ABSTRACT
Sequencing approaches for biodiversity studies include shallow targeted sequencing, expressed sequence tag approaches, and whole genome approaches. Whole genome approaches have been used for yeast, flies, and bacteria. Bacterial phylogenomics poses specific problems: whether a tree of life really exists for bacteria, and whether all genes can be used in a concatenated analysis. When the number of taxa becomes unmanageable, various supertree approaches are used. Grafting breaks down a problem into a series of smaller problems. Matrix representation allows trees in different studies to be linked together in a supertree matrix that summarizes each subtree as a series of nodes. The divide-and-conquer approach is similar to grafting, but no a priori assumptions about relationships are made. Metagenomics uses high-throughput DNA sequencing approaches to identify the majority of microbe species in a sample without culturing individual species.
