Experimental evolution
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Experimental evolution. The outcome of selection for high and low oil content in the Illinois corn experiment. William Dallinger 1880-1886 Selected for thermotolerance of microorganisms 60 F  158 F. How experimental evolution works. Batch (serial) culture Chemostat Turbidostat

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Experimental evolution

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Experimental evolution

Experimental evolution


Experimental evolution

The outcome of selection for high and low oil content

in the Illinois corn experiment.


Experimental evolution

William Dallinger

1880-1886

Selected for thermotolerance of microorganisms

60 F  158 F


How experimental evolution works

How experimental evolution works

  • Batch (serial) culture

  • Chemostat

  • Turbidostat

  • Static culture (liquid or solid)


Experimental evolution

Chemostat


Chemostats select for nutrient affinity

Chemostats select for nutrient affinity


Static culture

Static culture


What are the key variables brainstorm

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?


Some questions addressed by experimental evolution

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?


Is evolution repeatable

Is evolution repeatable?

“I call this experiment ‘replaying life’s 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)


We can replay evolution

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?


Some more questions

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?


Experimental evolution

The most conspicuous evidence of evolution by natural selection is the fit of organisms to their environment.

Yet quantifying adaptation continues to elude biologists.


Experimental evolution

Fitness = Ln [ N 1 (Day 1) / N1 (Day 0) ]

Ln [ N 2 (Day 1) / N2 (Day 0) ]

Adaptation may be quantified directly

Day 0

Day 1

Evolved

Ancestor

Determine

1 :2

Plate on agar to determine the ratio of 1 :2


Experimental evolution

-

+

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


Mutation rate itself evolves in certain populations

Mutation rate itself evolves in certain populations

Non-mutator

Mutator

Population

Generations

Sniegowski et al., Nature 387, 703-705 (1997)


Experimental evolution

“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)


Q1 is the folk wisdom true

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


Why is this association so elusive

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.


Is adaptation associated with loss of function

Is adaptation associated with loss of function?

?


Important environmental factors

Important environmental factors

Glucose

37° C


Experimental evolution

·

·

·

Fitness

I used Biolog plates to measure diet breadth

Time (Generations)


Experimental evolution

What are the consequences of adaptation?


Hypothetical curves describing loss of function

Hypothetical curves describing loss of function:

Total Catabolic Function

Time (Generations)


Parallel and convergent changes across lineages are hallmarks of adaptive evolution

?

ancestors

evolved

Parallel and convergent changes across lineages are hallmarks of adaptive evolution


Is the pattern consistent with ap

Is the pattern consistent with AP?


Diet breadth decays over time

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 407:736-739.


Specialization in diet breadth was caused mostly by antagonistic pleiotropy

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.


Experimental evolution

Evolution of thermal niche

Generation time

Vmax

Temperature (°C)

Cooper, Bennett, and Lenski. (2001) Evolution 55(5):889-896.


Adaptation to moderate temperatures leads to reduced performance at extreme temperatures

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.


Case study what explains the rapid loss of d ribose catabolism

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: 2834–2841.


Ribose function is hypermutable

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.


Experimental evolution

A.

IS150

G6

G5

G267

G268

G76

rbsD

rbsA

rbsC

rbsB

rbsK

rbsR

yieO

left IS150

G266

adjacent sequence

G269

G77

right IS150

adjacent sequence

HincII

HincII

HincII

HincII

HincII

HincII

B.

Hyb.

PCR

Extent of the deletion

(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

Ara+1

1,972

2,867

Ara+3

3,332

2,591

Ara+4

4,163

5,058

Ara+5

2,999

3,894

Ara+6

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: 2834–2841.


Rbs mutation alone improves fitness

1.05

1.04

1.03

1.02

l

l

l

l

l

l

1.01

l

1

0.99

0.98

1

2

3

4

5

6

7

Rbs- mutation alone improves fitness

Fitness

Independent Rbs-mutants of ancestor


What accounts for the rapid loss of ribose catabolism

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 (< 500 generations)


Experimental evolution

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


Summary

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.


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