In silico experimental evolution: a tool to test evolutionary scenarios

Bérénice Batut, D. P. Parsons, S. Fischer, G. Beslon, C. Knibbe

Adaptation from [Hindré et al 2012]

Elaboration of hypothetical evolutionary scenarios with comparative genomics

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Elaboration of hypothetical evolutionary scenarios with comparative genomics

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Elaboration of hypothetical evolutionary scenarios with comparative genomics

Changes in lifestyle

Changes in environmental conditions? Changes in population structure?

Changes in mutation rates?

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Adaptation from [Hindré et al 2012]

In vitro

Weaknesses Long-term experiments Difficulty to interpret the events Difficulty to reproduce any real environmental conditions and their variations

Experimental evolution to test evolutionary scenarios coming from comparative genomics

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Experimental evolution to test evolutionary scenarios coming from comparative genomics

[Hindré et al 2012]

In vitro

In silico

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In silico experimental evolution

Population of sequences / Phenotype

Selection process Variation process

Changes in lifestyle

Changes in mutation

processes Evolutionary

loop

Analysis of evolved “organisms”

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Aevol: an in silico experimental evolution platform - www.aevol.fr evol

Selection

Replication (mutations,

rearrangements) Population

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Selection

Replication (mutations,

rearrangements) Population

Selection

Replication (mutations,

rearrangements) Population

 

Aevol: an in silico experimental evolution platform - www.aevol.fr evol

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An organism => a structured genome with a variable number of genes in a variable order a variable amount of non coding sequences a variable number of operons …

Aevol: an in silico experimental evolution platform - www.aevol.fr evol

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Changes in lifestyle

Changes in environmental conditions? Changes in population structure?

Change in mutation rates?

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Changes in lifestyle and/or in mutation processes

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evol

Comparative genomics

In silico experimental

evolution

Using aevol to test evolutionary scenarios

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evolUsing aevol to test evolutionary scenarios

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Smoother distribution of growth rates

Control k = 750

Scenario k = 250

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Genome shrinkage under relaxed selection

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Genome shrinkage under relaxed selection

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Genome shrinkage under relaxed selection

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Genome shrinkage under relaxed selection

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Smaller and more compact genomes

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Smaller and more compact genomes

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Smaller and more compact genomes

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Comparison with endosymbionts and Prochlorococcus

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An exact “fossil record” is saved during each run

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Mutational events on winning lineage

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150,000⇧200,000

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Mutational events on winning lineage

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Control  

Scenario  

150,000⇧200,000

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Mutational events on winning lineage

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Control  

Scenario  

5 ⋅10−6 per  base   5 ⋅10−5 per  base  

In silico experimental evolution: a tool to test evolutionary scenarios

Adaptation from [Wagner 2009]

In silico experimental evolution: a tool to test evolutionary scenarios

Adaptation from [Wagner 2009]

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www.aevol.fr

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