Experimental evolution

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Experimental evolution
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The outcome of selection for high and low oil
content in the Illinois corn experiment.
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William Dallinger 1880-1886 Selected for
thermotolerance of microorganisms 60 F ? 158 F
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How experimental evolution works

• Batch (serial) culture
• Chemostat
• Turbidostat
• Static culture (liquid or solid)

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Chemostat
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Chemostats select for nutrient affinity
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Static culture
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What are the key variables? (brainstorm)

• Population size (N), and effective population
  size (Ne)
• Mutation rate
• Recombination?
• Parasites?
• Constant or fluctuating environment?
• Mass-action or structured environment?

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Some questions addressed by experimental evolution

• What is the tempo and mode of evolution? (gradual
  or punctuated, limits, etc?)
• What factors promote or constrain adaptation?
• What are the consequences of adaptation?
• What are the mechanisms of adaptation?
• Is the mutation rate optimal or minimal?
• How do mutations interact?

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Is evolution repeatable?

• I call this experiment replaying lifes tape.
  You press the rewind button and, making sure you
  thoroughly erase everything that actually
  happened, go back to any time and place in the
  past say to the seas of the Burgess Shale.
  Then let the tape run again and see if the
  repetition looks at all like the original.
• The bad news is that we cannot possibly perform
  the experiment
• -S.J. Gould, Wonderful Life the Burgess Shale
  and the nature of history (1989)

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We CAN replay evolution

• Replicate populations evolving under identical
  conditions address whether evolution is
  repeatable.
• Do you predict phenotypic repeatability
  (parallelism)?
• Do you predict genetic repeatability?

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Some more questions

• Why has sex evolved?
• Why do we age?
• How does virulence evolve?
• How does cooperation (or cheating) evolve?
• How does speciation begin?
• Is evolution Wrightian (many different outcomes)
  or Fisherian (one universal solution)?
• How do competitors coexist?

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• The most conspicuous evidence of evolution by
  natural selection is the fit of organisms to
  their environment.
• Yet quantifying adaptation continues to elude
  biologists.

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Adaptation may be quantified directly
Day 0
Day 1
Evolved
Ancestor
Determine 1 2
Plate on agar to determine the ratio of 1 2

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Generation 0 -------------------------
Generation 20,000 è

• Experimental
• Conditions
• 12 replicate cultures
• single genotype of Escherichia coli B
• daily serial transfer
• single resource and temperature
• no sex

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Mutation rate itself evolves in certain
populations
Non-mutator
Mutator
Population
Generations
Sniegowski et al., Nature 387, 703-705 (1997)
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Part of the folk wisdom of evolutionary biology
is that specialization leads to adaptive decay
for environments outside the domain of
specialization. -R.D. Holt, Evol. Ecol.
(1996)
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Q1 Is the folk wisdom true?

• Does specialization lead to adaptive decay? (Can
  we find such an association?)
• Specialization adaptation by an organism to a
  subset of its original environment
• Adaptive decay decay in niche breadth that is
  associated with adaptation

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Why is this association so elusive?

• To determine if specialization leads to adaptive
  decay, we need to
• quantify adaptation
• know the history of adaptation
• Both have proven challenging in most natural and
  experimental systems.

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Is adaptation associated with loss of function?
?
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Important environmental factors
37 C
Glucose
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I used Biolog plates to measure diet breadth
Time (Generations)
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What are the consequences of adaptation?
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Hypothetical curves describing loss of function
Total Catabolic Function
Time (Generations)
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Parallel and convergent changes across lineages
are hallmarks of adaptive evolution
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Is the pattern consistent with AP?
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Diet breadth decays over time
Red mutators White non-mutators
Total Catabolic Function
0 2,000 10,000 20,000
Time (Generations)
Cooper and Lenski (2000) Nature 407736-739.
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Specialization in diet breadth was caused mostly
by antagonistic pleiotropy

• Antagonistic pleiotropy
• Most losses of catabolic function occurred in
  replicate populations (parallelism) and when
  adaptation was most rapid (early in the
  experiment).
• Mutation accumulation
• Mutator populations tend to lose more catabolic
  functionality
• but this additional loss is not proportional to
  the increase in mutation rate.

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Evolution of thermal niche
Generation time
Vmax
Temperature (C)
Cooper, Bennett, and Lenski. (2001) Evolution
55(5)889-896.
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Adaptation to moderate temperatures leads to
reduced performance at extreme temperatures
Relative Vmax
Time (Generations)
Cooper, Bennett, and Lenski. (2001) Evolution
55(5)889-896.
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Case study What explains the rapid loss of
D-ribose catabolism?
Frequency Rbs-
Time (Generations)
Cooper, V. S., D. Schneider, M. Blot, and R. E.
Lenski. (2001) J. Bact. 183 28342841.
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Ribose function is hypermutable

• Mutation rate for ribose loss 5.4 X 10-5 per
  generation.
• 2-5 orders of magnitude higher than mutation
  rates measured for other traits.
• Time required to reach a frequency of 50 under
  mutation pressure alone 18,519 generations.

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A.
IS150
G6
G5
G267
G268
G76
rbsD
rbsA
rbsC
rbsB
rbsK
rbsR
yieO
left IS150
G266
adjacent sequence
G77
G269
right IS150
adjacent sequence
HincII
HincII
HincII
HincII
HincII
HincII
B.
Extent of the deletion
Hyb.

PCR

(bp
)
(bp
)
Ara-1
2,812
2,071
Ara-2
3,043
2,302
Ara-3
3,854
7,373
Ara-4
3,338
2,597
Ara-5
2,483
3,378
Ara-6
3,034
2,293
Ara1
1,972
2,867
Ara3
3,332
2,591
Ara4
4,163
5,058
Ara5
2,999
3,894
Ara6
3,329
2,588
2,662
9,005
Ancestor
1 k
b
Cooper, V. S., D. Schneider, M. Blot, and R. E.
Lenski. (2001) J. Bact. 183 28342841.
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Rbs- mutation alone improves fitness
Fitness
Independent Rbs- mutants of ancestor
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What accounts for the rapid loss of ribose
catabolism?

• Time to 50 of population
• MA alone 18,519 generations
• Selection 1,774 generations
• Selection plus MA 781 generations
• Genetic hitchhiking priceless (lt
  500 generations)

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Loss of succinate, fumarate, malate function

• suite of functions compromised in part by IS
  insertion in pykF
• different pykF mutations found in other
  populations same reversibility?
• suggests selection to regain succinate function
  and study of evolution of phenotypic plasticity

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Summary

• Is specialization caused more by AP or MA?
• Antagonistic pleiotropy explains the majority of
  change in diet breadth and thermal range.
• Mutation accumulation is only detectable among
  mutator populations may require more time?
• Should adaptive decay be folk wisdom?
• Most functions were retained.
• Selection in permissive environments may yield a
  greater frequency of specialists.
• The mechanisms responsible for loss of function
  cannot be assumed.