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Champagne: Whole-genome phylogenomic character matrix method places Myomorpha basal in Rodentia

https://doi.org/10.1101/803957
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What this work says

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

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A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
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Towards a molecular resolution of the ordinal phylogeny of the eutherian mammals
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The gene tree delusion
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Phylogenetic relationships of the species of Plagioscion Gill, 1861 (Eupercaria, Sciaenidae)
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Mammalian phytogeny: shaking the tree
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Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model
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Reply to Gatesy and Springer: The multispecies coalescent model can effectively handle recombination and gene tree heterogeneity
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A functional enrichment test for molecular convergent evolution finds a clear protein-coding signal in echolocating bats and whales
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Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes
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Phylogenetic relationships among cetartiodactyls based on insertions of short and long interpersed elements: Hippopotamuses are the closest extant relatives of whales
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MrBayes 3: Bayesian phylogenetic inference under mixed models
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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
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ASTRAL: genome-scale coalescent-based species tree estimation
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A Retroposon Analysis of Afrotherian Phylogeny
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Confirming the Phylogeny of Mammals by Use of Large Comparative Sequence Data Sets
inferredcites →https://doi.org/10.1093/molbev/msq019openalex-snapshot
Rodent Evolution: Back to the Root
inferredcites →https://doi.org/10.1093/molbev/msr121openalex-snapshot
MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
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PhyloNetworks: A Package for Phylogenetic Networks
inferredcites →https://doi.org/10.1093/nar/gkh340openalex-snapshot
MUSCLE: multiple sequence alignment with high accuracy and high throughput
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026379openalex-snapshot
Where Do Rodents Fit? Evidence from the Complete Mitochondrial Genome of Sciurus vulgaris
inferredcites →https://doi.org/10.1093/sysbio/27.4.401openalex-snapshot
Cases in which Parsimony or Compatibility Methods will be Positively Misleading
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NEXUS: An Extensible File Format for Systematic Information
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Are Transposable Element Insertions Homoplasy Free?: An Examination Using the Avian Tree of Life
inferredcites →https://doi.org/10.1093/sysbio/syu063openalex-snapshot
Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting
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Inferring Phylogenetic Networks Using PhyloNet
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Horizontal gene transfer in evolution: facts and challenges
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Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny
inferredcites →https://doi.org/10.1098/rspb.2018.1632openalex-snapshot
Improvements in the fossil record may largely resolve current conflicts between morphological and molecular estimates of mammal phylogeny
inferredcites →https://doi.org/10.1098/rstb.2008.0144openalex-snapshot
Dealing with incongruence in phylogenomic analyses
inferredcites →https://doi.org/10.1098/rstb.2015.0140openalex-snapshot
Mammal madness: is the mammal tree of life not yet resolved?
inferredcites →https://doi.org/10.1101/gr.114751.110openalex-snapshot
Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection
inferredcites →https://doi.org/10.1101/gr.125864.111openalex-snapshot
Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis
inferredcites →https://doi.org/10.1101/gr.2800104openalex-snapshot
Reconstructing large regions of an ancestral mammalian genome in silico
inferredcites →https://doi.org/10.1111/j.1096-0031.1989.tb00573.xopenalex-snapshot
THE RETENTION INDEX AND THE RESCALED CONSISTENCY INDEX
inferredcites →https://doi.org/10.1111/j.1096-0031.2005.00059.xopenalex-snapshot
A review of long‐branch attraction
inferredcites →https://doi.org/10.1126/science.1067179openalex-snapshot
Resolution of the Early Placental Mammal Radiation Using Bayesian Phylogenetics
inferredcites →https://doi.org/10.1126/science.1086292openalex-snapshot
Phylogenomics: Intersection of Evolution and Genomics
inferredcites →https://doi.org/10.1126/science.1229237openalex-snapshot
The Placental Mammal Ancestor and the Post–K-Pg Radiation of Placentals
inferredcites →https://doi.org/10.1126/science.1253451openalex-snapshot
Whole-genome analyses resolve early branches in the tree of life of modern birds
inferredcites →https://doi.org/10.1126/science.1257570openalex-snapshot
Phylogenomics resolves the timing and pattern of insect evolution
inferredcites →https://doi.org/10.1146/annurev-animal-020518-115005openalex-snapshot
Whole-Genome Alignment and Comparative Annotation
inferredcites →https://doi.org/10.1371/journal.pbio.1000602openalex-snapshot
Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough
inferredcites →https://doi.org/10.1371/journal.pcbi.0030002openalex-snapshot
A Phylogenomic Study of Human, Dog, and Mouse
inferredcites →https://doi.org/10.1371/journal.pcbi.0030074openalex-snapshot
Dog as an Outgroup to Human and Mouse
inferredcites →https://doi.org/10.1371/journal.pgen.0030007openalex-snapshot
Genomic Relationships and Speciation Times of Human, Chimpanzee, and Gorilla Inferred from a Coalescent Hidden Markov Model
inferredcites →https://doi.org/10.1371/journal.pone.0000384openalex-snapshot
Robust Time Estimation Reconciles Views of the Antiquity of Placental Mammals
inferredcites →https://doi.org/10.1371/journal.pone.0060019openalex-snapshot
Coalescent-Based Genome Analyses Resolve the Early Branches of the Euarchontoglires

What points at this work

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

inferred← citeshttps://doi.org/10.1016/j.cub.2021.02.057openalex-snapshot
Genomic and anatomical comparisons of skin support independent adaptation to life in water by cetaceans and hippos
inferred← citeshttps://doi.org/10.1016/j.ympev.2021.107344openalex-snapshot
Gene-tree misrooting drives conflicts in phylogenomic coalescent analyses of palaeognath birds
inferred← citeshttps://doi.org/10.1093/jhered/esz076openalex-snapshot
ILS-Aware Analysis of Low-Homoplasy Retroelement Insertions: Inference of Species Trees and Introgression Using Quartets
inferred← citeshttps://doi.org/10.1093/sysbio/syab086openalex-snapshot
Theoretical and Practical Considerations when using Retroelement Insertions to Estimate Species Trees in the Anomaly Zone
inferred← citeshttps://doi.org/10.1109/sc41405.2020.00043openalex-snapshot
SegAlign: A Scalable GPU-Based Whole Genome Aligner
inferred← citeshttps://doi.org/10.1146/annurev-animal-061220-023149openalex-snapshot
Phylogenomics and the Genetic Architecture of the Placental Mammal Radiation
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