Plant DNA barcodes: Species identification and community phylogenies

Background/Question/Methods A DNA barcode is a universally accepted short DNA sequence normally employed for the identification of species.  Several gene regions are now being routinely used in plants to provide a rapid and repeatable method for species identification and DNA barcode libraries are being assembled to address specific questions in ecology and evolutionary biology.  In plant communities species number, functional traits, and phylogenetic history all contribute to characterizing biological diversity.  Until now the phylogenetic component of community diversity has been particularly difficult to quantify in species-rich tree assemblages.  Here we ask the question: Can sequence data from plant DNA barcodes be used to construct highly resolved community phylogenies for tree species in forest dynamics plots? And can these phylogenies provide the evolutionary component for understanding community assembly? We use the plant DNA barcodes rbcL, matK, and trnH-psbA in a supermatrix approach along with phylogenetic constraint trees to generate community phylogenies in both temperate and tropical environments.

Results/Conclusions Our results employing these methods of phylogenetic reconstruction provide a high degree of congruence between the barcode phylogeny and broadly accepted hypotheses on the phylogeny of flowering plants (i.e., APG III) regardless of the number and taxonomic breadth of the taxa sampled.  The conserved barcode gene region rbcL along with the constraint trees provide the phylogenetic backbone at the family and ordinal level for the community analyses while the faster-evolving barcode gene regions matK and trnH-psbA permit the high resolution of the terminal twigs of the tree, i.e., the species.   These results for forest dynamics plots in Panama, Puerto Rico, Maryland and Virginia illustrate that highly resolved phylogenies derived from DNA barcode sequence data combined with constraint trees are particularly useful in comparative analyses of phylogenetic diversity and enhance research on the interface between community ecology and evolution.