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README
pbj-phylogeny.svg
pbj-phylogeny.tre
pbj.vcd

README

This illustration was used as figure 2 in our open-access paper:
http://www.plosone.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0078213&representation=PDF

	Wedel, Mathew J., and Michael P. Taylor. 2013. Caudal
	pneumaticity and pneumatic hiatuses in the sauropod dinosaurs
	Giraffatitan and Apatosaurus.PLOS ONE 8(10):e78213. 14
	pages. doi:10.1371/journal.pone.0078213

The figure caption is:

	Figure 2. The phylogenetic distribution of caudal pneumaticity
	in sauropods and other dinosaurs is complex. Boxes represent
	proximal, middle, and distal caudal vertebrae, arbitrarily
	defined for sauropods as caudals 1-10, 11-20, and 21 on,
	respectively; blue boxes indicate that pneumaticity is present
	in that part of the tail. Pneumaticity data for theropods come
	from Benson et al [15] -- note that although Theropoda is
	collapsed to a single node in this figure, caudal pneumaticity
	is not primitive for the clade, but evolved independently
	several times in both non-avian theropods and birds
	[6,15,29]. Data from sauropods come from the sources listed in
	Table 1. The figure also shows the phylogenetic framework we
	use in this paper. The phylogenetic framework is drawn from
	Whitlock [44] for diplodocoids, Mannion et al [30] for basal
	macronarians and Xianshanosaurus, Calvo et al [96] for most
	titanosaurs, and Campos et al [93] for Trigonosaurus. Basal
	sauropodomorphs are a grade, not a clade, but they are listed
	together here for convenience since they all lack caudal
	pneumaticity.

The published illustration
http://svpow.files.wordpress.com/2013/11/wedel-taylor-2013b-figure-2-phylogenetic-distribution-of-caudal-pneumaticity.jpg
is a combination (edited together by hand) of two computer-generated
SVG files:

1. A phylogenetic tree built using Treeview. For reference, we include
that tree here both as the hand-edited Nexus file that was the source
code (pbj-phylogeny.tre) and as the SVG file generated by Treeview
(pbj-phylogeny.svg).

2. The pneumaticity diagram built using VertFigure.

Working from the generated vertebral-column picture, we moved the
captions to the right of the vertebrae by hand. This editing was done
using Inkscape, as was the merge with the phylogenetic tree.

In this VCD file, we used two very simple glyphs: a solid light-blue
rectangle that fills the box for pneumatic vertebrae; and a pale grey
dash for apneumatic vertebrae.