Cenozoic macroperforate planktonic foraminifera phylogeny of Aze & others (2011). Relational database for TimeScale Creator Evolutionary Tree. Corrected Version, July 2018

TypeCollection
TitleCenozoic macroperforate planktonic foraminifera phylogeny of Aze & others (2011). Relational database for TimeScale Creator Evolutionary Tree. Corrected Version, July 2018
Brief TitleAze & others (2011) phylogeny database; Corrected Version, July 2018
Collection TypeDataset
Access PrivilegesStratophylogenies
DOI - Digital Object Identifier10.25911/5b8df4bfb5ac9
Metadata LanguageEnglish
Data LanguageEnglish
Significance StatementThe TSCEvolTree_Aze&2011_CorrJul2018 database provides the means by which to transfer the evolutionary trees of the Cenozoic macroperforate planktonic foraminifera phylogeny from Aze & others [1] to the TimeScale Creator visualisation platform, while preserving the currency of that 2011 dataset as a case study. A key element therefore is to prepare the stratigraphic ranges for recalibration, allowing the trees to persist authentically into the future as international time scales are updated. The transfer also provides the opportunity to incorporate corrections or amendments as encountered during the transfer, and to enhance the 2011 dataset in several ways such as more explicitly linking timings between the morphospecies and lineage trees. These objectives are accomplished mainly by developing this relational database for the dataset and presenting much of the information in it via the evolutionary trees function of TimeScale Creator. However, the underlying aim remains to preserve the contemporaneity and intent of the original study — it is a “Corrected Version”, not a revision.

A key advantage of a relational-database approach for the 2011 dataset is the clear separation of primary from derived information, especially useful in managing the interplay between morphospecies and lineages and in delineating and calibrating dates from different zonation time scales.


1. Aze T, Ezard TH, Purvis A, Coxall HK, Stewart DR, Wade BS, et al. A phylogeny of Cenozoic macroperforate planktonic foraminifera from fossil data. Biological Reviews of the Cambridge Philosophical Society. 2011;86(4):900-27. doi: 10.1111/j.1469-185X.2011.00178.x.

Brief DescriptionThe TSCEvolTree_Aze&2011_CorrJul2018 database is based upon the phylogeny of Aze & others [1] (the "2011" study/paper/etc.) and comprises two main tables, one for morphospecies, MorphospeciesAze_TableS3, the other for lineages, BiospeciesAze_aL.

The morphospecies table [following 1, Appendix S1, Table S3] compiles stratigraphic ranges and indications of morphology, ecology, and geography from stated sources, as well as stratigraphic analyses made using the Neptune database. The main focus of the morphospecies table for this transfer to TimeScale Creator is upon the ranges. This includes augmenting the table to record corrections or amendments to some dates (always within the provision not to revise but to better represent the intensions of the 2011 study) and, for a few ranges, to add questionable or conjectured range extensions. To enable the ranges to be recalibrated for subsequent time scales, the date sources are here linked to an ancillary table (MorphospeciesAze_TableS3DateRef) that explicitly indicates time scales for these sources. This measure also is needed to support the transfer because corrections or amendments made to Ma values from the 2011 study during the transfer are not necessarily against the time scale employed by that study (i.e., that of Wade & others [2], calibrated to Cande & Kent [3]). The measure also facilitates clear differentiation in the database where more than one time scale may, in effect, be applied by or to the source. Also added via the morphospecies table are indications of levels of evidential support for the ancestor–descendant proposals; these indications are generalized and not meant to suggest new information but rather to highlight a small number of demonstrably less or better supported proposals, and also to provide future capability for more deliberate attention to this aspect.

The main feature provided by the lineage table which augments the 2011 study is to embed in the table any links which may have been exercised manually in the 2011 study between the stratigraphic range of a lineage and that of an associated morphospecies; this applied to approximately 40 % of start dates and almost all end dates of lineages. This is implemented in the database by assigning a morphospecies range point (start or end) to each lineage range point (start or end) and employing a field to turn on or off the link between the lineage and morphospecies range points; if this field is turned on, the lineage point adopts the Ma of the morphospecies range point; if turned off, the original Ma given in the 2011 study to the lineage point (or its replacement if corrected or amended) is retained but the time scale of the morphospecies point is employed for calibration of the Ma. This measure enables correspondences between the timing of the morphospecies and lineage trees to be made transparent but also to easily retain these linkages if morphospecies ranges are changed. A similar embedding feature has been added which allows the database to work out the lineage memberships of each morphospecies, thus obviating the need to manually construct these lists (and inevitably make human errors).

