Related papers: Systematics and symmetry in molecular phylogenetic…
This thesis develops and expands upon known techniques of mathematical physics relevant to the analysis of the popular Markov model of phylogenetic trees required in biology to reconstruct the evolutionary relationships of taxonomic units…
Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation…
Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…
Models of random phylogenetic networks have been used since the inception of the field, but the introduction and rigorous study of mathematically tractable models is a much more recent topic that has gained momentum in the last 5 years.…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
A phylogenetic birth-and-death model is a probabilistic graphical model for a so-called phylogenetic profile, i.e., the size distribution for a homolog gene family at the terminal nodes of a phylogeny. Profile datasets are used in…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
Phylogenetic inference-the derivation of a hypothesis for the common evolutionary history of a group of species- is an active area of research at the intersection of biology, computer science, mathematics, and statistics. One assumes the…
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…
Basic principles of mathematical modeling are reviewed in this book, with the focus on physics and its practical applications, and examples of selected mathematical methods are presented. Most of the models have been imported from physics…
The evolutionary relationships among organisms have traditionally been represented using rooted phylogenetic trees. However, due to reticulate processes such as hybridization or lateral gene transfer, evolution cannot always be adequately…
Phylogenetics is the study of the evolutionary relationships between organisms. One of the main challenges in the field is to take biological data for a group of organisms and to infer an evolutionary tree, a graph that represents these…
Phylogenetic invariants are certain polynomials in the joint probability distribution of a Markov model on a phylogenetic tree. Such polynomials are of theoretical interest in the field of algebraic statistics and they are also of practical…
Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees relating species. Along branches, sequence evolution is modelled using a continuous-time Markov process characterised by an instantaneous rate…
By providing a framework of accounting for the shared ancestry inherent to all life, phylogenetics is becoming the statistical foundation of biology. The importance of model choice continues to grow as phylogenetic models continue to…
Mathematical modelling has a long history in the context of collective cell migration, with applications throughout development, disease and regenerative medicine. The aim of modelling in this context is to provide a framework in which to…
Phylogenomics is a new field which applies to tools in phylogenetics to genome data. Due to a new technology and increasing amount of data, we face new challenges to analyze them over a space of phylogenetic trees. Because a space of…
We introduce new methods for phylogenetic tree quartet construction by using machine learning to optimize the power of phylogenetic invariants. Phylogenetic invariants are polynomials in the joint probabilities which vanish under a model of…
We propose a novel method for the inference of phylogenetic trees that utilises point configurations on hyperbolic space as its optimisation landscape. Each taxon corresponds to a point of the point configuration, while the evolutionary…