A phylogeny is a tree representing the ancestry of an evolving population. They are a powerful technique for observing large-scale patterns in evolution. Phylogenies group extant organisms by ancestral relatedness, showing the history of hierarchical lineage branching events within an evolving system. These relationships reveal the evolutionary trajectories of populations through a genotypic or phenotypic space. As such, phylogenies open a direct window through which to observe ecology, differential selection, genetic potentiation, emergence of complex traits, and other evolutionary dynamics in artificial life (ALife) systems .

In biology, phylogenies must usually be reconstructed based on comparisons amongst existing species (and sometimes information from the fossil record). In artificial life systems, however, they can usually be directly measured. This perfect observability is a major strength of artificial life systems, but means that comparisons between phylogenies from nature and phylogenies from artificial life must be handled with care . Biologists have developed many sophisticated and powerful phylogeny-based analysis techniques. For example, existing work uses properties of tree topology to infer characteristics of the evolutionary processes acting on a population. With an understanding of the differences between biology and artificial life, these approaches can be imported into ALife systems. For example, phylodiversity metrics can be used to detect diversity-maintaining ecological interactions and ongoing generation of significant evolutionary innovations.

Tools

Phylogenies in biology are a bio-product of natural selection that arise, mostly, through our desire to make sense of what we see and the relationship between creatures. In simulation, however, we have access to the whole “fossil record” and so we know the ground truth.

This makes it possible to actually study the higher-level dynamics of groups of individuals (which we may or may not call species) and form informative trees (or graphs) about their relationships.

The following are some standalone tools that enable analysis of phylogenetic data, particularly from artificial life systems:

• APOGeT
• hstrat
• PhyloTrackPy

There are also artificial life systems that have specific support for phylogenies or have been used to investigate phylogenetic dynamics previously:

• Aevol
• Avida
• Symbulation

References