DOI: 10.25911/5b8df4ddb9497
title: Cenozoic macroperforate planktonic foraminifera phylogeny of Aze & others (2011).  TimeScale Creator Evolutionary Tree.  Corrected Version, July 2018.  Five datapacks for Java software package.

description: The Timescale Creator platform is an interactive user environment in which the chart, in our case the evolutionary tree [1, see p. 22–25, 88–92], can be refreshed as options are selected (such as stratigraphic or Earth-history columns) and, given its vector graphics design, unlimited zoom and pop-ups can be employed on the fly.  For example the morphospecies and lineage trees of the 2011 study can now be displayed against a time scale comprising not only standard epochs but a comprehensive gamut of Earth-history columns, not just the standard chrono- and bio-stratigraphic units figured in the 2011 paper.  And interactively, mouse-over pop-ups allow display of further details of these units (e.g., access to their up-to-date internationally agreed definitions).

At the broadest view, the Timescale Creator versions of the 2011 trees can displayed against a monochrome background or projected against a background coloured by stages, the latter especially useful to keep track of the time interval while zooming in.  A cursory look over the original 2011 and Timescale Creator versions of the whole trees reveals some variation in tree shape:  for both sets of trees, spacing of clades is specific to each manifestation of a tree, it being determined by graphical programming algorithms dependent on, for example, the length of labels within the tree.  A similar artifactual effect on tree shape to note (again, applicable to both sets of trees) is the left- or right-hand positioning (rotation) of descendant clades relative to ancestors.


1.	Ogg JG, Gradstein FM, Chunduru NV, Gangi P, Lugowski A, Ault A. Manuals for Timescale Creator use, and for making TSC datapacks. West Lafayette (Indiana): Geologic TimeScale Foundation Inc., 2012  https://engineering.purdue.edu/Stratigraphy/tscreator/download/TSC_Manuals_April2012.pdf.
description: Timescale Creator–database customization

Features provided by Timescale Creator enhance the information which can be gleaned from the 2011 trees.  These features can be provided either from functions already built into Timescale Creator, or via “in-house” programming within the database which has exploited the built-in functions to provide data and information on key issues of interest to the case study.  It is this flexibility provided by the combination of Timescale Creator functions and datapacks programmed from the back-end relational database which is showcased below.


Groups

Colours were used in the original 2011 trees [1, Appendices 2, 3 ], and now in the Timescale Creator trees, to display eco- and morpho-groups (respectively).  The Timescale Creator trees also add coloured group labels (rather than colouring the range labels as in the original trees), and this allows identification of groups without recourse to the legend.  These group labels are positioned on ancestor–descendant branches, but have here been programmed to display only when the group membership changes from ancestor to descendant.  As a result, they have the added advantage of highlighting origins and reappearances of the selected groups or properties in a phylogenetic context.  A handy use of this feature is when, for example, this is programmed to apply to the generic assignment of morphospecies, making polyphyletic morphogenera, intentioned or otherwise, easy to spot.


Lineage labels

To label range lines on the lineage tree, the Timescale Creator version has been programmed to augment each lineage code with its list of contained morphospecies, e.g., the listing appended to Lineage N1-N3 is “H. holmdelensis &gt; G. archeocompressa &gt; G. planocompressa &gt; G. compressa“.  The morphospecies series in these listings is ordered by lowest occurrence, and so the &gt;’s denote stratigraphic succession.  (The &gt;’s do not necessarily represent ancestor–descendant relationships; of course only a single line of descent could be expressed in such a format.)  This allows the lineage and its proposed morphological succession to be grasped much more easily, including a ready comparison with the morphospecies tree.


Pop-ups

Pop-ups provide the most ample opportunity within Timescale Creator to provide access to supporting information for trees.  Because pop-up windows are flexibly resizable and are coded in html, textual content has in effect few quota limitations and, in fact, can be employed to view external sources such as Internet sites and image files without the need to store them in the pop-up itself.  They can also be programmed to follow a format tailored for the subject matter, as is done here.

