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Phylogenomics Uncovers Confidence and Conflict in the Rapid Radiation of Australo-Papuan Rodents
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Embracing Uncertainty in Reconstructing Early Animal Evolution
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Multigene phylogeny of the Old World mice, Murinae, reveals distinct geographic lineages and the declining utility of mitochondrial genes compared to nuclear genes
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Pliocene colonization and adaptive radiations in Australia and New Guinea (Sahul): Multilocus systematics of the old endemic rodents (Muroidea: Murinae)
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Applications of next-generation sequencing to phylogeography and phylogenetics
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Divergent maximum-likelihood-branch-support values for polytomies
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Repeated biome transitions in the evolution of Australian rodents
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Genome-scale approaches to resolving incongruence in molecular phylogenies
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Full-length transcriptome assembly from RNA-Seq data without a reference genome
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jModelTest 2: more models, new heuristics and parallel computing
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ModelFinder: fast model selection for accurate phylogenetic estimates
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De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity
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Understanding the origin of species with genome-scale data: modelling gene flow
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Contentious relationships in phylogenomic studies can be driven by a handful of genes
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Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model
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Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics
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Partitioned Likelihood Support and the Evaluation of Data Set Conflict
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A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
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Phylogeny and Divergence-Date Estimates of Rapid Radiations in Muroid Rodents Based on Multiple Nuclear Genes
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Approximate Likelihood-Ratio Test for Branches: A Fast, Accurate, and Powerful Alternative
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Inconsistency of Phylogenetic Estimates from Concatenated Data under Coalescence
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The Sequence Alignment/Map format and SAMtools
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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
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Trimmomatic: a flexible trimmer for Illumina sequence data
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Quartet Inference from SNP Data Under the Coalescent Model
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ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes
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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
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Ultrafast Approximation for Phylogenetic Bootstrap
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OrthoMaM v8: A Database of Orthologous Exons and Coding Sequences for Comparative Genomics in Mammals
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ExaBayes: Massively Parallel Bayesian Tree Inference for the Whole-Genome Era
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IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
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An Exon-Capture System for the Entire Class Ophiuroidea
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Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies
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StarBEAST2 Brings Faster Species Tree Inference and Accurate Estimates of Substitution Rates
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Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta)
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UFBoot2: Improving the Ultrafast Bootstrap Approximation
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Phylogenetic Analysis in the Anomaly Zone
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Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes
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Exon capture phylogenomics: efficacy across scales of divergence
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Resources for phylogenomic analyses of Australian terrestrial vertebrates
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MICROEVOLUTIONARY PROCESSES GENERATE PHYLOGENOMIC DISCORDANCE AT ANCIENT DIVERGENCES
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Irrational exuberance for resolved species trees
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CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP
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LocText: relation extraction of protein localizations to assist database curation
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ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees
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Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants
inferredcites →https://doi.org/10.1371/10.1371/currents.tol.8d41ac0f13d1abedf4c4a59f5d17b1f7openalex-snapshot
Concatenation Analyses in the Presence of Incomplete Lineage Sorting
inferredcites →https://doi.org/10.1371/currents.tol.8d41ac0f13d1abedf4c4a59f5d17b1f7openalex-snapshot
Concatenation Analyses in the Presence of Incomplete Lineage Sorting
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Bushes in the Tree of Life
inferredcites →https://doi.org/10.1371/journal.pgen.0020068openalex-snapshot
Discordance of Species Trees with Their Most Likely Gene Trees
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Anatomical Brain Images Alone Can Accurately Diagnose Chronic Neuropsychiatric Illnesses
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Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Phylogenomics reveals extreme gene tree discordance in a lineage of dominant trees: hybridization, introgression, and incomplete lineage sorting blur deep evolutionary relationships despite clear species groupings in Eucalyptus subgenus Eudesmia
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Climate‐influenced boreotropical survival and rampant introgressions explain the thriving of New World grapes in the north temperate zone
inferred← citeshttps://doi.org/10.1111/jse.13137openalex-snapshot
Target enrichment data reveal rapid divergence with reticulate evolution of Maianthemum (Asparagaceae: Convallarioideae) in the Himalayan‐Hengduan Mountains and eastern Asia
inferred← citeshttps://doi.org/10.1111/mec.16787openalex-snapshot
Initiation of speciation across multiple dimensions in a rock‐restricted, tropical lizard
inferred← citeshttps://doi.org/10.1111/mec.17119openalex-snapshot
Genetic mixing in conservation translocations increases diversity of a keystone threatened species, Bettongia lesueur
inferred← citeshttps://doi.org/10.1111/mec.17301openalex-snapshot
Speciation across biomes: Rapid diversification with reproductive isolation in the Australian delicate mice
inferred← citeshttps://doi.org/10.1111/mec.70038openalex-snapshot
Caves as Species Pumps: Key Innovations, Isolation and Periodic Introgression Drive the World's Largest Cavefish Radiation in a Dynamic Karstic Landscape
inferred← citeshttps://doi.org/10.1111/mec.70235openalex-snapshot
Two Contrasting Demographic Processes Shape the Divergence and Evolution of the Widespread Arid Zone Specialist, Petrogale lateralis
inferred← citeshttps://doi.org/10.1111/syen.12490openalex-snapshot
The phylogeny of robber flies (Asilidae) inferred from ultraconserved elements
inferred← citeshttps://doi.org/10.1186/s12915-024-02031-8openalex-snapshot
The evolution of ectomycorrhizal symbiosis and host-plant switches are the main drivers for diversification of Amanitaceae (Agaricales, Basidiomycota)
inferred← citeshttps://doi.org/10.3389/fevo.2022.931644openalex-snapshot
Sequence Capture From Historical Museum Specimens: Maximizing Value for Population and Phylogenomic Studies
inferred← citeshttps://doi.org/10.3389/fgene.2024.1414074openalex-snapshot
Phylogenomic analysis and molecular identification of true fruit flies
inferred← citeshttps://doi.org/10.3389/fpls.2021.820997openalex-snapshot
Synthesis of Nuclear and Chloroplast Data Combined With Network Analyses Supports the Polyploid Origin of the Apple Tribe and the Hybrid Origin of the Maleae—Gillenieae Clade
inferred← citeshttps://doi.org/10.53846/goediss-9151openalex-snapshot
The Evolution of the Australian Amitermes group
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