Another key table (Wade & others, 2011 Datum) compiles the datums from Wade & others [2]. Here their tables are augmented to separately depict the zonations of Berggren & others (1995) [4] and Berggren & Pearson (2005) [5] in addition to the Wade & others zonation in its two versions (calibrated to Cande & Kent, 1995 [3], and to Gradstein & others, 2004 [6]). The remaining tables in the database include those (“global”) shared with other databases to provide, amongst other information, species and genus nomenclature, links to portals, and TimeScale Creator time units and datums.

From the tables: derived data and information, and datapacks

Much of the essential data needed for tree construction — names, dates, ancestors — are tabular or relational (or nearly so) and so mostly amounts to employing SQL queries to recast or combine elements from the database tables. This includes, from the main tables, the selection of ancestors, dates, and sources and associated commentary where, for instance, there are multiple options (e.g., corrected or amended entries), and then linking with accessory tables to add key determinants such as zonation time scales, accessory information such as taxonomic and grouping details, and paraphernalia such as colours.

Time-scale calibration of morphospecies and lineage dates employed a nested series of queries progressively recalibrating from those dates against the earlier published zonations to those against subsequent schemes, based on the augmented compilation of datums of Wade & others [2] (database table Wade & others, 2011 Datum). Proportional calibration between the zonations of Berggren & others (1995) [4], Berggren & Pearson (2005) [5], and finally Wade & others, calibrated to Cande & Kent (1995) [3], employed zonal index (marker) datums only. So these calibrations, based only on sometimes relatively coarsely spaced planktonic-foraminiferal events, should be considered minimally adequate. For the jump to GTS2004, that is, from the scales of Cande & Kent (1995) to Gradstein & others (2004) [6], all datums of Wade & others were used, providing a finely tuned conversion, at least in terms of planktonic-foraminiferal events. Later GTS conversions, from GTS2004 to GTS2012 and finally GTS2016, employed planktonic-foraminiferal zonal index datums using tables augmented from TimeScale Creator spreadsheet data.

Programming, coded in the database’s Visual Basic, is then used to integrate tables and queries into derived tables from which TimeScale Creator datapacks can be formulated. The programming includes procedural programming which is especially needed to generate the textural information provided in pop-ups as this is mostly nonrelational. Although the programming was developed inexpertly “in-house” and is code-intensive, it had the advantage of being able to be developed specifically to purpose and, being nonproprietary, able to be made available for scrutiny.




1. Aze T, Ezard TH, Purvis A, Coxall HK, Stewart DR, Wade BS, et al. A phylogeny of Cenozoic macroperforate planktonic foraminifera from fossil data. Biological Reviews of the Cambridge Philosophical Society. 2011;86(4):900-27. doi: 10.1111/j.1469-185X.2011.00178.x.
2. Wade BS, Pearson PN, Berggren WA, Pälike H. Review and revision of Cenozoic tropical planktonic foraminiferal biostratigraphy and calibration to the geomagnetic polarity and astronomical time scale. Earth-Science Reviews. 2011;104(1-3):111-42. doi: 10.1016/j.earscirev.2010.09.003.
3. Cande SC, Kent DV. Revised calibration of the geomagnetic polarity timescale for the Late Cretaceous and Cenozoic. Journal of Geophysical Research: Solid Earth. 1995;100(B4):6093-5. doi: 10.1029/94JB03098.
4. Berggren WA, Kent DV, Swisher CC, III, Aubry M-P. A revised Cenozoic geochronology and chronostratigraphy. In: Berggren WA, Kent DV, Aubry M-P, Hardenbol J, editors. Geochronology, time scales and global stratigraphic correlations. Tulsa (Oklahoma, USA): Society for Sedimentary Geology, Special Publication. No. 54.; 1995. p. 129-212.
5. Berggren WA, Pearson PN. A revised tropical to subtropical Paleogene planktonic foraminiferal zonation. Journal of Foraminiferal Research. 2005;35(4):279-98. doi: 10.2113/35.4.279.
6. Gradstein FM, Ogg JG, Smith AG, editors. A Geologic Time Scale 2004. Cambridge: Cambridge University Press; 2004.

