Related papers: Quantifying the difference between phylogenetic di…
Measuring diversity accurately is important for many scientific fields, including machine learning (ML), ecology, and chemistry. The Vendi Score was introduced as a generic similarity-based diversity metric that extends the Hill number of…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
Diversities are a generalization of metric spaces, where instead of the non-negative function being defined on pairs of points, it is defined on arbitrary finite sets of points. Diversities have a well-developed theory. This includes the…
In recent years, the concepts of ``diversity'' and ``inclusion'' have attracted considerable attention across a range of fields, encompassing both social and biological disciplines. To fully understand these concepts, it is critical to not…
In comparison to phylogenetic trees, phylogenetic networks are more suitable to represent complex evolutionary histories of species whose past includes reticulation such as hybridisation or lateral gene transfer. However, the reconstruction…
Statistical consistency in phylogenetics has traditionally referred to the accuracy of estimating phylogenetic parameters for a fixed number of species as we increase the number of characters. However, as sequences are often of fixed length…
In evolutionary biology, phylogenetic trees are commonly inferred from a set of characters (partitions) of a collection of biological entities (e.g., species or individuals in a population). Such characters naturally arise from molecular…
Graphs are interesting structures: extremely useful to depict real-life problems, extremely easy to understand given a sketch, extremely complicated to represent formally, extremely complicated to compare. Phylogeny is the study of the…
In order to conduct a statistical analysis on a given set of phylogenetic gene trees, we often use a distance measure between two trees. In a statistical distance-based method to analyze discordance between gene trees, it is a key to decide…
Diversity is a concept relevant to numerous domains of research varying from ecology, to information theory, and to economics, to cite a few. It is a notion that is steadily gaining attention in the information retrieval, network analysis,…
There are many metrics available to compare phylogenetic trees since this is a fundamental task in computational biology. In this paper, we focus on one such metric, the $\ell^\infty$-cophenetic metric introduced by Cardona et al. This…
Gene innovation is a key mechanism on the evolution and phenotypic diversity of life forms. There is a need for tools able to study gene innovation across an increasingly large number of genomic sequences to maximally capitalise our…
The concept of $k$-compatibility measures how many phylogenetic trees it would take to display all splits in a given set. A set of trees that display every single possible split is termed a \textit{universal tree set}. In this note, we find…
Understanding functional diversity, the range and variability of species' roles and actions within their communities, is key to predicting and preserving the functions that sustain both nature and human well-being. In this paper, we provide…
Extensive research shows that more species-rich assemblages are generally more productive and efficient in resource use than comparable assemblages with fewer species. But the question of how diversity simultaneously affects the wide…
Phylogenetic networks are rooted acyclic directed graphs in which the leaves are identified with members of a set X of species. The cluster of a vertex is the set of leaves that are descendants of the vertex. A network is "distinct-cluster"…
Based on the normal distribution and its properties, i.e., average and variance, Fisher works have provided a conceptual framework to identify genotype-phenotype associations. While Fisher intuition has proved fruitful over the past…
We consider the problem of identifying jointly the ancestral sequence, the phylogeny and the parameters in models of DNA sequence evolution with insertion and deletion (indel). Under the classical TKF91 model of sequence evolution, we…
Rooted binary perfect phylogenies provide a generalization of rooted binary unlabeled trees in which each leaf is assigned a positive integer value that corresponds in a biological setting to the count of the number of indistinguishable…
For many taxa, the current high rates of extinction are likely to result in a significant loss of biodiversity. The evolutionary heritage of biodiversity is frequently quantified by a measure called phylogenetic diversity (PD). We predict…