Supertree construction in the genomic age

Supertree construction is the process whereby overlapping phylogenetic trees, and not character data, are combined to yield a larger, more comprehensive phylogeny. In this chapter, I review the logic and methodology behind supertree construction and argue that it holds a necessary place in phylogenetic inference. Much of the justification for supertrees is admittedly practical. As I show with an empirical example, most large groups have insufficient sequence data to build complete phylogenies for them. By being able to indirectly combine diverse forms of phylogenetic information, supertrees are the best method for constructing complete phylogenies of groups with hundreds of species. However, supertree construction can also be justified on theoretical grounds. As whole genomic data are obtained for increasing numbers of species, the theoretical and practical advantages of supertrees together will ensure that the method will play a necessary analytical role as part of a divide-and-conquer strategy to reconstructing the Tree of Life.