Among the primary contributions of phylogenetic systematics to the synthesis of developmental biology and evolution are phylogenetic hypotheses. Phylogenetic hypotheses are critical in interpreting the patterns of evolution of developmental genes and processes, as are morphological data. Using a robust phylogeny, the evolutionary history of individual morphological or developmental features can be traced and ancestral conditions inferred. Multiple characters (e.g., morphological and developmental) can be mapped together on the phylogeny, and patterns of character association can be quantified and tested for correlation.

Using the vertebrate forelimb as an example, I show that by mapping accurate morphological data (homologous skeletal elements of the vertebrate forelimb) onto a phylogeny, an alternative interpretation of Hox gene expression emerges. Teleost fishes and tetrapods may share no homologous skeletal elements in their forelimbs, and thus similarities and differences in Hox patterns during limb development must be reinterpreted. Specifically, the presence of the phase III Hox pattern in tetrapods may not be correlated with digits but rather may simply be the normal expression pattern of a metapterygium in fishes. This example illustrates the rigorous hypotheses that can be developed using morphological data and phylogenetic methods.

“Creating a general reference system and investigating the relations that extend from it to all other possible and necessary systems in biology is the task of systematics.” (Hennig, 1966, p.7)