Files -

Database:
TSCEvolTree_Aze&2011_CorrJul2018.accdb
- Microsoft Access database

Snips:
TSCEvolTree_Aze&2011_CorrJul2018_SnipRelationships.png
- snip of Relationships window from database


Full DescriptionSummary of relational tables in the TSCEvolTree_Aze&2011_CorrJul2018 database

MorphospeciesAze_TableS3

Details for the 339 morphospecies of the Aze & others paper [1], augmented from [1, Appendix S1, Table S3 and Appendix S5, worksheet aM]. The main focus is on clarifying the choice of stratigraphic ranges and ancestry, and incorporating post-publication corrections by the authors of Aze & others or selective corrections/amendments during conversion to TimeScale Creator.

Stratigraphic ranges are given in Ma values; the time scales of the sources for the Ma values are made explicit (via links to table, MorphospeciesAze_TableS3DateRef). Almost all ranges are simple, as per those provided by the 2011 paper, delineated by lowest (start date) and highest occurrence (end date). However, a small number of ranges more closely represent those given by the nominated sources by also including range extensions: “questioned” or “questioned (rare)” for less confident stratigraphic occurrences; and “conjectured”, where a range extension is hypothesized, usually to support an ancestry proposal lacking contiguous stratigraphic occurrences. A proportion (~15 %) of Ma values are corrected where minor differences in Ma values were found between the 2011 paper and the nominated source; however, a systematic check was not conducted across the dataset. A further proportion (~15 %) of Ma values are amended where alternative sources appear to better represent the intention of the 2011 paper; these include a few instances where there would be a conflict with the index (marker) datum sequence of the Wade & others [2] zonation. Corrections to Ma values are accompanied by brief explanatory comments. Minor changes to Ma values were also made by one of us (TA) for a proportion (~17 %) of entries; most of these corresponded to the already invoked corrections or amendments.

Entries for ancestors follow the 2011 paper, with two exceptions in which adjustments to Ma values have removed the overlap in range between ancestor and descendant: a correction made by Tracy Aze (for Pulleniatina finalis, P. obliquiloculata replaced P. spectabilis); and an amendment (for Paragloborotalia pseudokugleri, Dentoglobigerina galavisi is amended to D. globularis). Levels of evidential support for the ancestor–descendant proposals were not critically appraised as part of the TimeScale Creator conversion. However, column [PhylogenyMethod] was employed to distinguish a small number of proposals which were distinctly less (“not well”) or better (“strongly”) supported than the typical “well supported” proposals presumed for this group.

All other information given in [1, Table S3] was incorporated, including indications of morphology, ecology, geography, and analyses made using the Neptune database. This information from Table S3 also included the lists of segments from both morphospecies (ID) and lineage (LID) trees within which each morphospecies occurred; in terms of relational logic, these could be supplanted by a single entry, the code for the lineage containing the highest occurrence of the morphospecies, and this was added manually for the TimeScale Creator conversion.

BiospeciesAze_aL

Details for the 210 lineages of the 2011 paper, augmented from [1, Appendix S5, worksheet aL]. The main focus is to maximize and maintain consistency and transparency between morphospecies and lineages for Ma values of their stratigraphic ranges. This is achieved for the TimeScale Creator conversion by nominating a morphospecies whose Ma value (start or end date) potentially defines the date (start or end) for a lineage; each morphospecies chosen for this is based on the apparent link between morphospecies and lineage dates used in the 2011 paper; this morphospecies is given by column [StartDateOrigLinkMph]. For start dates, ~40 % of lineages could be linked in this way; for end dates, almost all (93 %) were. Where a lineage range point of the 2011 study did not correspond to a morphospecies range point, then this morphospecies is at least used to provide the time scale applied to the date for the lineage.

