fix the format of PhyloXML references

The PhyloXML specification indicates that references should
match the following regular expression pattern:

[a-zA-Z0-9_]+:[a-zA-Z0-9_\.\-\s]+

In order to do so, we now prepend "VTK:" to the beginning of the
array name.

Change-Id: Ie898e19dc10ec6edd2b67a5b493f55521e15c63d