Polyhedral Geometry of Phylogenetic Rogue Taxa

Cueto, María Angélica; Matsen, F. A.

doi:10.1007/s11538-010-9556-x

Cited by 17 publications

(17 citation statements)

References 33 publications

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“…That is, we will show that for every topology of the in-group, there is a set of arbitrarily distant outliers that can lead to this topology when using neighbour joining. These results are similar to those of Cueto and Matsen (2011) for the BME algorithm, though our proof for NJ is independent of theirs and more elementary.…”

Section: Neighbour Joining Is Out-group Volatilesupporting

confidence: 84%

“…A related line of work is concerned with properties of consensus functions, which provide a way to summarise the agreement between two or more trees, by Bryant (1997) and Eulenstein (2006), among others. Lastly, our results on the volatility of neighbour joining bear resemblance to the work of Cueto and Matsen (2011) on the BME algorithm. However, our results were obtained independently and we provide simpler proofs.…”

Section: Previous Worksupporting

confidence: 65%

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Effects of rooting via out-groups on in-group topology in phylogeny

Ackerman

Brown²,

Loker³

2014

IJBRA

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Users of phylogenetic methods require rooted trees, because the direction of time depends on the placement of the root. While phylogenetic trees are typically rooted by using an out-group, this mechanism is inappropriate when the addition of an out-group changes the in-group topology. We perform a formal analysis of phylogenetic algorithms under the inclusion of distant out-groups. It turns out that linkage-based algorithms (including UPGMA) and a class of bisecting methods do not modify the topology of the in-group when an out-group is included. By contrast, the popular neighbour joining algorithm fails this property in a strong sense: every data set can have its structure destroyed by some arbitrarily distant outlier. Furthermore, including multiple outliers can lead to an arbitrary topology on the in-group. The standard rooting approach that uses out-groups may be fundamentally unsuited for neighbour joining.

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Section: Neighbour Joining Is Out-group Volatilesupporting

confidence: 84%

Section: Previous Worksupporting

confidence: 65%

Effects of rooting via out-groups on in-group topology in phylogeny

Ackerman

Brown²,

Loker³

2014

IJBRA

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“…Their study indicated that 29% of four taxa phylogenies would be reconstructed differently had a fifth taxa been added. These percentages increased to 50% for five taxa trees and 62% for six taxa trees (Cueto and Matson, 2011). However, Cueto and Matson point out that their estimated rogue frequencies may have been greater given the use of random branch lengths (2011).…”

Section: Introductionmentioning

confidence: 98%

“…They found that the rogue taxa effect was common when the added taxa were chosen without reference to the original tree (arbitrarily) and that the effect worsened as the number of taxa increased (Cueto and Matson, 2011). Their study indicated that 29% of four taxa phylogenies would be reconstructed differently had a fifth taxa been added.…”

Section: Introductionmentioning

confidence: 99%

“…In similar work to Cueto and Matson (2011), Eikmeyer et al estimated how frequently the rapid neighbor joining (NJ) algorithm obtained the same solution as the more time consuming Balanced Minimum Evolution (BME) method whose solution NJ is designed to approximate (2008). Their study found that for five taxa trees NJ and BME reconstructed the same tree for 98% of four taxa data samples (Eikenmeyer et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

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Rogue taxa phenomenon: A biological companion to simulation analysis

Westover

Rusinko

Hoin

et al. 2013

Molecular Phylogenetics and Evolution

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To provide a baseline biological comparison to simulation study predictions about the frequency of rogue taxa effects, we evaluated the frequency of a rogue taxa effect using viral data sets which differed in diversity. Using a quartet-tree framework, we measured the frequency of a rogue taxa effect in three data sets of increasing genetic variability (within viral serotype, between viral serotype, and between viral family) to test whether the rogue taxa was correlated with the mean sequence diversity of the respective data sets. We found a slight increase in the percentage of rogues as nucleotide diversity increased. Even though the number of rogues increased with diversity, the distribution of the types of rogues (friendly, crazy, or evil) did not depend on the diversity and in the case of the order-level data set the net rogue effect was slightly positive. This study, assessing frequency of the rogue taxa effect using biological data, indicated that simulation studies may over-predict the prevalence of the rogue taxa effect. Further investigations are necessary to understand which types of data sets are susceptible to a negative rogue effect and thus merit the removal of taxa from large phylogenetic reconstructions.

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Discrete coalescent trees

et al. 2021

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In many phylogenetic applications, such as cancer and virus evolution, time trees, evolutionary histories where speciation events are timed, are inferred. Of particular interest are clock-like trees, where all leaves are sampled at the same time and have equal distance to the root. One popular approach to model clock-like trees is coalescent theory, which is used in various tree inference software packages. Methodologically, phylogenetic inference methods require a tree space over which the inference is performed, and the geometry of this space plays an important role in statistical and computational aspects of tree inference algorithms. It has recently been shown that coalescent tree spaces possess a unique geometry, different from that of classical phylogenetic tree spaces. Here we introduce and study a space of discrete coalescent trees. They assume that time is discrete, which is natural in many computational applications. This tree space is a generalisation of the previously studied ranked nearest neighbour interchange space, and is built upon tree-rearrangement operations. We generalise existing results about ranked trees, including an algorithm for computing distances in polynomial time, and in particular provide new results for both the space of discrete coalescent trees and the space of ranked trees. We establish several geometrical properties of these spaces and show how these properties impact various algorithms used in phylogenetic analyses. Our tree space is a discretisation of a previously introduced time tree space, called t-space, and hence our results can be used to approximate solutions to various open problems in t-space.

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Polyhedral Geometry of Phylogenetic Rogue Taxa

Cited by 17 publications

References 33 publications

Effects of rooting via out-groups on in-group topology in phylogeny

Effects of rooting via out-groups on in-group topology in phylogeny

Rogue taxa phenomenon: A biological companion to simulation analysis

Discrete coalescent trees

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