  Since the advent of modern bioinformatics, the challenging, multifaceted
problem of reconstructing phylogenetic history from biological sequences has
hatched perennial statistical and algorithmic innovation. Studies of the
phylogenetic dynamics of digital, agent-based evolutionary models motivate a
peculiar converse question: how to best engineer tracking to facilitate fast,
accurate, and memory-efficient lineage reconstructions? Here, we formally
describe procedures for phylogenetic analysis in both serial and distributed
computing scenarios. With respect to the former, we demonstrate
reference-counting-based pruning of extinct lineages. For the latter, we
introduce a trie-based phylogenetic reconstruction approach for "hereditary
stratigraphy" genome annotations. This process allows phylogenetic
relationships between genomes to be inferred by comparing their similarities,
akin to reconstruction of natural history from biological DNA sequences.
Phylogenetic analysis capabilities significantly advance distributed
agent-based simulations as a tool for evolutionary research, and also benefit
application-oriented evolutionary computing. Such tracing could extend also to
other digital artifacts that proliferate through replication, like digital
media and computer viruses.
