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

Full description

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

Notes

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Significance statement

Our graphics program just might provide common ground for evolutionary biologists and paleontologists to examine, together, evolutionary change though deep time; and in so doing gain valuable insights from each other. There is currently a burgeoning literature in molecular phylogenetics, richly detailing genetic complexity within living species and species complexes. But lesser known, at least to biological communities, is what’s coming out of that branch of paleontological research that is funded mainly because of the fundamental reliance of paleoclimatology on high-resolution microfossil stratigraphy. These microfossil studies typically embrace sequences of fossil-rich planktonic oozes extending over the past several tens of millions of years. And, like the molecular-phylogenetic literature, the microfossil studies also richly detail complexity — but within past species lineages, and in terms of morphology, geochemistry, and so on, profiled through long stretches of deep time. Recently this research area has produced quite a macroevolutionary breakthrough (by Aze & others, 2011): joint morphospecies and lineage phylogenetic trees for the same microfossil group (macroperforate planktonic foraminifera; some 340 morphospecies and 210 lineages in total), covering the entire Cenozoic Era from 66 millions years ago to the present living representatives. And, in parallel with this work, vigorous molecular-phylogenetic research has been conducted on the same microfossil group, resulting in very detailed genotypic characterisation of the living species. So, at least for these microfossils, there is an exciting opportunity to bring together these two branches of research — paleontological and molecular. However, synthesizing those morphospecies (phenon) and lineage (species) trees of Aze & others is a visual brain teaser. As a result, even though the lineage tree has proved a very rich source of macroevolutionary research in the intervening years, little has been done to uncover the rich interplay within these trees between morphologic change and lineage evolution and speciation, including any relationship with patterns emerging from the molecular studies. Our integrated species–phenon tree aims to redress this situation by augmenting a tree-drawing feature within a widely used Earth-history visualization platform (TimeScale Creator) and realizing a new, visually engaging representation of lineage evolution that will be accessible and relevant to both paleontologists and molecular biologists. In so doing, we hope to help bridge a gulf between these two research areas and mutually enrich both.