Pop-ups for the morphospecies tree display the contents of the 2011 paper’s summary table [1, Appendix S1, Table S3], including decoding of eco- and morpho-group numbers, range statistics from the Neptune portal, and tailoring the reference list to each morphospecies.  They also incorporate the ancestor [from 1, Appendix S5, worksheet aM], specify the type of cladogenetic event (all are, in fact, budding for this budding/bifurcating topology [2]), and level of support for the ancestor–descendant proposal (see § Branches).  Lineages containing the morphospecies are listed, along with their morphospecies content and age range (for details, see § Linkages between morphospecies and lineage trees [3]).  Also included are the binomen’s original assignation and, where available, links to portals, Chronos [4][5-7] and the World Register of Marine Species (WoRMS) [8].


Range lines

Range-line styles have been used for the Timescale Creator version of the 2011 trees to depict four levels of confidence for ranges.  Apart from accepted ranges (lines of usual thickness), two less-confident records of stratigraphic occurrence are depicted:  “questioned” (thin line) and “questioned-and-rare” (broken line).  For extensions to ranges that are not based on stratigraphic occurrences but are hypothesized (for various reasons), a “conjectured” range is separately recognised (dotted line) to ensure that stratigraphic and hypothesized categories are not conflated.  There is an option to attach age labels (in Ma) to range lines, providing the chart with an explicit deep-time positioning throughout.


Branches

Similarly to ranges, branch-line styles have been used to depict three levels of stratophenetic support for ancestry.  Almost all ancestor–descendant proposals for the 2011 study are presumed to be “Well Supported” (correspondence between detailed stratigraphic sequences and plausible phyletic series; drawn as a broken line).  A small number have been categorised as less or better supported than the usual:  “Not Well Supported” (only broad correspondence between stratigraphic order and suggestive phyletic series; drawn as a dotted line); or “Strongly Supported” (detailed morphometric–stratigraphic sequences from ancestor to descendant; continuous line).


Linkages between morphospecies and lineage trees

Many range points of the lineages of the 2011 study are herein directly linked to those of included morphospecies:  not quite half of start dates and almost all of end dates.  Brief details of this linkage are displayed in the “Stratigraphic Range (continued)” section of the pop-up, where the linkage will usually result in the same precalibrated Ma value between lineage and morphospecies range points, but these values will differ where there has been a correction or amendment of the original Ma value.  The reason for choosing the morphospecies range point is usually briefly indicated.  Where the original Ma value of the lineage range point is retained and not directly linked to a morphospecies point, the morphospecies and its time scale that are employed nonetheless for calibration are indicated.

Pop-ups are also employed to more easily appreciate the linkages between morphospecies and lineages, following from the morphospecies content of lineages.  These are displayed both in terms of the lineages in which a morphospecies occurs and in terms of the morphospecies included in a lineage, along with other information to help track these interrelationships.


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.	see § Data, topologies, and taxa of the 2011 study’s trees:  Tree topologies, above
3.	a morphospecies contained in more than one lineage is depicted in Figure 20a
4.	Support for on-going activity on the foraminiferal section of Chronos [116] no longer appears viable; other portals may need to be linked in later versions e.g., pforams@mikrotax [117, 118]
5.	Huber BT. Foraminiferal databases (Mesozoic Paleocene, Eocene Planktonic Foraminifera Taxonomic databases), Chronos Portal Washington (DC, USA): Consortium for Ocean Leadership for the Chronos Internal Coordinating Committee (Iowa State University and the National Science Foundation). Available from: http://portal.chronos.org/gridsphere/gridsphere?cid=foram_working_group (not updated in recent years).
6.	Young J, Huber BT, Bown P, Wade BS. pforams@mikrotax (UK Natural Environment Research Council), within mikrotax.org London: University College London. Available from: http://www.mikrotax.org/pforams/index.html.
7.	Huber BT, Petrizzo MR, Young JR, Falzoni F, Gilardoni SE, Bown PR, et al. Pforams@microtax:  a new online taxonomic database for planktonic foraminifera. Micropaleontology. 2017;62(6):429-38.
8.	Hayward BW, Le Coze F, Gross O. World Foraminifera Database, World Register of Marine Species (WoRMS) Vlaams Instituut voor de Zee (Flanders Marine Institute), Oostende (Belgium): WoRMS Editorial Board; 2018 [2018-01-09]. Available from: http://www.marinespecies.org/foraminifera, http://www.marinespecies.org doi:10.14284/170