Evolutionary SA search for likely environment and biomass

General concept

The reductive evolution simulation can be modified to identify the environment and biomass that best fits the gene content and the time of gene loss as inferred from a phylogenetic reconstruction. A simulated annealing procedure is used with the reductive evolutionary simulation embedded in. The minimal growth medium was augmented with randomly selected metabolites, and with the original biomass function, the search is started for the ancestral metabolic network. For each iteration of the search the biomass is fixed and the optimal environment is identified (assessed by the consistency of the timing of gene loss with the actual timing as suggested by a phylogenetic analysis). The optimal environment is then fixed and biomass compositions are identified that correlate the best with phylogeny. These steps are repeated until there is no improvement in the simulated annealing fitness score.

Items to consider when implementing

Software packages with this method

Applications of interest

Description of study and link to study:

What was learned with this method:

Relevant references

Yizhak, et al.

Related methods

Reductive evolution simulation

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