Related papers: On properties driving diversity index selection
Phylogenetically decisive collections of taxon sets have the property that if trees are chosen for each of their elements, as long as these trees are compatible, the resulting supertree is unique. This means that as long as the trees…
Phylogenetic inference, grounded in molecular evolution models, is essential for understanding the evolutionary relationships in biological data. Accounting for the uncertainty of phylogenetic tree variables, which include tree topologies…
Whether or not biodiversity dynamics tend toward stable equilibria remains an unsolved question in ecology and evolution with important implications for our understanding of diversity and its conservation. Phylo/population genetic models…
Understanding the patterns and processes of diversification of life in the planet is a key challenge of science. The Tree of Life represents such diversification processes through the evolutionary relationships among the different taxa, and…
A phylogenetic tree is a way to organize a finite set of species, individuals or other sources of related data. The species for which we have existing DNA data make up the set of leaves of the tree. The balanced minimal evolution method of…
Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…
The selection of the most suitable evolutionary model to analyze the given molecular data is usually left to biologist's choice. In his famous book, J Felsenstein suggested that certain linear equations satisfied by the expected…
Diversity plays a crucial role in evolutionary computation. While diversity has been mainly used to prevent the population of an evolutionary algorithm from premature convergence, the use of evolutionary algorithms to obtain a diverse set…
A number of methods have been developed to infer differential rates of species diversification through time and among clades using time-calibrated phylogenetic trees. However, we lack a general framework that can delineate and quantify…
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. It has recently been proved by Fuchs and Jin to…
Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains…
Phylogenetic trees elucidate evolutionary relationships among species, but phylogenetic inference remains challenging due to the complexity of combining continuous (branch lengths) and discrete parameters (tree topology). Traditional Markov…
Phylogenetic comparative analysis is an approach to inferring evolutionary process from a combination of phylogenetic and phenotypic data. The last few years have seen increasingly sophisticated models employed in the evaluation of more and…
The aim of this review is to present and analyze the probabilistic models of mathematical phylogenetics which have been intensively used in recent years in biology as the cornerstone of attempts to infer and reconstruct the ancestral…
The current rate of species extinction is rapidly approaching unprecedented highs and life on Earth presently faces a sixth mass extinction event driven by anthropogenic activity, climate change and ecological collapse. The field of…
We derive an invertible transform linking two widely used measures of species diversity: phylogenetic diversity and the expected proportions of segregating (non-constant) sites. We assume a bi-allelic, symmetric, finite site model of…
The phylogenetic Mean Pairwise Distance (MPD) is one of the most popular measures for computing the phylogenetic distance between a given group of species. More specifically, for a phylogenetic tree T and for a set of species R represented…
Measures of phylogenetic balance, such as the Colless and Sackin indices, play an important role in phylogenetics. Unfortunately, these indices are specifically designed for phylogenetic trees, and do not extend naturally to phylogenetic…
In phylogenetic networks, it is desirable to estimate edge lengths in substitutions per site or calendar time. Yet, there is a lack of scalable methods that provide such estimates. Here we consider the problem of obtaining edge length…
Datasets encountered when examining deeper issues in ecology and evolution are often complex. This calls for careful strategies for both model building, model selection, and model averaging. Our paper aims at motivating, exhibiting, and…