology' panel and discussion.  The program covers the costs of travel, registration, food and accommodation at the meetings. The application deadline is 1 March, but admissions will be reviewed as they are received, and so the earlier you apply, the better.  Applications are welcomed from all undergraduates, and the admissions goal is to create a diverse pool of students.  An overview of the program and student eligibility can be found at: http://www.oeb.harvard.edu/faculty/edwards/community/application.html Apply online at: www.nescent.org/Evolution2011_application Applications consist of a short statement of interest, a letter of recommendation and the title and abstract of the poster to be presented. In addition, we will be soliciting names of graduate students, postdocs and faculty members who would like to serve as mentors during the meetings.  Mentors take pairs of students and attend talks with them, introduce them to colleagues, network and generally make the meetings a welcoming place for them.  Although costs are not covered for mentors it is an unusually rewarding experience. Contact Richard Kliman <rmkliman@cedarcrest.edu> if you are interested in serving as a mentor. For inquires contact one of the organizers: Scott Edwards - sedwards@oeb.harvard.edu Richard Kliman - rmkliman@cedarcrest.edu JoryWeintraub - jory@nescent.org

20. Monday (1/31):Detailed description of project details and general fundamentals • Read: • Elena & Lenski, 2003. Nature Reviews Genetics. Evolution experiments with microorganisms: The dynamics and genetic bases of adaptation • Lee et al., 2010. Nature. Bacterial charity work leads to population-wide resistance