Entries for ancestral lineages follow the 2011 paper, with two exceptions necessitated by changes in Ma values which place the ancestral lineage outside the date of origin of the descendant lineage: N150-N151-T153, involving the origin of morphospecies Paragloborotalia pseudokugleri; and N52-N54-T53, involving the origin of morphospecies Hirsutella cibaoensis. Levels of evidential support for the ancestor–descendant proposals were not critically appraised as part of the TimeScale Creator conversion. However, column [PhylogenyMethod] was employed to distinguish two proposals that were distinctly less (“not well”) or better (“strongly”) supported than the typical “well supported” proposals presumed for this group. The assignment of branching type as bifurcating or budding in the 2011 paper is incorporated.

Ecogroup and morphogroup allocations follow the 2011 paper (these data were not provided with the 2011 paper, but were indicated by colours employed in [1, Appendices S2, S3]; some colours for lineage morphogroups needed to be corrected; the ecogroup and morphogroup data for lineages were provided for the TimeScale Creator conversion by one of us [TA]). Some minor exceptions to these ecogroup and morphogroups were invoked for the TimeScale Creator conversion, in order to better match those of the contained morphospecies.

MorphospeciesAze_TableS1_Morphogroup

Details for morphogroups used for morphospecies and lineages; as for [1, Appendix 1, Table S1, "Morphogroup"], with explicit colour codes.

MorphospeciesAze_TableS1_Ecogroup

Details for ecogroups used for morphospecies and lineages; as for [1, Appendix 1, Table S1, "Ecogroup"], with explicit colour codes.

MorphospeciesAze_TableS3_EcogroupReference

Sources for ecogroups assigned to morphospecies; as for "Ecogroup reference", taken from [1, Appendix 1, Table S3]; multiple references in the original entries are accorded a row each.

MorphospeciesAze_TableS3_AppendixS1C_References

References for [1, Appendix 1, Table S3 ].

MorphospeciesAze_TableS3DateRef

Sources, and their time-scales, used for Ma values (sources from [1, Appendix 1, Table S3, "Date reference"] "Date reference", Table S3, Appendix 1 of the 2011 paper). The key purpose is to make explicit the time scale against which the source has (apparently) provided the Ma value, essential in order to appropriately recalibrate to the current GTS time scale and also to maintain the capability to recalibrate to future time scales. An important example of this need is where dates from the Paleocene Atlas [3] have here been remeasured directly from the Atlas and so are against the time scale of Berggren & others [4], rather than calibrated to Wade & others [2] as in the 2011 study.

In the interests of transparency and to provide a pointer to recalibration steps needed, a further level of specificity is needed for those sources which imply more than one time scale for Ma values used. For the TimeScale Creator conversion, references to these sources also have the time scale specified. Examples include chapters from the Eocene Atlas [5]. For instance, in order for the TimeScale Creator conversion to record the questionable parts of the stratigraphic ranges given for some Clavigerinella morphospecies by Coxall & Pearson [6], additional start dates for these morphospecies have been measured directly from their Figure 8.1, drawn against the scale of Berggren & Pearson [7]. However, these dates need to be integrated with the Ma values from Coxall & Pearson already used in the 2011 paper, which were presented recalibrated by them to the scale of Wade & others. These two sets of sources are given as, respectively, “Coxall & Pearson (2006: BP05)” (against Berggren & Pearson) and “Coxall & Pearson (2006)” (against the time-scale option of Wade & others which was calibrated to Cande & Kent [8]). Analogous examples came from sources such as Berggren & others, which include some dates for which the usual recalibration is not applicable (reasons are specific to each instance and are indicated in comments fields in table, MorphospeciesAze_TableS3; Appendix S1b includes descriptions of these fields in worksheet, DesignMorphospeciesAze_TableS3, and corresponding data in worksheet, MorphospeciesAze_TableS3).

MorphospeciesAze_TableS3DateRef_DateScale

This simply gives full names for the four time scales requiring recalibration:
BKSA95: Berggren & others, 1995 [4]
BP05: Berggren & Pearson, 2005 [7]
WPBP11(CK95): Wade & others, 2011 [2]; calibrated to Cande & Kent, 1995 [8]
WPBP11(GTS04): Wade & others, 2011 [2]; calibrated to Gradstein & others, 2004 (GTS2004) [9].

