Related papers: Stochastic Models for Phylogenetic Trees on Higher…
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…
It is known that the Kimura 3ST model of sequence evolution on phylogenetic trees can be extended quite naturally to arbitrary split systems. However, this extension relies heavily on mathematical peculiarities of the K3ST model, and…
Earth's forests play an important role in the fight against climate change, and are in turn negatively affected by it. Effective monitoring of different tree species is essential to understanding and improving the health and biodiversity of…
We present convincing empirical evidence for an effective and general strategy for building accurate small models. Such models are attractive for interpretability and also find use in resource-constrained environments. The strategy is to…
Computer simulations are an important tool for studying the mechanics of biological evolution. In particular, in silico work with agent-based models provides an opportunity to collect high-quality records of ancestry relationships among…
The paper reviews the results obtained for spatial population models and the evolution of the genealogies of these populations during the last decade by the author and his coworkers. The focus is on their large scale behaviour and on the…
Construction of phylogenetic trees has traditionally focused on binary trees where all species appear on leaves, a problem for which numerous efficient solutions have been developed. Certain application domains though, such as viral…
The Persistent-Phylogeny Model is an extension of the widely studied Perfect-Phylogeny Model, encompassing a broader range of evolutionary phenomena. Biological and algorithmic questions concerning persistent phylogeny have been intensely…
A staged tree model is a discrete statistical model encoding relationships between events. These models are realised by directed trees with coloured vertices. In algebro-geometric terms, the model consists of points inside a toric variety.…
Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced…
Phylogenetic inference, the task of reconstructing how related sequences evolved from common ancestors, is a central objective in evolutionary genomics. The current state-of-the-art methods exploit probabilistic models of sequence evolution…
Latent tree models are graphical models defined on trees, in which only a subset of variables is observed. They were first discussed by Judea Pearl as tree-decomposable distributions to generalise star-decomposable distributions such as the…
Spatially explicit data layers of tree species assemblages, referred to as forest types or forest type groups, are a key component in large-scale assessments of forest sustainability, biodiversity, timber biomass, carbon sinks and forest…
A class of models for large-scale evolution and mass extinctions is presented. These models incorporate environmental changes on all scales, from influences on a single species to global effects. This is a step towards a unified picture of…
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…
The alpha model, a parametrized family of probabilities on cladograms (rooted binary leaf labeled trees), is introduced. This model is Markovian self-similar, deletion-stable (sampling consistent), and passes through the Yule, Uniform and…
We present an algorithm for learning decision trees using stochastic gradient information as the source of supervision. In contrast to previous approaches to gradient-based tree learning, our method operates in the incremental learning…
Species' interactions are shaped by their traits. Thus, we expect traits -- in particular, trait (dis)similarity -- to play a central role in determining whether a particular set of species coexists. Traits are, in turn, the outcome of an…
Many biological studies involve inferring the evolutionary history of a sample of individuals from a large population and interpreting the reconstructed tree. Such an ascertained tree typically represents only a small part of a…
We give a overview of stochastic models of evolution that have found applications in genetics, ecology and linguistics for an audience of nonspecialists, especially statistical physicists. In particular, we focus mostly on neutral models in…