Combinatorial perspectives on Dollo-k characters in phylogenetics

Bouckaert, Remco; Fischer, Mareike; Wicke, Kristina

doi:10.1016/j.aam.2021.102252

Cited by 1 publication

(2 citation statements)

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“…Just as the Fitch parsimony score was used to define the Fitch-labeling and the large Fitch parsimony problem, we can define similar concepts for the Dollo and Camin-Sokal parsimony scores. The following result about Dollo-labelings is the basis of a linear-time algorithm presented by Bouckaert et al [ 28 ] for computing Dollo ( T , c ).…”

Section: Introductionmentioning

confidence: 99%

“…(Theorem 1 in [ 28 ]) Let T be a rooted, binary tree and let c be an ordered, binary character with no missing values, both on the same species set. A Dollo-labeling for ( T , c ) must assign state 1 to every internal vertex on a path from the LCA of all leaves assigned state 1 (including the LCA) to any leaf assigned state 1 and assign state 0 to all remaining vertices.…”

Section: Introductionmentioning

confidence: 99%

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Dollo-CDP: a polynomial-time algorithm for the clade-constrained large Dollo parsimony problem

Dai,

Rubel,

Han

et al. 2024

Algorithms Mol Biol

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The last decade of phylogenetics has seen the development of many methods that leverage constraints plus dynamic programming. The goal of this algorithmic technique is to produce a phylogeny that is optimal with respect to some objective function and that lies within a constrained version of tree space. The popular species tree estimation method ASTRAL, for example, returns a tree that (1) maximizes the quartet score computed with respect to the input gene trees and that (2) draws its branches (bipartitions) from the input constraint set. This technique has yet to be used for parsimony problems where the input are binary characters, sometimes with missing values. Here, we introduce the clade-constrained character parsimony problem and present an algorithm that solves this problem for the Dollo criterion score in $$O(|\Sigma |^{3.726}(n+k) + |\Sigma |^{1.726}nk)$$ O ( | Σ | 3.726 ( n + k ) + | Σ | 1.726 n k ) time, where n is the number of leaves, k is the number of characters, and $$\Sigma$$ Σ is the set of clades used as constraints. Dollo parsimony, which requires traits/mutations to be gained at most once but allows them to be lost any number of times, is widely used for tumor phylogenetics as well as species phylogenetics, for example analyses of low-homoplasy retroelement insertions across the vertebrate tree of life. This motivated us to implement our algorithm in a software package, called Dollo-CDP, and evaluate its utility for analyzing retroelement insertion presence / absence patterns for bats, birds, toothed whales as well as simulated data. Our results show that Dollo-CDP can improve upon heuristic search from a single starting tree, often recovering a better scoring tree. Moreover, Dollo-CDP scales to data sets with much larger numbers of taxa than branch-and-bound while still having an optimality guarantee, albeit a more restricted one. Lastly, we show that our algorithm for Dollo parsimony can easily be adapted to Camin-Sokal parsimony but not Fitch parsimony.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%