  Evolutionary dynamics are shaped by a variety of fundamental, generic
drivers, including spatial structure, ecology, and selection pressure. These
drivers impact the trajectory of evolution, and have been hypothesized to
influence phylogenetic structure. Here, we set out to assess (1) if spatial
structure, ecology, and selection pressure leave detectable signatures in
phylogenetic structure, (2) the extent, in particular, to which ecology can be
detected and discerned in the presence of spatial structure, and (3) the extent
to which these phylogenetic signatures generalize across evolutionary systems.
To this end, we analyze phylogenies generated by manipulating spatial
structure, ecology, and selection pressure within three computational models of
varied scope and sophistication. We find that selection pressure, spatial
structure, and ecology have characteristic effects on phylogenetic metrics,
although these effects are complex and not always intuitive. Signatures have
some consistency across systems when using equivalent taxonomic unit
definitions (e.g., individual, genotype, species). Further, we find that
sufficiently strong ecology can be detected in the presence of spatial
structure. We also find that, while low-resolution phylogenetic reconstructions
can bias some phylogenetic metrics, high-resolution reconstructions
recapitulate them faithfully. Although our results suggest potential for
evolutionary inference of spatial structure, ecology, and selection pressure
through phylogenetic analysis, further methods development is needed to
distinguish these drivers' phylometric signatures from each other and to
appropriately normalize phylogenetic metrics. With such work, phylogenetic
analysis could provide a versatile toolkit to study large-scale evolving
populations.
