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. Our integrated species–phenon tree merges ancestor–descendant proposals for fossil morphotaxa (phena) with reconstructed phylogenies of lineages (species), to digitally visualize infraspecific diversity within species through deep time. Aze & others’ important macroevolutionary dataset provides a case example to encourage mutual learnings between paleontological and molecular approaches. 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
Type
Collection
Title
Zehady, A. K., Fordham, B. G., & Ogg J. G. (2019). Integrated species–phenon trees: visualizing infraspecific diversity within lineages. Data repository for published article
Brief Title
Zehady & others (2019). Integrated species–phenon trees. Data repository for published article
Collection Type
Collection
Access Privileges
Stratophylogenies
DOI - Digital Object Identifier
10.25911/5db66fd8c5127
Metadata Language
English
Data Language
English
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.
Brief Description
The integrated species–phenon tree merges ancestor–descendant proposals for fossil morphotaxa (phena) with reconstructed phylogenies of lineages (species), to digitally visualize infraspecific diversity within species through deep time.
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. Our integrated species–phenon tree merges ancestor–descendant proposals for fossil morphotaxa (phena) with reconstructed phylogenies of lineages (species), to digitally visualize infraspecific diversity within species through deep time. Aze & others’ important macroevolutionary dataset provides a case example to encourage mutual learnings between paleontological and molecular approaches. 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
Contact Email
barry.fordham@anu.edu.au
Contact Address
Research School of Earth Sciences Jaeger 8, Building 142, Mills Road Australian National University Canberra, ACT 2601 Australia
Contact Phone Number
+61 (0)421 611 913
Principal Investigator
Abdullah Khan Zehady
Supervisors
James G. Ogg
Collaborators
Barry G. Fordham
Fields of Research
040308 - Palaeontology (incl. Palynology); 060309 - Phylogeny and Comparative Analysis; 040311 - Stratigraphy (incl. Biostratigraphy and Sequence Stratigraphy); 040605 - Palaeoclimatology; 0603 - Evolutionary Biology
Socio-Economic Objective
960304 - Climate Variability (excl. Social Impacts)
Keywords
evolutionary tree; phylogeny; timescale calibration; data visualization; morphospecies; lineages; stratophenetics; biostratigraphy; macroevolution; TimeScale Creator
Type of Research Activity
Strategic basic research
Date Coverage
2014-08
2019-05
Date of data creation
2019-05
Year of data publication
2019
Creator(s) for Citation
Abdullah Khan
Zehady
Barry G.
Fordham
James G.
Ogg
Publisher for Citation
The Australian National University Data Commons
Publications
doi
10.1371/journal.pone.0204625
Future-proofing the Cenozoic macroperforate planktonic foraminifera phylogeny of Aze & others (2011)
Fordham, B. G., Aze, T., Haller, C., Zehady, A. K., Pearson, P. N., Ogg, J. G., & Wade, B. S. (2018). Future-proofing the Cenozoic macroperforate planktonic foraminifera phylogeny of Aze & others (2011). PLoS One, 13(10), e0204625.
doi
10.1111/j.1469-185X.2011.00178.x
A phylogeny of Cenozoic macroperforate planktonic foraminifera from fossil data
Aze, T., Ezard, T. H., Purvis, A., Coxall, H. K., Stewart, D. R., Wade, B. S., & Pearson, P. N. (2011). A phylogeny of Cenozoic macroperforate planktonic foraminifera from fossil data. Biological Reviews of the Cambridge Philosophical Society, 86(4), 900-927.
Access Rights
Open Access
Access Rights Type
Open
Rights held in and over the data
Creative Commons Licence (CC BY) is assigned to this data. Details of the licence can be found at http://creativecommons.org.au/licences.
Licence Type
CC-BY - Attribution
Retention Period
Indefinitely
Disposal Date
Never
Extent or Quantity
13
Data Size
9.13 MB
Data Management Plan
No
Status: Published
Published to:
  • Australian National University
  • Australian National Data Service