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

TypeCollection
TitleZehady, A. K., Fordham, B. G., & Ogg J. G. (2019). Integrated species–phenon trees: visualizing infraspecific diversity within lineages. Data repository for published article
Brief TitleZehady & others (2019). Integrated species–phenon trees. Data repository for published article
Collection TypeCollection
Access PrivilegesStratophylogenies
DOI - Digital Object Identifier10.25911/5db66fd8c5127
Metadata LanguageEnglish
Data LanguageEnglish
Significance StatementOur 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 DescriptionThe 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 DescriptionThe 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 Emailbarry.fordham@anu.edu.au
Contact AddressResearch 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 InvestigatorAbdullah Khan Zehady
SupervisorsJames G. Ogg
CollaboratorsBarry G. Fordham
Fields of Research040308 - Palaeontology (incl. Palynology)
060309 - Phylogeny and Comparative Analysis
040311 - Stratigraphy (incl. Biostratigraphy and Sequence Stratigraphy)
040605 - Palaeoclimatology
0603 - Evolutionary Biology
Socio-Economic Objective960304 - Climate Variability (excl. Social Impacts)
Keywordsevolutionary tree
phylogeny
timescale calibration
data visualization
morphospecies
lineages
stratophenetics
biostratigraphy
macroevolution
TimeScale Creator
Type of Research ActivityStrategic basic research
Date Coverage
Date FromDate To
2014-082019-05
Date of data creation2019-05
Year of data publication2019
Creator(s) for Citation
Given NameSurname
Abdullah KhanZehady
Barry G.Fordham
James G.Ogg
Publisher for CitationThe Australian National University Data Commons
Publications

Identifier Type
Digital Object Identifier
Identifier Value
10.1371/journal.pone.0204625
Publication Title
Future-proofing the Cenozoic macroperforate planktonic foraminifera phylogeny of Aze & others (2011)
Publication Reference
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.


Identifier Type
Digital Object Identifier
Identifier Value
10.1111/j.1469-185X.2011.00178.x
Publication Title
A phylogeny of Cenozoic macroperforate planktonic foraminifera from fossil data
Publication Reference
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 RightsOpen Access
Access Rights TypeOpen
Rights held in and over the dataCreative Commons Licence (CC BY) is assigned to this data. Details of the licence can be found at http://creativecommons.org.au/licences.
Licence TypeCC-BY - Attribution
Retention PeriodIndefinitely
Disposal DateNever
Extent or Quantity13
Data Size9.13 MB
Data Management PlanNo
Status: Published
Published To:
- Australian National University
- Australian National Data Service
Identifier: anudc:5982
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  • Files: 13
  • Size: 9.13 MB

Data Files

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