*2.3. Phylogenetic Reconstruction*

To enforce taxonomic relationships based on the global dataset from the Angiosperm Phylogeny Group III [70], a constraint tree using the R20120829 tree was built in Phylomatic version 3 [71]. In Mesquite [72], the tree was edited so each family was a polytomy and that the barcode data could then be used to infer the relationships of the species below the level of family, consistent with the methods of Shapcott [17].

The 3-marker alignment for the 1576 heath and rainforest species and constraint tree were uploaded to the CIPRES portal [73], and the RAxML-HPC2onXSEDE tool was used with a mixed partition model to search for the best scoring ML tree. This was repeated for eight runs and the best tree with the smallest likelihood score was selected. This tree was rooted in Geneious and dated in PATHd8 [74], with the ages of nine orders found using fossil dates and an age for angiosperms of 250 mya after the methods of Shapcott [16,17] to produce a final dated tree with calibrated molecular branch lengths for the 1576 heath and rainforest species. This tree was pruned in PICANTE in R to produce a dated tree for the 366 regional heath species of the Sunshine Coast [75].
