Related papers: Estimating Trees from Filtered Data: Identifiabili…

Phylogenetic comparative methods are well established tools for using inter-species variation to analyse phenotypic evolution and adaptation. They are generally hampered, however, by predominantly univariate approaches and failure to…

Identifiability of evolutionary tree models has been a recent topic of discussion and some models have been shown to be non-identifiable. A coalescent-based rooted population tree model, originally proposed by Nielsen et al. 1998 [2], has…

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 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…

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 trees are widely used to understand the evolutionary history of organisms. Tree shapes provide information about macroevolutionary processes. However, macroevolutionary models are unreliable for inferring the true processes…

Phylogenetic trees are frequently used to model evolution. Such trees are typically reconstructed from data like DNA, RNA, or protein alignments using methods based on criteria like maximum parsimony (amongst others). Maximum parsimony has…

The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data.…

With the advance of experimental techniques such as time-lapse fluorescence microscopy, the availability of single-cell trajectory data has vastly increased, and so has the demand for computational methods suitable for parameter inference…

Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…

Eliciting preferences from human judgements is inherently imprecise, yet most decision analysis methods force a single priority vector from pairwise comparisons, discarding the information embedded in inconsistencies. We instead leverage…

Covarion models of character evolution describe inhomogeneities in substitution processes through time. In phylogenetics, such models are used to describe changing functional constraints or selection regimes during the evolution of…

Diversification models describe the random growth of evolutionary trees, modeling the historical relationships of species through speciation and extinction events. One class of such models allows for independently changing traits, or types,…

Probability estimation of tree topologies is one of the fundamental tasks in phylogenetic inference. The recently proposed subsplit Bayesian networks (SBNs) provide a powerful probabilistic graphical model for tree topology probability…

Phylogenetic trees are used to model evolution: leaves are labelled to represent contemporary species ("taxa") and interior vertices represent extinct ancestors. Informally, convex characters are measurements on the contemporary species in…

There have been many studies to examine whether one trait is correlated with another trait across a group of present-day species (for example, do species with larger brains tend to have longer gestation times. Since the introduction of the…

Estimating phylogenetic trees is an important problem in evolutionary biology, environmental policy and medicine. Although trees are estimated, their uncertainties are discarded by mathematicians working in tree space. Here we explicitly…

Staged trees are probabilistic graphical models capable of representing any class of non-symmetric independence via a coloring of its vertices. Several structural learning routines have been defined and implemented to learn staged trees…

In phylogenetic studies, biologists often wish to estimate the ancestral discrete character state at an interior vertex $v$ of an evolutionary tree $T$ from the states that are observed at the leaves of the tree. A simple and fast…

To the known fact that Parsimony method sometimes fails on the problem of inferring species trees from gene trees, here we proved that no mater of what topology the true 9-taxon and greater species tree is the only thing one needs to break…