Zehady, A. K., Fordham, B. G., & Ogg J. G. (2019). Integrated species–phenon trees: visualizing infraspecific diversity within lineages. Data repository for published article

The unprecedented detail with which contemporary molecular phylogenetics are visualizing infraspecific relationships within living species and species complexes cannot as yet be reliably extended into deep time. Yet paleontological systematics has routinely dealt in (mainly) morphotaxa envisaged in various ways to have been components of past species lineages. Bridging these perspectives can only enrich both. We present a visualization tool that digitally depicts infraspecific diversity within species through deep time. Our integrated species–phenon tree merges ancestor–descendant trees for fossil morphotaxa (phena) into reconstructed phylogenies of lineages (species) by expanding the latter into “species boxes” and placing the phenon trees inside. A key programming strategy to overcome the lack of a simple overall parent–child hierarchy in the integrated tree has been the progressive population of a species–phenon relationship map which then provides the graphical footprint for the overarching species boxes. Our initial case has been limited to planktonic foraminfera via Aze & others’ important macroevolutionary dataset. The tool could potentially be appropriated for other organisms, to detail other kinds of infraspecific granularity within lineages, or more generally to visualize two nested but loosely coupled trees.

Supporting Data
Functional Specification _ Integrated Species – Phenon Tree.docx
Figure Datapacks:
TSCEvolTree_IntTree2019Fig1ia,b.dpk
TSCEvolTree_IntTree2019Fig1ic.dpk
TSCEvolTree_IntTree2019Fig1iiia,b.dpk
TSCEvolTree_IntTree2019Fig1iiic.dpk
Figure Datasets:
TSCEvolTree_IntTree2019Fig1ia,b.txt
TSCEvolTree_IntTree2019Fig1ic.txt
TSCEvolTree_IntTree2019Fig1iiia,b.txt
TSCEvolTree_IntTree2019Fig1iiic.txt
Figure Settings:
TSCEvolTree_IntTree2019Fig1ia,b.tsc
TSCEvolTree_IntTree2019Fig1ic.tsc
TSCEvolTree_IntTree2019Fig1iiia,b.tsc
TSCEvolTree_IntTree2019Fig1iiic.tsc