Wade & others, 2011 Datum

Details for datums relative to zonations, compiled from [2, Tables 1, 3, 4 ].

Zonal (marker) datums are indicated, but other datums are also included, almost all of which provide intrazonal intervals employed for calibration between time scales. Datums specific to the BKSA95 zonation are separately tabulated from those of BP05, allowing calibration between zonations BKSA95, BP05, WPBP11(CK95), and WPBP11(GTS04) (see MorphospeciesAze_TableS3DateRef_DateScale, above). The WPBP11(GTS04) zonation corresponds to GTS2004 and so allows calibration to later GTS time scales (GTS2012, GTS2016).

Additional columns provide brief indications of adjustments needed for calibration, including a small number of alternative datums resulting from revised definitions of zonations. Nomenclatural links are provided for datum-naming taxa.

Global tables:

SpeciesGroupName
GenusGroupName
ChronosPortal
ColoursClofordWebSafeByHue

augmented from TimeScale Creator spreadsheet data:

TimeUnit_ReferenceUnit
TimeUnit
TSCPlanktonicForaminifersDatum
TSCPlanktonicForaminifersDatumMorphospecies

Datapack tables:

TSCMorphospeciesAzeTableS3
TSCBiospeciesAze
TSCAzeIntegratedTree


1. Aze T, Ezard TH, Purvis A, Coxall HK, Stewart DR, Wade BS, et al. A phylogeny of Cenozoic macroperforate planktonic foraminifera from fossil data. Biological Reviews of the Cambridge Philosophical Society. 2011;86(4):900-27. doi: 10.1111/j.1469-185X.2011.00178.x.
2. Wade BS, Pearson PN, Berggren WA, Pälike H. Review and revision of Cenozoic tropical planktonic foraminiferal biostratigraphy and calibration to the geomagnetic polarity and astronomical time scale. Earth-Science Reviews. 2011;104(1-3):111-42. doi: 10.1016/j.earscirev.2010.09.003.
3. Olsson RK, Hemleben C, Berggren WA, Huber BT, editors. Atlas of Paleocene planktonic foraminifera. Smithsonian Contributions to Paleobiology, 85. Washington (DC, USA): Smithsonian Institution Press; 1999.
4. Berggren WA, Kent DV, Swisher CC, III, Aubry M-P. A revised Cenozoic geochronology and chronostratigraphy. In: Berggren WA, Kent DV, Aubry M-P, Hardenbol J, editors. Geochronology, time scales and global stratigraphic correlations. Tulsa (Oklahoma, USA): Society for Sedimentary Geology, Special Publication. No. 54.; 1995. p. 129-212.
5. Pearson PN, Olsson RK, Huber BT, Hemleben C, Berggren WA, editors. Atlas of Eocene planktonic foraminifera. Fredericksburg (Virginia, USA): Cushman Foundation for Foraminiferal Research Special Publication, vol. 41; 2006.
6. Coxall HK, Pearson PN. Taxonomy, biostratigraphy, and phylogeny of the Hantkeninidae (Clavigerinella, Hantkenina, and Cribrohantkenina). In: Pearson PN, Olsson RK, Huber BT, Hemleben C, Berggren WA, editors. Atlas of Eocene planktonic foraminifera. Fredericksburg (Virginia, USA): Cushman Foundation for Foraminiferal Research Special Publication, vol. 41; 2006. p. 213-56.
7. Berggren WA, Pearson PN. A revised tropical to subtropical Paleogene planktonic foraminiferal zonation. Journal of Foraminiferal Research. 2005;35(4):279-98. doi: 10.2113/35.4.279.
8. Cande SC, Kent DV. Revised calibration of the geomagnetic polarity timescale for the Late Cretaceous and Cenozoic. Journal of Geophysical Research: Solid Earth. 1995;100(B4):6093-5. doi: 10.1029/94JB03098.
9. Gradstein FM, Ogg JG, Smith AG, editors. A Geologic Time Scale 2004. Cambridge: Cambridge University Press; 2004.
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
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 creation2012-07
Year of data publication2018
Creator(s) for Citation
Given NameSurname
Barry G.Fordham
Publisher for CitationThe Australian National University Data Commons
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 Quantity2
Data Size70.1 MB
Data Management PlanNo

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