相关论文: Species tree inference by the STAR method, and gen…

Efforts to reconstruct phylogenetic trees and understand evolutionary processes depend fundamentally on stochastic models of speciation and mutation. The simplest continuous-time model for speciation in phylogenetic trees is the Yule…

Many population genetic models have been developed for the purpose of inferring population size and growth rates from random samples of genetic data. We examine two popular approaches to this problem, the coalescent and the…

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…

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…

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 is one of the fundamental tasks in statistics and machine learning. However, standard methods for probability estimation on discrete objects do not handle object structure in a satisfactory manner. In this paper, we…

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…

When hybridization or other forms of lateral gene transfer have occurred, evolutionary relationships of species are better represented by phylogenetic networks than by trees. While inference of such networks remains challenging, several…

This paper extends earlier work by Cox and Durrett, who studied the coalescence times for two lineages in the stepping stone model on the two-dimensional torus. We show that the genealogy of a sample of size n is given by a time change of…

A well-established model for the genealogy of a large population in equilibrium is Kingman's coalescent. For the population together with its genealogy evolving in time, this gives rise to a time-stationary tree-valued process. We study 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…

We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…

A metric phylogenetic tree relating a collection of taxa induces weighted rooted triples and weighted quartets for all subsets of three and four taxa, respectively. New intertaxon distances are defined that can be calculated from these…

Simple stochastic models for phylogenetic trees on species have been well studied. But much paleontology data concerns time series or trees on higher-order taxa, and any broad picture of relationships between extant groups requires use of…

Phylogenetic comparative methods correct for shared evolutionary history among a set of non-independent organisms by modeling sample traits as arising from a diffusion process along on the branches of a possibly unknown history. To…

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…

We answer two questions raised by Bryant, Francis and Steel in their work on consensus methods in phylogenetics. Consensus methods apply to every practical instance where it is desired to aggregate a set of given phylogenetic trees (say,…

Understanding the evolution of binary traits, which affects the birth and survival of species and also the rate of molecular evolution, remains challenging. A typical example is the evolution of mating systems in plant species. In this…

Unraveling the co-expression of genes across studies enhances the understanding of cellular processes. Inferring gene co-expression networks from transcriptome data presents many challenges, including spurious gene correlations, sample…

An early burst of speciation followed by a subsequent slowdown in the rate of diversification is commonly inferred from molecular phylogenies. This pattern is consistent with some verbal theory of ecological opportunity and adaptive…