Reversible polymorphism-aware phylogenetic models and their application to tree inference

DOI10.1016/J.JTBI.2016.07.042MaRDI QIDQ309245zbMATH OpenOpenAlexWikidataFDO

Authors Dominik Schrempf, Bui Quang Minh, Nicola De Maio, Arndt von Haeseler, Carolin Kosiol

Publication date 7 September 2016

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

Copyright license Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International

Full work available at URL https://doi.org/10.1016/j.jtbi.2016.07.042

zbMATH Keywords

phylogeneticsincomplete lineage sortingreversible polymorphism-aware phylogenetic modelspecies treesubstitution model

Mathematics Subject Classification ID

Applications of Markov chains and discrete-time Markov processes on general state spaces (social mobility, learning theory, industrial processes, etc.) (60J20) Genetics and epigenetics (92D10) Problems related to evolution (92D15)

Recommendations

• Consistency and identifiability of the polymorphism-aware phylogenetic models
• Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites
• Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and Loss
• Identifiability and inference of non-parametric rates-across-sites models on large-scale phylo\-genies
• Maximum tree: a consistent estimator of the species tree

Cites work

• scientific article; zbMATH DE number 2126323 (Why is no real title available?)
• scientific article; zbMATH DE number 3943611 (Why is no real title available?)
• scientific article; zbMATH DE number 3656855 (Why is no real title available?)
• scientific article; zbMATH DE number 961607 (Why is no real title available?)
• Diffusion models in population genetics
• Line-of-descent and genealogical processes, and their applications in population genetics models
• Markov Chains
• Mathematical population genetics. I: Theoretical introduction.
• On the number of segregating sites in genetical models without recombination
• Probability Models for DNA Sequence Evolution
• The Differential Equation of the Distribution of Gene Frequencies
• The allele-frequency spectrum in a decoupled Moran model with mutation, drift, and directional selection, assuming small mutation rates
• The coalescent

Cited in

(4)

• An alternative derivation of the stationary distribution of the multivariate neutral Wright-Fisher model for low mutation rates with a view to mutation rate estimation from site frequency data
• Bayesian estimation of the phylogeography of African gorillas with genome-differentiated population trees
• Inference in population genetics using forward and backward, discrete and continuous time processes
• Consistency and identifiability of the polymorphism-aware phylogenetic models

Describes a project that uses

Uses Software

• PHYLIP
• MrBayes
• RAxML
• IQ-TREE
• SimPhy

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