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Selecting Question-Specific Genes to Reduce Incongruence in Phylogenomics: A Case Study of Jawed Vertebrate Backbone Phylogeny

https://doi.org/10.1093/sysbio/syv059
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Ending incongruence
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Genome-scale approaches to resolving incongruence in molecular phylogenies
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The African coelacanth genome provides insights into tetrapod evolution
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Naive binning improves phylogenomic analyses
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An Improved General Amino Acid Replacement Matrix
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A Phylogenomic Approach to Resolve the Arthropod Tree of Life
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Mammalian Evolution May not Be Strictly Bifurcating
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Evolution of Modern Birds Revealed by Mitogenomics: Timing the Radiation and Origin of Major Orders
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Multiple Genome Alignments Facilitate Development of NPCL Markers: A Case Study of Tetrapod Phylogeny Focusing on the Position of Turtles
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Pancrustacean Phylogeny in the Light of New Phylogenomic Data: Support for Remipedia as the Possible Sister Group of Hexapoda
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Retroposon Insertion Patterns of Neoavian Birds: Strong Evidence for an Extensive Incomplete Lineage Sorting Era
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Impact of Missing Data on Phylogenies Inferred from Empirical Phylogenomic Data Sets
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One Thousand Two Hundred Ninety Nuclear Genes from a Genome-Wide Survey Support Lungfishes as the Sister Group of Tetrapods
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Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference
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Diversification of Neoaves: integration of molecular sequence data and fossils
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Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis
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Highly conserved low‐copy nuclear genes as effective markers for phylogenetic analyses in angiosperms
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Difficult phylogenetic questions: more data, maybe; better methods, certainly
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Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition
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The Tree of Life and a New Classification of Bony Fishes
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What points at this work

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

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Topological support and data quality can only be assessed through multiple tests in reviewing Blattodea phylogeny
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Global Rate Variation in Bony Vertebrates
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Whole Genome Sequencing of the Pirarucu (Arapaima gigas) Supports Independent Emergence of Major Teleost Clades
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BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data
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Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life
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Evolutionary Rate Variation among Lineages in Gene Trees has a Negative Impact on Species-Tree Inference
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Defining Coalescent Genes: Theory Meets Practice in Organelle Phylogenomics
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Conserved Nonexonic Elements: A Novel Class of Marker for Phylogenomics
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Model Choice, Missing Data, and Taxon Sampling Impact Phylogenomic Inference of Deep Basidiomycota Relationships
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Quartet-Based Computations of Internode Certainty Provide Robust Measures of Phylogenetic Incongruence
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Phylogenetic Conflicts, Combinability, and Deep Phylogenomics in Plants
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Multiple hidden processes complicate phylogenomic inference of deep Basidiomycota relationships
