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Polymorphism-Aware Species Trees with Advanced Mutation Models, Bootstrap, and Rate Heterogeneity

https://doi.org/10.1093/molbev/msz043
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/jez.b.21026openalex-snapshot
Inferring species phylogenies from multiple genes: Concatenated sequence tree versus consensus gene tree
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Information Theory and an Extension of the Maximum Likelihood Principle
inferredcites →https://doi.org/10.1007/978-3-642-81046-6_52openalex-snapshot
Stochastic Processes and Population Growth
inferredcites →https://doi.org/10.1007/bf00160154openalex-snapshot
Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
inferredcites →https://doi.org/10.1007/bf02101694openalex-snapshot
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
inferredcites →https://doi.org/10.1016/0025-5564(81)90043-2openalex-snapshot
Comparison of phylogenetic trees
inferredcites →https://doi.org/10.1016/j.jtbi.2016.07.042openalex-snapshot
Reversible polymorphism-aware phylogenetic models and their application to tree inference
inferredcites →https://doi.org/10.1016/j.tpb.2012.01.001openalex-snapshot
The allele-frequency spectrum in a decoupled Moran model with mutation, drift, and directional selection, assuming small mutation rates
inferredcites →https://doi.org/10.1016/j.tpb.2016.12.001openalex-snapshot
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
inferredcites →https://doi.org/10.1016/j.tree.2009.01.009openalex-snapshot
Gene tree discordance, phylogenetic inference and the multispecies coalescent
inferredcites →https://doi.org/10.1017/s0305004100033193openalex-snapshot
Random processes in genetics
inferredcites →https://doi.org/10.1038/nature12228openalex-snapshot
Great ape genetic diversity and population history
inferredcites →https://doi.org/10.1038/nmeth.4285openalex-snapshot
ModelFinder: fast model selection for accurate phylogenetic estimates
inferredcites →https://doi.org/10.1038/nrg.2016.104openalex-snapshot
Genetic drift, selection and the evolution of the mutation rate
inferredcites →https://doi.org/10.1093/acprof:oso/9780198567028.001.0001openalex-snapshot
Computational Molecular Evolution
inferredcites →https://doi.org/10.1093/bioinformatics/13.3.235openalex-snapshot
Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
inferredcites →https://doi.org/10.1093/bioinformatics/btn484openalex-snapshot
BEST: Bayesian estimation of species trees under the coalescent model
inferredcites →https://doi.org/10.1093/bioinformatics/btu462openalex-snapshot
ASTRAL: genome-scale coalescent-based species tree estimation
inferredcites →https://doi.org/10.1093/genetics/164.4.1645openalex-snapshot
Bayes Estimation of Species Divergence Times and Ancestral Population Sizes Using DNA Sequences From Multiple Loci
inferredcites →https://doi.org/10.1093/molbev/msp274openalex-snapshot
Bayesian Inference of Species Trees from Multilocus Data
inferredcites →https://doi.org/10.1093/molbev/msu300openalex-snapshot
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
inferredcites →https://doi.org/10.1093/molbev/msx281openalex-snapshot
UFBoot2: Improving the Ultrafast Bootstrap Approximation
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040126openalex-snapshot
A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040517openalex-snapshot
Relationships between gene trees and species trees.
