Common Ancestry, Contemporary Phylogenetics, and Process Ontology

Recent advances in systematics and evolutionary biology have revealed extraordinary complexity in phylogenetic diversification, challenged our traditional views of the Tree of Life, and changed our understanding of the nature of phylogenetic entities themselves. These empirical advances call for an updated conceptual basis for phylogenetics. Phylogeny is best conceptualized as a complex multidimensional system - encompassing spatial, temporal, and hierarchical dimensions. The hierarchical dimension confers important but poorly studied influences - such as emergence, constraint, non-linearity, and non-extrapolationism - on phylogenetic possibilities. Spatially and temporally, phylogenetic diversification patterns should be viewed as resulting from multimodal phenomena - i.e., as a consequence of both vertical and horizontal modes of evolution. Further, phylogeny should not be viewed as a single absolute history - it comprises interacting, multi-layered lineage histories (i.e., genomes, cells, organisms, species). Causal interactions and feedback dynamics amongst these dimensions represent a classic biocomplexity system. Therefore, we suggest that this is an opportune time for development of a phylogenetic systems theory. Because our view of phylogeny comprises a complex interacting system of multiple lineage histories, we also argue that a process ontology provides the logical foundation for contemporary phylogenetics. A process ontology framework also reconciles recent observations that the boundaries of biological entities (including the boundaries of genomes, cells, organisms, and species lineages) are fuzzy and open to varying degrees of exchange at various points in their histories. While these fuzzy boundaries accommodate the biocomplexity and multimodal evolutionary processes described above, they also pose challenges for our notions of phylogenetic entities themselves and their biological individuality - leading to exciting new areas of study in systematics, theoretical biology and philosophy of biology.