The Foundations of Concordance Views of Phylogeny

Despite the enormous importance and widespread use of the term, it is unclear exactly what a phylogeny of organisms represents. Precision in terminology is especially important given widespread genetic discordance between different gene trees and between gene trees, organismal pedigrees, and population histories. Here, we will focus on methods in which a tree is determined by input gene trees. We compare various possibilities of how to do this including consensus trees, the R* triplet method, and concordance methods. We then focus on the use of concordance factors as one way to make precise the notion of a phylogenetic tree as representing the ‘dominant history’. We make precise the notion of a concordance factor and then compare various concordance ideas in the literature and then compare such trees to so-called ‘species trees’ which attempt to track population histories through time. A number of papers have previously shown some connections between concordance trees and species tree