Evolutionary Placement Analysis (EPA, Berger et al. 2011) would be a more appropriate method here than using consensus sequences derived from environmental samples to generate a phylogeny. This method was developed for exactly this type of analysis. Consensus sequences from environmental samples may be chimeras of different sequences, however no attempt appears to be made to identify chimera sequences. Additionally, inclusion of shorter environmental sequences in generating the phylogeny will lead to reduced support. A better approach is to create a reference tree, then place the environmental sequences on the tree using Evolutionary Placement Analysis.