Given that a PLoS article is an XML document, it would be great if the tree diagram was itself XML, in particular SVG. But, in one sense, we don't want just a diagram, we want access to the underlying tree (for example, so we can play with it in other software). The tree may or may not be available in TreeBASE, but what if the diagram itself was the tree? In other words, imagine a tree viewing program could output SVG, structured in such a way that with a XSLT stylesheet the underlying tree could be extracted (say in Newick or, gack, NexXML) from the SVG, but users could take the SVG and embellish it (in Adobe Illustrator or Inkscape). The nice illustration and the tree data structure would be one and the same thing! No getting tree and illustration out of sync, and no hoping authors have put tree in a database somewhere -- the article contains the tree.
In order for this to happen, we need a tree viewer that exports SVG, and ideally would allow annotation so that the author could do most of the work within that program (ensuring that the underlying tree object isn't broken by graphic editing). Then export the SVG, add extract bits in Illustrator/Inkscape if needed, and have it incorporated into the article XML (which is what the publisher uses to render the article on the web). Simples.