Evolution in Action (OEB 100)
Instructor: Christopher Marx
Teaching fellow: Dipti Nayak
Weekly meeting: NW B127
Time: Mondays 4 – 5:30 pm
Please let me out
of here: my
barnacles and
pigeons need me!
Laboratory: NW 152
Time: 24/7/365 open access
Website: http://isites.harvard.edu/k77185
OEB 100 – 11.01.24
Integration of systems-level physiology and
evolution
Molecular, cell &
developmental
biology, biochem.
genotype
physiology
phenotype
environment
Integration of systems-level physiology and
evolution
Evolutionary
biology, ecology
genotype
genotype
genotype
selection &
drift
mutation
phenotype
phenotype
phenotype
ecological
interactions
environment
Integration of systems-level physiology and
evolution
“Biology”
genotype
genotype
Use adaptation
of laboratory
populations ofgenotype
microbes as a forum
to explore how biological systems
physiology
selection &
evolve.
drift
phenotype
phenotype
phenotype
The “functional synthesis”
(Dean & Thornton, 2007)
ecological
interactions
mutation
environment
Could tackle all levels through various aspects of
the project…
genotype
genotype
genotype
Competition
assays;
tradeoffs &
recovery of
past abilities?
Global gene
expression?
Sequence
genomes;
parallelism?;
mutational
trajectories?
phenotype
phenotype
phenotype
Adaptive
diversification?
Assay external
medium conditions
Model system: Methylobacterium
• M. extorquens is a plant epiphyte
• Model for C1 growth (~50 years):
CH3-R
HCHO
biomass
CO2
• 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)
Experimental evolution
You’ll use 48-t=1
t=2
t=…….
well plates in
an automated,
robotic system
Ancestor
1/64 dilution every 2 days (initially 4 days), N = ~2x109
final
Selection largely for
growth rate
Evolved
isolates
Living fossil record
Fitness assayed via competitions
Competition
Evolved
T0
Flow Cytometry
Fluor. ancestor
Evolved
Fluor. ancestor
T0
fluorescence
T1
fluorescence
Competitive
growth
T1
(Lee et al., 2009. Evolution)
Project: Using evolution to study bacterial
resistance growth on the toxic chemical
formaldehyde
Methylobacterium
Formaldehyde is a key metabolic
intermediate….
Living Cell
Formaldehyde (1mM)
But the cells cannot
grow on it….
Evolution to Grow on Formaldehyde…
..We now have 4 populations that can grow on 30 mM formaldehyde
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.
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.
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)
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.
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.
From first time in 2009…
Last spring…
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
Jory Weintraub - jory@nescent.org
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