Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites

DOI10.1016/j.jtbi.2015.03.006zbMath1341.92047arXiv1406.4811OpenAlexW2046132104WikidataQ41191336 ScholiaQ41191336MaRDI QIDQ2630306

Julia Chifman, Laura S. Kubatko

Publication date: 27 July 2016

Published in: Journal of Theoretical Biology (Search for Journal in Brave)

Full work available at URL: https://arxiv.org/abs/1406.4811

zbMATH Keywords

identifiabilityphylogeneticsalgebraic statistics

Mathematics Subject Classification ID

Problems related to evolution (92D15) Taxonomy, cladistics, statistics in mathematical biology (92B10) Genetics and epigenetics (92D10)

Related Items (14)

Identifiability of species network topologies from genomic sequences using the logDet distance ⋮ A stochastic Farris transform for genetic data under the multispecies coalescent with applications to data requirements ⋮ Site pattern probabilities under the multispecies coalescent and a relaxed molecular clock: theory and applications ⋮ Classes of explicit phylogenetic networks and their biological and mathematical significance ⋮ Distinguishing Phylogenetic Networks ⋮ Phylogenomic Models from Tree Symmetries ⋮ Evaluation of the relative performance of the subflattenings method for phylogenetic inference ⋮ Split probabilities and species tree inference under the multispecies coalescent model ⋮ Modeling the distribution of distance data in Euclidean space ⋮ Distance to the stochastic part of phylogenetic varieties ⋮ Identifiability and reconstructibility of species phylogenies under a modified coalescent ⋮ Hypothesis tests for phylogenetic quartets, with applications to coalescent-based species tree inference ⋮ Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent ⋮ Bayesian-weighted triplet and quartet methods for species tree inference

Cites Work

• Unnamed Item
• Unnamed Item
• Unnamed Item
• Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent
• Line-of-descent and genealogical processes, and their applications in population genetics models
• The coalescent
• Construction of linear invariants in phylogenetic inference
• Determining species tree topologies from clade probabilities under the coalescent
• Identifying evolutionary trees and substitution parameters for the general Markov model with invariable sites
• Tree Construction using Singular Value Decomposition
• Identifiability of a Markovian model of molecular evolution with gamma-distributed rates

This page was built for publication: Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites