Ecology, Spatial Structure, and Selection Pressure Induce Strong Signatures in Phylogenetic Structure

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.