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Phylogeny

We use PhylogeneticTrees.jl for phylogeny tracking. This package includes efficient algorithms for calculating distances between taxa and pruning the tree of taxa with no living descendants to free up memory.

Why do we care about Phylogeny?

In short, phylogeny is the evolutionary history of a group of organisms. This has myriad uses:

  • Analysis: We can easily observe how population dynamics change throughout evolution and visualize extinctions and sub-species. See Interpreting the Tape of Life by Dolson et.al for more.
  • Optimization: We can estimate performance of individuals based on their phylogenetic distance from other individuals to achieve substantial reductions in compute required. See evolutionary and co-evolutionary applications of this idea.

Phylogenetic Operators

Phylogeny is managed using four operators:

  • InitializePhylogeny: Adds current members of the population as roots of a phylogenetic tree. Runs on the first generation
  • UpdatePhylogeny: Updates the phylogeny for the current population, runs on all generations. Should run after children are produced.
  • LogPhylogeny: A bit misnamed for now, this operator writes phylogeny data to disk in the ALIFE Data Standard format. Should run before pruning individuals
  • PurgePhylogeny: Removes individuals from the phylogeny that have no living descendants. Should run after children are produced and optionally, all individuals have been written to disk. Essential for reducing memory usage.

Deltas and DeltaCaches

Stores the difference between an individual and its parent for all edges in the tree.

  • InitializeDeltaCache: Initializes the delta cache for the current population. Runs on the first generation.
  • UpdateDeltaCache: Updates the delta cache for the current population. Should run after children are produced.

Gene Pool

The GenePool is a subset of genes in the population, typically the most recent genes. Used for runtime techniques that leverage information about the population, like adaptive mutation rates.

  • UpdateGenePool: Creates/updates the gene pool for the current population.