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). Data repository for published article.

TypeCollection
TitleFordham, 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). Data repository for published article.
Brief TitleFordham & others (2018). Data repository for published article
Collection TypeCollection
Access PrivilegesStratophylogenies
DOI - Digital Object Identifier10.25911/5b8df50c1f2bd
Metadata LanguageEnglish
Data LanguageEnglish
Significance StatementThe Aze & others (2011) phylogeny of Cenozoic macroperforate planktonic foraminifera has proved an important macroevolutionary dataset: especially because it proposed evolutionary trees of both morphospecies and lineages for a large taxonomic group. Having trees for both concepts for the same group provides a unique opportunity to examine macroevolutionary phenomena conjointly from both morphospatial and phylogenetic perspectives. The utility of these trees are further enhanced because the group chosen occupies the entire Cenozoic Era, has the richest and most intensively studied fossil record of any group, and is a primary group for Cenozoic biostratigraphic zonations and paleoceanographic proxies.

However, the 2011 work has remained static with regard to subsequent advances, including timescale updates and phylogenetic knowledge. This is starting to impact on its currency for ongoing macroevolutionary analysis. In addition, the biostratigraphic and paleoceanographic communities have made only minor use of the Aze & others study mainly because positioning it within Earth history contexts is not straightforward. The work’s unique employment of both morphospecies and lineages has also been misunderstood by some macroevolutionary analysts.

We have addressed these issues by transferring the Aze & others dataset onto TimeScale Creator, the data-visualisation platform used for the last decade and a half to integrate and publish the international Geological Time Scale (GTS). This has allowed the trees and their contents to be calibrated through the series of time-scale upgrades encompassed by the dataset, making it current and ready for future time scales. In so doing the dataset has been improved and enhanced, while preserving its historical integrity (but also positioned for subsequent versions), and a number of lessons have been learnt to guide future work.

By introducing an evolutionary-tree function into the TimeScale Creator platform, the dataset contents are now accessible visually on the tree, via enhanced graphical devices and labeling and, especially, by presentation of taxonomic, biostratigraphic, paleoceanographic, and other information in pop-ups linked to individual taxa displayed on the trees. This makes the internals of the database transparent to the research community, including details of age calibrations on which the trees, and their application, depends. But the database contents have also been corrected, enlarged, and improved, including linking of morphospecies and lineages to ensure internal consistency and to enable sharing with the research community.

Both macroevolutionary and biostratigraphic communities are now equipped with an enduring phylogenetic database of Cenozoic macroperforate planktonic foraminiferal morphospecies and lineages for which both graphics and content can be visualised together.
Brief DescriptionData repository for published article - 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. https://doi.org/10.1371/journal.pone.0204625

Files -

NewSpreadsheets:
spreadsheets (for details see worksheet, Contents)
- some generated from database, TSCEvolTree_Aze&2011_CorrJul2018

-TSCEvolTree_Aze&2011_CorrJul2018_BasicData.xlsx
- TSCEvolTree_Aze&2011_CorrJul2018_DBDesign.xlsx

Aze&2011_OriginalAppendices:
Appendices from Aze & others, 2011, Supporting Information
- Aze&2011_Orig_AppendixS1.pdf
- Aze&2011_Orig_AppendixS2.pdf
- Aze&2011_Orig_AppendixS3.pdf
- Aze&2011_Orig_AppendixS4.pdf
- Aze&2011_Orig_AppendixS5.xls

Links to -
anudc:5528 database,TSCEvolTree_Aze&2011_CorrJul2018
anudc:5529 datapacks
Full DescriptionArticle Abstract - The unique macroevolutionary dataset of Aze & others has been transferred onto the TimeScale Creator visualisation platform while, as much as practicable, preserving the original unrevised content of its morphospecies and lineage evolutionary trees. This is a “Corrected Version” (not a revision), which can serve as an on-going historical case example because it is now updatable with future time scales. Both macroevolutionary and biostratigraphic communities are now equipped with an enduring phylogenetic database of Cenozoic macroperforate planktonic foraminiferal morphospecies and lineages for which both graphics and content can be visualised together. Key to maintaining the currency of the trees has been specification of time scales for sources of stratigraphic ranges; these scales then locate the range dates within the calibration series. Some ranges or their sources have undergone mostly minor corrections or amendments. Links between lineage and morphospecies trees have been introduced to improve consistency and transparency in timing within the trees. Also, Aze & others’ dual employment of morphospecies and lineage concepts is further elaborated here, given misunderstandings that have ensued. Features displayed on the trees include options for line styles for additional categories for range extensions or degrees of support for ancestor–descendant proposals; these have been applied to a small number of instances as an encouragement to capture more nuanced data in the future. In addition to labeling of eco- and morpho-groups on both trees, genus labels can be attached to the morphospecies tree to warn of polyphyletic morphogenera, and the lineage codes have been decoded to ease their recognition. However, it is the mouse-over pop-ups that provide the greatest opportunity to embed supporting information in the trees. They include details for stratigraphic ranges and their recalibration steps, positions relative to the standard planktonic-foraminiferal zonation, and applications as datums, as well as mutual listings between morphospecies and lineages which ease the tracing of their interrelated contents. The elaboration of the original dataset has been captured in a relational database, which can be considered a resource in itself, and, through queries and programming, serves to generate the TimeScale Creator datapacks.
Contact Emailbarry.fordham@anu.edu.au
Contact AddressBarry G. Fordham
Research School of Earth Sciences
Jaeger 8, Building 142, Mills Road
Australian National University
Acton, ACT 2601 Australia

Contact Phone Number+61 (0)421 611 913
Principal InvestigatorBarry G. Fordham
CollaboratorsTracy Aze
Christian Haller
Abdullah Khan Zehady
Paul N. Pearson
James G. Ogg
Bridget S. Wade
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 visualisation
morphospecies
lineages
planktonic foraminifera
stratophenetics
biostratigraphy
macroevolution
TimeScale Creator
relational database
Cenozoic
Type of Research ActivityStrategic basic research
Date Coverage
Date FromDate To
18262014
Time Period2012 - 2016
Date of data creation2018-07
Year of data publication2018
Creator(s) for Citation
Given NameSurname
Barry G.Fordham
TracyAze
ChristianHaller
Abdullah KhanZehady
Paul N.Pearson
James G.Ogg
Bridget S.Wade
Publisher for CitationThe Australian National University Data Commons
Publications

Identifier Type

Identifier Value

Publication Title

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. https://doi.org/10.1371/journal.pone.0204625


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 Quantity7
Data Size1.38 MB
Data Management PlanNo

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