Phylogenetic Analyses of Ecological Communities Using DNA Barcode Data

Ecologists and conservation biologists are increasingly focusing on quantifying the phylogenetic component of biodiversity in order to inform basic and applied research. A major obstacle of this approach in tropical ecosystems has been the difficulty of generating high-quality phylogenetic trees for the vast numbers of species in these systems. Phylogenetic trees inferred from DNA barcodes hold the potential to overcome this obstacle. Here, I present a methodological framework for analyzing the phylogenetic alpha and beta diversity of ecological communities using a phylogenetic tree. The analytical approach is presented using the freely available and widely used software platform “R”.