Related papers: Diversity, disparity, and evolutionary rate estima…
One approach to estimating a species tree from a collection of gene trees is to first estimate probabilities of clades from the gene trees, and then to construct the species tree from the estimated clade probabilities. While a greedy…
There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression trees.…
Phylogenetic mixture models are statistical models of character evolution allowing for heterogeneity. Each of the classes in some unknown partition of the characters may evolve by different processes, or even along different trees. The…
Recently there has been renewed interest in phylogenetic inference methods based on phylogenetic invariants, alongside the related Markov invariants. Broadly speaking, both these approaches give rise to polynomial functions of sequence site…
We introduce a model for the evolution of species triggered by generation of novel features and exhaustive combination with other available traits. Under the assumption that innovations are rare, we obtain a bursty branching process of…
Gene trees are evolutionary trees representing the ancestry of genes sampled from multiple populations. Species trees represent populations of individuals -- each with many genes -- splitting into new populations or species. The coalescent…
The reconstruction of large phylogenetic trees from data that violates clocklike evolution (or as a supertree constructed from any m input trees) raises a difficult question for biologists - how can one assign relative dates to the vertices…
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…
In this paper we present a new way to understand the timing of branching events in phylogenetic trees. Our method explicitly considers the relative timing of diversification events between sister clades; as such it is complimentary to…
The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in…
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…
Phylogenetic networks are necessary to represent the tree of life expanded by edges to represent events such as horizontal gene transfers, hybridizations or gene flow. Not all species follow the paradigm of vertical inheritance of their…
Planning for the protection of species often involves difficult choices about which species to prioritize, given constrained resources. One way of prioritizing species is to consider their "evolutionary distinctiveness", i.e. their relative…
Inferring the ancestral state at the root of a phylogenetic tree from states observed at the leaves is a problem arising in evolutionary biology. The simplest technique -- majority rule -- estimates the root state by the most frequently…
Yule's 1925 paper introducing the branching model that bears his name was a landmark contribution to the biodiversity sciences. In his paper, Yule developed stochastic models to explain the observed distribution of species across genera and…
Phylogenetic networks are a generalisation of phylogenetic trees that allow for more complex evolutionary histories that include hybridisation-like processes. It is of considerable interest whether a network can be considered `tree-like' or…
Tree shape statistics provide valuable quantitative insights into evolutionary mechanisms underpinning phylogenetic trees, a commonly used graph representation of evolution systems ranging from viruses to species. By developing limit…
The reconstruction of phylogenetic trees based on viral genetic sequence data sequentially sampled from an epidemic provides estimates of the past transmission dynamics, by fitting epidemiological models to these trees. To our knowledge,…
In biology, a phylogenetic tree is a tool to represent the evolutionary relationship between species. Unfortunately, the classical Schr\"oder tree model is not adapted to take into account the chronology between the branching nodes. In…
Scientific studies in many areas of biology routinely employ evolutionary analyses based on the probabilistic inference of phylogenetic trees from molecular sequence data. Evolutionary processes that act at the molecular level are highly…