 We began by noting that a phylogeny reconstructs evolutionary history and that different types of entities have an evolutionary history—for example, genes, organisms, populations, and species all have genealogical histories. Assume that we are trying to reconstruct the history of species or higher taxa (indeed, “phylogeny” itself is sometimes defined this way, e.g., Wiley 1981; S. Edwards 2009). Standard methods such as parsimony, likelihood, and bayesian methods all directly infer the history of characters. So what is the connection between the history of these characters and the phylogeny of the species? The unstated assumption is that the histories of these characters are the same and line up with the species history. We conclude this entry by acknowledging that this unstated assumption is often violated and we consider what effect this has on the theory and practice of phylogenetic inference. As we will see, examining this unstated assumption forces us to directly face the question of what a phylogeny actually represents and thus what “phylogenetic inference” even means.