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Phylogenetic signal is associated with the degree of variation in root-to-tip distances
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When species trees disagree: an approach consistent with the coalescent that quantifies phylogenomic support for contentious relationships
inferred← citeshttps://doi.org/10.1101/2021.09.22.461455openalex-snapshot
The Influence of Model Violation on Phylogenetic Inference: A Simulation Study
inferred← citeshttps://doi.org/10.1101/2024.05.06.592828openalex-snapshot
Predicting locus phylogenetic utility using machine learning
inferred← citeshttps://doi.org/10.1101/371930openalex-snapshot
Phylogenetic conflicts, combinability, and deep phylogenomics in plants
inferred← citeshttps://doi.org/10.1101/601237openalex-snapshot
Phylogenetic Synecdoche Demonstrates Optimality of Subsampling and Improves Recovery of the Blaberoidea Phylogeny
inferred← citeshttps://doi.org/10.1101/765610openalex-snapshot
Exons, Introns, and UCEs Reveal Conflicting Phylogenomic Signals in a Rapid Radiation of Frogs (Ranidae: Hylarana )
inferred← citeshttps://doi.org/10.1109/kse53942.2021.9648748openalex-snapshot
fastTIGER: A rapid method for estimating evolutionary rates of sites from large datasets
inferred← citeshttps://doi.org/10.1109/kse56063.2022.9953767openalex-snapshot
A protein secondary structure-based algorithm for partitioning large protein alignments
inferred← citeshttps://doi.org/10.1109/rivf48685.2020.9140797openalex-snapshot
A protein alignment partitioning method for protein phylogenetic inference
inferred← citeshttps://doi.org/10.1111/azo.12378openalex-snapshot
Ovary structure and oogenesis in internally and externally fertilizing Osteoglossiformes (Teleostei:Osteoglossomorpha)
inferred← citeshttps://doi.org/10.1111/cla.12232openalex-snapshot
When did the ancestor of true bugs become stinky? Disentangling the phylogenomics of Hemiptera–Heteroptera
inferred← citeshttps://doi.org/10.1111/cla.12540openalex-snapshot
Quantification of congruence among gene trees with polytomies using overall success of resolution for phylogenomic coalescent analyses
inferred← citeshttps://doi.org/10.1111/jse.12664openalex-snapshot
Phylogenetic relationships and the maternal donor ofRoegneria(Triticeae: Poaceae) based on three nuclear DNA sequences (ITS,Acc1, andPgk1) and one chloroplast region (trnL‐F)
inferred← citeshttps://doi.org/10.1111/syen.12217openalex-snapshot
Phylotranscriptomics resolves ancient divergences in the Lepidoptera
inferred← citeshttps://doi.org/10.1111/syen.12406openalex-snapshot
Phylogenomics — principles, opportunities and pitfalls of big‐data phylogenetics
inferred← citeshttps://doi.org/10.1111/syen.12454openalex-snapshot
Assessing support for Blaberoidea phylogeny suggests optimal locus quality
inferred← citeshttps://doi.org/10.1111/syen.12582openalex-snapshot
Phylogeny of the flea beetles (Galerucinae: Alticini) and the position of Aulacothorax elucidated through anchored phylogenomics (Coleoptera: Chrysomelidae: Alticini)
inferred← citeshttps://doi.org/10.1111/syen.12685openalex-snapshot
Whole genome shotgun phylogenomics resolve the diving beetle tree of life
inferred← citeshttps://doi.org/10.1111/zsc.12210openalex-snapshot
Phylogenomic subsampling: a brief review
inferred← citeshttps://doi.org/10.1111/zsc.12512openalex-snapshot
Gene tree quality affects empirical coalescent branch length estimation
inferred← citeshttps://doi.org/10.1111/zsc.12521openalex-snapshot
End of a mystery: Integrative approach reveals the phylogenetic position of an enigmatic Antarctic tardigrade genus Ramajendas (Tardigrada, Eutardigrada)
inferred← citeshttps://doi.org/10.1111/zsc.12703openalex-snapshot
Integrative description of Grevenius annulatus (Eutardigrada, Isohypsibioidea) from North‐West Russia with new data on the species cuticular structure leads to the institution of a new genus
inferred← citeshttps://doi.org/10.1126/sciadv.adl0989openalex-snapshot
A macroevolutionary role for chromosomal fusion and fission in Erebia butterflies
inferred← citeshttps://doi.org/10.1126/science.abq4257openalex-snapshot
Genome structures resolve the early diversification of teleost fishes
inferred← citeshttps://doi.org/10.1146/annurev-ecolsys-122120-122554openalex-snapshot
The Emerging Phylogenetic Perspective on the Evolution of Actinopterygian Fishes
inferred← citeshttps://doi.org/10.1186/s12862-017-0958-3openalex-snapshot
Phylogenetic classification of bony fishes
inferred← citeshttps://doi.org/10.1186/s12862-019-1534-9openalex-snapshot
The effect of alignment uncertainty, substitution models and priors in building and dating the mammal tree of life
inferred← citeshttps://doi.org/10.1186/s12915-024-01848-7openalex-snapshot
Gene flow and an anomaly zone complicate phylogenomic inference in a rapidly radiated avian family (Prunellidae)
inferred← citeshttps://doi.org/10.1186/s13104-019-4577-5openalex-snapshot
Treehouse: a user-friendly application to obtain subtrees from large phylogenies
inferred← citeshttps://doi.org/10.1186/s40246-022-00429-5openalex-snapshot
Placing human gene families into their evolutionary context
inferred← citeshttps://doi.org/10.1360/n052018-00222openalex-snapshot
Recent progress in phylogenomic methods
inferred← citeshttps://doi.org/10.1371/journal.pbio.3002632openalex-snapshot
The promise and pitfalls of synteny in phylogenomics
inferred← citeshttps://doi.org/10.1371/journal.pone.0202729openalex-snapshot
Noise and biases in genomic data may underlie radically different hypotheses for the position of Iguania within Squamata
inferred← citeshttps://doi.org/10.1371/journal.pone.0338893openalex-snapshot
Investigating adaptation to environmental variability in forest trees through molecular phylogenetic analysis
inferred← citeshttps://doi.org/10.23860/diss-ada-eren-2023openalex-snapshot
Utilization of Large-Scale Genomic Data and Phylogenetic Methods in Studying Evolutionary Radiations
inferred← citeshttps://doi.org/10.31610/zsr/2023.32.1.50openalex-snapshot
Some have drops and some do not, but can we rely on that? Re-investigation of Diphascon tenue (Tardigrada: Eutardigrada) with discussion of the phylogeny and taxonomy of the superfamily Hypsibioidea
inferred← citeshttps://doi.org/10.32942/osf.io/yrdsfopenalex-snapshot
Reconciliation of evidence for the Portulacineae “backbone” phylogeny
inferred← citeshttps://doi.org/10.3374/014.065.0101openalex-snapshot
Phylogenetic Classification of Living and Fossil Ray-Finned Fishes (Actinopterygii)
inferred← citeshttps://doi.org/10.3389/fgene.2020.506749openalex-snapshot
Can We Reliably Calibrate Deep Nodes in the Tetrapod Tree? Case Studies in Deep Tetrapod Divergences
inferred← citeshttps://doi.org/10.3390/ani13223449openalex-snapshot
Evolutionary Insights into the Relationship of Frogs, Salamanders, and Caecilians and Their Adaptive Traits, with an Emphasis on Salamander Regeneration and Longevity
inferred← citeshttps://doi.org/10.3390/d11070115openalex-snapshot
Comparative Phylogenomics, a Stepping Stone for Bird Biodiversity Studies
inferred← citeshttps://doi.org/10.3390/genes10010038openalex-snapshot
Highly Resolved Phylogenetic Relationships within Order Acipenseriformes According to Novel Nuclear Markers
inferred← citeshttps://doi.org/10.3390/genes17040455openalex-snapshot
Morphological and Cyto-Nuclear Conflicting Signals Across Non-Sister Lineages in Darkling Beetles (Tenebrionidae: Akis)
inferred← citeshttps://doi.org/10.3390/toxins13110779openalex-snapshot
Morphology of the Cutaneous Poison and Mucous Glands in Amphibians with Particular Emphasis on Caecilians (Siphonops annulatus)
inferred← citeshttps://doi.org/10.48550/arxiv.1904.03826openalex-snapshot
Species Tree Estimation Using ASTRAL: Practical Considerations
inferred← citeshttps://doi.org/10.5204/thesis.eprints.207248openalex-snapshot
A genomics perspective of species and speciation in an Atyid shrimp (Paratya australiensis)
inferred← citeshttps://doi.org/10.5802/crbiol.150openalex-snapshot
Solving an enigma in the tree of life, at the origins of teleost fishes
inferred← citeshttps://doi.org/10.5802/crbiol.150-fropenalex-snapshot
Résolution d’une énigme dans l’arbre du vivant, aux origines des poissons téléostéens
inferred← citeshttps://doi.org/10.6084/m9.figshare.25302933openalex-snapshot
Additional file 1 of Gene flow and an anomaly zone complicate phylogenomic inference in a rapidly radiated avian family (Prunellidae)
inferred← citeshttps://doi.org/10.64898/2026.02.13.705779openalex-snapshot
Phylogenomics and the origins of sharks
inferred← citeshttps://doi.org/10.64898/2026.03.30.714540openalex-snapshot
Signal, noise, and bias in phylogenetic inference: potential and limits to the resolution of phylogenetic trees in the phylogenomic era
inferred← citeshttps://doi.org/10.64898/2026.06.28.735080openalex-snapshot
Genomic Distortion of Jawed Vertebrate Phylogeny
inferred← citeshttps://doi.org/10.64898/2026.08.25.747154openalex-snapshot
Non-convergent aridity adaptation despite pervasive linked selection in Eucalyptus
inferred← citeshttps://doi.org/10.7287/peerj.preprints.27521v1openalex-snapshot
Timing the extant avian radiation: The rise of modern birds, and the importance of modeling molecular rate variation
inferred← citeshttps://doi.org/10.7717/peerj.6399openalex-snapshot
Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics
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