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A matroid associated with a phylogenetic tree [PDF]
Discrete Mathematics & Theoretical Computer Science, 2014 Special issue PRIMA 2013 A (pseudo-)metric D on a finite set X is said to be a \textquotelefttree metric\textquoteright if there is a finite tree with leaf set X and non-negative edge weights so that, for all x,y ∈X, D(x,y) is the path distance in the tree between x and y. It is well known that not every metric is a tree metric. However, when
Dress, Andreas +2 more
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Invertibility of the TKF model of sequence evolution [PDF]
, 2006 We consider character sequences evolving on a phylogenetic tree under the TKF91 model. We show that as the sequence lengths tend to infinity the the topology of the phylogenetic tree and the edge lengths are determined by any one of (a) the alignment of ...
Thatte, Bhalchandra D.
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A metric on phylogenetic tree shapes [PDF]
Systematic Biology, 2016 AbstractThe shapes of evolutionary trees are influenced by the nature of the evolutionary process, but comparisons of trees from different processes are hindered by the challenge of completely describing tree shape. We present a full characterization of the shapes of rooted branching trees in a form that lends itself to natural tree comparisons.
Colijn, C, Plazzotta, G
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A new resolution function to evaluate tree shape statistics.
PLoS ONE, 2019 Phylogenetic trees are frequently used in biology to study the relationships between a number of species or organisms. The shape of a phylogenetic tree contains useful information about patterns of speciation and extinction, so powerful tools are needed ...
Maryam Hayati +2 more
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Understanding the tree of life: an overview of tree-reading skill frameworks
Evolution: Education and Outreach, 2019 Diagrammatic depictions of evolutionary relationships play an increasingly important role in scientific and educational literature. Reading evolutionary trees is seen as a major challenge for biologists in learning about evolution and its applications in
Thilo Schramm +2 more
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Conflicting phylogenetic signals in plastomes of the tribe Laureae (Lauraceae) [PDF]
PeerJ, 2020 Background Gene tree discordance is common in phylogenetic analyses. Many phylogenetic studies have excluded non-coding regions of the plastome without evaluating their impact on tree topology. In general, plastid loci have often been treated as a single
Tian-Wen Xiao +5 more
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Mean and Variance of Phylogenetic Trees [PDF]
Systematic Biology, 2019 Abstract We describe the use of the Fréchet mean and variance in the Billera–Holmes–Vogtmann (BHV) treespace to summarize and explore the diversity of a set of phylogenetic trees. We show that the Fréchet mean is comparable to other summary methods, and, despite its stickiness property, is more likely to be binary than the majority-rule ...
Daniel G. Brown, Megan Owen
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The Fair Proportion is a Shapley Value on phylogenetic networks too
, 2018 The Fair Proportion of a species in a phylogenetic tree is a very simple measure that has been used to assess its value relative to the overall phylogenetic diversity represented by the tree.
Coronado, Tomás M. +2 more
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eLifeEnvironmental factors can influence ecological networks, but these effects are poorly understood in the realm of the phylogeny of host-parasitoid interactions.
Ming-Qiang Wang +22 more
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Confidence Sets for Phylogenetic Trees [PDF]
Journal of the American Statistical Association, 2018 Inferring evolutionary histories (phylogenetic trees) has important applications in biology, criminology and public health. However, phylogenetic trees are complex mathematical objects that reside in a non-Euclidean space, which complicates their analysis.
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