inferredcites →https://doi.org/10.1093/sysbio/46.3.523openalex-snapshot
Gene Trees in Species Trees
inferredcites →https://doi.org/10.1093/sysbio/syp061openalex-snapshot
Estimating Species Trees: Methods of Phylogenetic Analysis When There Is Incongruence across Genes
inferredcites →https://doi.org/10.1093/sysbio/syq010openalex-snapshot
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
inferredcites →https://doi.org/10.1093/sysbio/syt023openalex-snapshot
Anomalous Unrooted Gene Trees
inferredcites →https://doi.org/10.1093/sysbio/syv021openalex-snapshot
A New Hierarchy of Phylogenetic Models Consistent with Heterogeneous Substitution Rates
inferredcites →https://doi.org/10.1093/sysbio/syv048openalex-snapshot
PoMo: An Allele Frequency-Based Approach for Species Tree Estimation
inferredcites →https://doi.org/10.1093/sysbio/syv082openalex-snapshot
SimPhy : Phylogenomic Simulation of Gene, Locus, and Species Trees
inferredcites →https://doi.org/10.1098/rstb.1925.0002openalex-snapshot
II.—A mathematical theory of evolution, based on the conclusions of Dr. J. C. Willis, F. R. S
inferredcites →https://doi.org/10.1111/j.1558-5646.1985.tb00420.xopenalex-snapshot
CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP
inferredcites →https://doi.org/10.1111/j.2517-6161.1949.tb00032.xopenalex-snapshot
Stochastic Processes and Population Growth
inferredcites →https://doi.org/10.1146/annurev-ecolsys-110316-022645openalex-snapshot
The Utility of Single Nucleotide Polymorphism (SNP) Data in Phylogenetics
inferredcites →https://doi.org/10.1186/1471-2148-10-302openalex-snapshot
A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
inferredcites →https://doi.org/10.1186/1471-2148-7-214openalex-snapshot
BEAST: Bayesian evolutionary analysis by sampling trees
inferredcites →https://doi.org/10.1214/aos/1176344136openalex-snapshot
Estimating the Dimension of a Model
inferredcites →https://doi.org/10.1214/aos/1176344552openalex-snapshot
Bootstrap Methods: Another Look at the Jackknife
inferredcites →https://doi.org/10.7312/nei-92038openalex-snapshot
Molecular Evolutionary Genetics

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Homoploid hybrid speciation and recurrent hybridization along the northwestern Iberian mountain chains
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Nucleotide Usage Biases Distort Inferences of the Species Tree
inferred← citeshttps://doi.org/10.1093/molbev/msaa015openalex-snapshot
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
inferred← citeshttps://doi.org/10.1093/molbev/msae138openalex-snapshot
Polymorphism-Aware Models in RevBayes: Species Trees, Disentangling Balancing Selection, and GC-Biased Gene Conversion
inferred← citeshttps://doi.org/10.1093/mollus/eyaa004openalex-snapshot
The complete mitochondrial genomes of four Baikal molluscs from the endemic family Baicaliidae (Caenogastropoda: Truncatelloida)
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ncOrtho: efficient and reliable identification of miRNA orthologs
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Mutation, Randomness, and Evolution
inferred← citeshttps://doi.org/10.1093/oso/9780198844457.002.0004openalex-snapshot
Copyright Page
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List of Figures
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List of Tables and Boxes
inferred← citeshttps://doi.org/10.1093/oso/9780198844457.003.0001openalex-snapshot
Introduction: a curious disconnect
inferred← citeshttps://doi.org/10.1093/oso/9780198844457.003.0002openalex-snapshot
Ordinary randomness
inferred← citeshttps://doi.org/10.1093/oso/9780198844457.003.0003openalex-snapshot
Practical Randomness
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Evolutionary Randomness
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Mutational mechanisms and evolvability
inferred← citeshttps://doi.org/10.1093/oso/9780198844457.003.0006openalex-snapshot
Randomness as Irrelevance
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The problem of variation
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Climbing Mount Probable
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The revolt of the clay
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Moving on
inferred← citeshttps://doi.org/10.1093/oso/9780198844457.005.0001openalex-snapshot
Mutation exemplars
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Counting the universe of mutations
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Randomness quotations
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Geographic isolation enables recurrent pollinator shifts despite hybridisation in the Cape’s hyperdiverse heathers
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Host specialization defines the emergence of new fungal plant pathogen populations
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Bactrocera dorsalis in the Indian Ocean: A tale of two invasions
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Range-wide population genomics of common seadragons shows secondary contact over a former barrier and insights on illegal capture
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Genetic characterization of the first Deltacoronavirus from wild birds around Qinghai Lake
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The North Asian Genus Kolhymamnicola Starobogatov and Budnikova 1976 (Gastropoda: Amnicolidae), Its Extended Diagnosis, Distribution, and Taxonomic Relationships
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Additional file 1 of Range-wide population genomics of common seadragons shows secondary contact over a former barrier and insights on illegal capture
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Modelling the articulation of selective and neutral mechanisms in the evolution of protein-coding DNA sequences
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Pervasive duplication of tumor suppressors in Afrotherians during the evolution of large bodies and reduced cancer risk
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