Directed next generation sequencing for phylogenetics: An example using Decapoda (Crustacea)

We propose a method using next generation sequencing technology for phylogenetics. The method is PCR based, requires little training beyond basic lab skills and is both cost and time effective. With this method we generated data for and produced a phylogeny of Decapoda that demonstrates this method's potential, the quality of the data, and the ability for the method to fit or even replace current Sanger based methods of generating DNA data for phylogenetic reconstruction. Finally, we discuss advantages and current challenges of the directed next generation sequencing approach.