by Olaf R. P. Bininda-Emonds
The dominant approach to the analysis of phylogenomic data is the concatenation of the individual gene data sets into a giant supermatrix that is analyzed en masse. Nevertheless, there remain compelling arguments for a partitioned approach in which individual partitions (usually genes) are instead analyzed separately and the resulting trees are combined to yield the final phylogeny. For instance, it has been argued that this supertree framework, which remains controversial, can better account for natural evolutionary processes like horizontal gene transfer and incomplete lineage sorting that can cause the gene trees, although accurate for the evolutionary history of the genes, to differ from the species tree. In this chapter, I review the different methods of supertree construction (broadly defined), including newer model-based methods based on a multispecies coalescent model. In so doing, I elaborate on some of their strengths and weaknesses relative to one another as well as provide a rough guide to performing a supertree analysis before addressing criticisms of the supertree approach in general. In the end, however, rather than dogmatically advocating supertree construction and partitioned analyses in general, I instead argue that a combined, “global congruence” approach in which data sets are analyzed under both a supermatrix (unpartitioned) and supertree (partitioned) framework represents the best strategy in our attempts to uncover the Tree of Life.