Review Paper: The Shape of Phylogenetic Treespace

Abstract

Trees are a canonical structure for representing evolutionary histories. Many popular criteria used to infer optimal trees are computationally hard, and the number of possible tree shapes grows super-exponentially in the number of taxa. The underlying structure of the spaces of trees yields rich insights that can improve the search for optimal trees, both in accuracy and in running time, and the analysis and visualization of results. We review the past work on analyzing and comparing trees by their shape as well as recent work that incorporates trees with weighted branch lengths.

New opabiniid diversifies the weirdest wonders of the euarthropod lower stem group

“…Such calculations have been effective in summarizing the taxonomic uncertainty in fossil placement (Klopfstein and Spasojevic, 2019). Furthermore, our visualization of the sample of optimal trees (Hillis, Heath and St. John, 2005; St. John, 2017; Wright and Lloyd, 2020) illustrates the distribution of topological distances between conflicting and overlapping hypotheses. This technique allows the strength of support for competing hypotheses of relationships to be more comprehensively evaluated beyond an arbitrary cutoff value.…”

“…Treespace analysis. Supplemental to traditional clade support metrics, we used classical multidimensional scaling (MDS) to plot treespace (Gower, 1966;Hillis, Heath and St. John, 2005;St. John, 2017;Wright and Lloyd, 2020), with the goal of identifying the distribution of trees resolving key clades formed with KUMIP 314087 ( Table 1).…”

Recording development with single cell dynamic lineage tracing

“…Custom algorithms have been developed to achieve this based on maximum likelihood (Chan et al, 2018) or network graphs (Spanjaard et al, 2018). Others have adapted methods from the field of phylogenetics (see Box 2), which has a long history of addressing conceptually similar problems and has developed a number of techniques and approximations to tackle the complexity of tree construction (St. John, 2017).…”

A Generalized Robinson-Foulds Distance for Clonal Trees, Mutation Trees, and Phylogenetic Trees and Networks

“…The comparison of phylogenetic trees and networks, on the one hand, has been studied for several decades now; see [31] for a recent review. To the best of our knowledge, there is only one other generalization of the RF metric for the comparison of phylogenetic trees [4,8].…”