Figure 5
Cluster and correlation analysis of phylogenetic inference strategies. Each leaf of the dendrogram corresponds to a different phylogenetic inference strategy for obtaining the rooted phylogeny of eight ingroup pine species. Blue squares directly below the dendrogram indicate the features used to construct a rooted phylogeny for the eight pine species. The first six rows below the dendrogram represent different species tree construction methods. The next four rows below the dendrogram represent gene tree inference methods. The following three rows below the dendrogram represent the outgroup species. The dendrogram was constructed by hierarchical clustering using the Ward algorithm [77] applied to a matrix of Euclidean distances between all pairs of 145-dimensional vectors (each dimension representing a distinct clade). The remaining nine rows below the outgroups show the results of K-means clustering applied to the 72 145-dimensional vectors with K clusters, K=2,3,…,9. Below the cluster analysis is a heat map of the correlation coefficients between all pairs of phylogenetic inference strategies. An entry in the heat map represents the Pearson correlation coefficient between a pair of strategies by only using points in the 145-dimensional vector that were nonzero in both strategies being compared.