相关论文: Stochastic Models for Speciation Events in Phyloge…

Joint distributions over many variables are frequently modeled by decomposing them into products of simpler, lower-dimensional conditional distributions, such as in sparsely connected Bayesian networks. However, automatically learning such…

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…

In data analysis, latent variables play a central role because they help provide powerful insights into a wide variety of phenomena, ranging from biological to human sciences. The latent tree model, a particular type of probabilistic…

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.…

Distances between sequences based on their $k$-mer frequency counts can be used to reconstruct phylogenies without first computing a sequence alignment. Past work has shown that effective use of k-mer methods depends on 1) model-based…

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…

We consider the problem of estimating species trees from unrooted gene tree topologies in the presence of incomplete lineage sorting, a common phenomenon that creates gene tree heterogeneity in multilocus datasets. One popular class of…

The Bayesian method is noted to produce spuriously high posterior probabilities for phylogenetic trees in analysis of large datasets, but the precise reasons for this over-confidence are unknown. In general, the performance of Bayesian…

In this article we propose a new method, which we name 'quartet neighbor joining', or 'quartet-NJ', to infer an unrooted species tree on a given set of taxa T from empirical distributions of unrooted quartet gene trees on all four-taxon…

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…

With the aim of considering models with persistent memory we propose a fractional nonlinear modification of the classical Yule model often studied in the context of macrovolution. Here the model is analyzed and interpreted in the framework…

This short paper presents an abstract, tunable model of genomic structural change within the cell lifecycle and explores its use with simulated evolution. A well-known Boolean model of genetic regulatory networks is extended to include…

In this paper, we propose some representations of a generalized linear birth process called fractional Yule process (fYp). We also derive the probability distributions of the random birth and sojourn times. The inter-birth time distribution…

As an alternative to parsimony analyses, stochastic models have been proposed (Lewis, 2001), (Nylander, et al., 2004) for morphological characters, so that maximum likelihood or Bayesian analyses may be used for phylogenetic inference. A…

The numerical integration of stochastic growth equations on non-Euclidean networks presents unique challenges due to the nonlinearities that occur in many relevant models and of the structural constraints of the networks. In this work, we…

In this paper we investigate the use of staged tree models for discrete longitudinal data. Staged trees are a type of probabilistic graphical model for finite sample space processes. They are a natural fit for longitudinal data because a…

Cancers follow a clonal Darwinian evolution, with fitter subclones replacing more quiescent cells, ultimately giving rise to macroscopic disease. High-throughput genomics provides the opportunity to investigate these processes and determine…

To introduce selection into a model of coalescence, I explore the use of modified integer partitions that allow the identification of a preferred lineage. I show that a partition-partition transition matrix, along with Monte Carlo discrete…

We consider the following question: how close to the ancestral root of a phylogenetic tree is the most recent common ancestor of $k$ species randomly sampled from the tips of the tree? For trees having shapes predicted by the Yule-Harding…

Phylogenetic networks provide a way to describe and visualize evolutionary histories that have undergone so-called reticulate evolutionary events such as recombination, hybridization or horizontal gene transfer. The level k of a network…