Tree comparison functions are widely used in phylogenetics for comparing evolutionary trees. Unrooted trees can be compared with rooted trees by identifying all rootings of the unrooted tree that minimize some provided comparison function between two rooted trees. The plateau property is satisfied by the provided function, if all optimal rootings form a subtree, or plateau, in the unrooted tree, from which the rootings along every path toward a leaf have monotonically increasing costs. This property is sufficient for the linear-time identification of all optimal rootings and rooting costs. However, the plateau property has only been proven for a few rooted comparison functions, requiring individual proofs for each function without benefitting from inherent structural features of such functions. Here, we introduce the consistency condition that is sufficient for a general function to satisfy the plateau property. For consistent functions, we introduce general linear-time solutions that identify optimal rootings and all rooting costs. Further, we identify novel relationships between consistent functions in terms of plateaus, especially the plateau of the well-studied duplication-loss function is part of a plateau of every other consistent function. We introduce a novel approach for identifying consistent cost functions by defining a formal language of Boolean costs. Formulas in this language can be interpreted as cost functions. Finally, we demonstrate the performance of our general linear-time solutions in practice using empirical and simulation studies.
Computational Biology and Bioinformatics, IEEE/ACM Transactions
Boolean functions,biology computing,evolution (biological),formal languages,genetics,genomics,trees (mathematics),Boolean cost,evolutionary tree,formal language,linear-time identification,linear-time solution,phylogenetics,plateau property,unrooted tree reconciliation,Bioinformatics,Boolean cost,Cost function,IEEE transactions,Phylogeny,Radio frequency,Reconciliation,Robinson-Foulds distance,Search problems,Vegetation,deep coalescence,evolutionary cost,formal language,gene duplication,gene loss,speciation,species tree,unrooted gene tree
Plateau,Boolean function,Monotonic function,Formal language,Phylogenetic tree,Computer science,Tree (data structure),Mathematical proof,Bioinformatics