Related papers: Sound Colless-like balance indices for multifurcat…
The study of species organization and their clustering by genetic or phenotypic similarity is carried out with the tools of phylogenetic trees. An important structural property of phylogenetic trees is the balance, which measures how taxa…
In recent years, there has been an effort to extend the classical notion of phylogenetic balance, originally defined in the context of trees, to networks. One of the most natural ways to do this is with the so-called $B_2$ index. In this…
Effects like selection in evolution as well as fertility inheritance in the development of populations can lead to a higher degree of asymmetry in evolutionary trees than expected under a null hypothesis. To identify and quantify such…
Phylogenetic diversity indices are commonly used to rank the elements in a collection of species or populations for conservation purposes. The derivation of these indices is typically based on some quantitative description of the…
Phylogenetic diversity indices such as the Fair Proportion (FP) index are frequently discussed as prioritization criteria in biodiversity conservation. They rank species according to their contribution to overall diversity by taking into…
One of the main applications of balance indices is in tests of null models of evolutionary processes. The knowledge of an exact formula for a statistic of a balance index, holding for any number n of leaves, is necessary in order to use…
Tree balance plays an important role in different research areas like theoretical computer science and mathematical phylogenetics. For example, it has long been known that under the Yule model, a pure birth process, imbalanced trees are…
Tree balance has received considerable attention in recent years, both in phylogenetics and in other areas. Numerous (im)balance indices have been proposed to quantify the (im)balance of rooted trees. A recent comprehensive survey…
Ecological studies have now gone beyond measures of species turnover towards measures of phylogenetic and functional dissimilarity with a main objective: disentangling the processes that drive species distributions from local to broad…
The reconstruction of a species phylogeny from genomic data faces two significant hurdles: 1) the trees describing the evolution of each individual gene--i.e., the gene trees--may differ from the species phylogeny and 2) the molecular…
Measures of tree balance play an important role in different research areas such as mathematical phylogenetics or theoretical computer science. The balance of a tree is usually quantified in a single number, called a balance or imbalance…
Although the analysis of rooted tree shape has wide-ranging applications, notions of tree balance have developed independently in different domains. In computer science, a balanced tree is one that enables efficient updating and retrieval…
Phylogenetic trees capture evolutionary relationships among species and reflect the forces that shaped them. While many studies rely on branch length information, the topology of phylogenetic trees (particularly their degree of imbalance)…
As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…
We investigate the use of additional 3D and phylogenetic non-3D tree balance indices for analyzing and monitoring forests using an exemplary "virtual forest" dataset from the Wytham Woods, Oxford, UK. This study assesses 3D model quality,…
Null models of binary phylogenetic trees are useful for testing hypotheses on real world phylogenies. In this paper we consider phylogenies as binary trees without edge lengths together with a sampling measure and encode them as algebraic…
In this paper we introduce and study three new measures for efficient discriminative comparison of phylogenetic trees. The NNI navigation dissimilarity $d_{nav}$ counts the steps along a "combing" of the Nearest Neighbor Interchange (NNI)…
The Shapley Value and the Fair Proportion Index of phylogenetic trees have been frequently discussed as prioritization tools in conservation biology. Both indices rank species according to their contribution to total phylogenetic diversity,…
Phylogenetic diversity is a popular measure for quantifying the biodiversity of a collection $Y$ of species, while phylogenetic diversity indices provide a way to apportion phylogenetic diversity to individual species. Typically, for some…
In phylogenomics, species-tree methods must contend with two major sources of noise; stochastic gene-tree variation under the multispecies coalescent model (MSC) and finite-sequence substitutional noise. Fast agglomerative methods such as…