相关论文: Identifiability of the Rooted Tree Parameter under…

Identifiability is a crucial property for a statistical model since distributions in the model uniquely determine the parameters that produce them. In phylogenetics, the identifiability of the tree parameter is of particular interest since…

For a model of molecular evolution to be useful for phylogenetic inference, the topology of evolutionary trees must be identifiable. That is, from a joint distribution the model predicts, it must be possible to recover the tree parameter.…

The inference of the evolutionary history of a collection of organisms is a problem of fundamental importance in evolutionary biology. The abundance of DNA sequence data arising from genome sequencing projects has led to significant…

Coalescent models of evolution account for incomplete lineage sorting by specifying a species tree parameter which determines a distribution on gene trees. It has been shown that the unrooted topology of the species tree parameter of the…

We give a combinatorial description of the toric ideal of invariants of the Cavender-Farris-Neyman model with a molecular clock (CFN-MC) on a rooted binary phylogenetic tree and prove results about the polytope associated to this toric…

A parameter of a mathematical model is structurally identifiable if it can be determined from noiseless experimental data. Here, we examine the identifiability properties of two important classes of linear compartmental models:…

Inference of evolutionary trees and rates from biological sequences is commonly performed using continuous-time Markov models of character change. The Markov process evolves along an unknown tree while observations arise only from the tips…

A foundational question in the theory of linear compartmental models is how to assess whether a model is structurally identifiable -- that is, whether parameter values can be inferred from noiseless data -- directly from the combinatorics…

Phylogenetic mixture models are statistical models of character evolution allowing for heterogeneity. Each of the classes in some unknown partition of the characters may evolve by different processes, or even along different trees. The…

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…

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…

The parameters of many classes of birth-death processes cannot be inferred uniquely from phylogenetic trees: infinitely many parameter combinations yield the same distribution of phylogenetic trees. Here, we show that parameter…

Linear compartmental models are a widely used tool for analyzing systems arising in biology, medicine, and more. In such settings, it is essential to know whether model parameters can be recovered from experimental data. This is the…

In phylogenetics, phylogenetic trees are rooted binary trees, whereas phylogenetic networks are rooted arbitrary acyclic digraphs. Edges are directed away from the root and leaves are uniquely labeled with taxa in phylogenetic networks. For…

Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees. Substitutions in sequences are modelled through a continuous-time Markov process, characterised by an instantaneous rate matrix, which standard…

Phylogenetic data arising on two possibly different tree topologies might be mixed through several biological mechanisms, including incomplete lineage sorting or horizontal gene transfer in the case of different topologies, or simply…

Understanding the evolutionary relationship among species is of fundamental importance to the biological sciences. The location of the root in any phylogenetic tree is critical as it gives an order to evolutionary events. None of the…

Inference of species networks from genomic data under the Network Multispecies Coalescent Model is currently severely limited by heavy computational demands. It also remains unclear how complicated networks can be for consistent inference…

In this work, we answer an open problem in the study of phylogenetic networks. Phylogenetic trees are rooted binary trees in which all edges are directed away from the root, whereas phylogenetic networks are rooted acyclic digraphs. For the…

Phylogenetic networks can model more complicated evolutionary phenomena that trees fail to capture such as horizontal gene transfer and hybridization. The same Markov models that are used to model evolution on trees can also be extended to…