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Bushes in the Tree of Life

https://doi.org/10.1371/journal.pbio.0040352

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What this work says

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

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DNA Archives and Our Nearest Relative: The Trichotomy Problem Revisited

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Limitations of Metazoan 18S rRNA Sequence Data: Implications for Reconstructing a Phylogeny of the Animal Kingdom and Inferring the Reality of the Cambrian Explosion

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Thermal Adaptation of the Small Subunit Ribosomal RNA Gene: A Comparative Study

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Mathematical Elegance with Biochemical Realism: The Covarion Model of Molecular Evolution

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Patterns of speciation and limits to phylogenetic resolution

inferredcites →https://doi.org/10.1016/j.cub.2006.07.016openalex-snapshot

Chaetognath phylogenomics: a protostome with deuterostome-like development

inferredcites →https://doi.org/10.1016/j.cub.2006.07.017openalex-snapshot

Broad taxon and gene sampling indicate that chaetognaths are protostomes

inferredcites →https://doi.org/10.1016/j.tplants.2005.03.006openalex-snapshot

The place of Amborella within the radiation of angiosperms

inferredcites →https://doi.org/10.1016/s0166-218x(98)00080-8openalex-snapshot

Reconstructing phylogenies from nucleotide pattern probabilities: A survey and some new results

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Rare genomic changes as a tool for phylogenetics

inferredcites →https://doi.org/10.1016/s0960-9822(02)01426-4openalex-snapshot

Gene Transfer: Gene Swapping Craze Reaches Eukaryotes

inferredcites →https://doi.org/10.1016/s1055-7903(03)00035-6openalex-snapshot

Afrotherian phylogeny as inferred from complete mitochondrial genomes

inferredcites →https://doi.org/10.1016/s1055-7903(03)00118-0openalex-snapshot

A new phylogenetic marker, apolipoprotein B, provides compelling evidence for eutherian relationships

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A critical reappraisal of the fossil record of the bilaterian phyla

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Inferring complex phytogenies

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Structural biology and phylogenetic estimation

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Adaptive protein evolution in Drosophila

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Testing the neutral theory of molecular evolution with genomic data from Drosophila

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Genome-scale approaches to resolving incongruence in molecular phylogenies

inferredcites →https://doi.org/10.1038/nature03158openalex-snapshot

Unexpected complexity of the Wnt gene family in a sea anemone

inferredcites →https://doi.org/10.1038/nature04637openalex-snapshot

The pectoral fin of Tiktaalik roseae and the origin of the tetrapod limb

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A Devonian tetrapod-like fish and the evolution of the tetrapod body plan

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Genetic evidence for complex speciation of humans and chimpanzees

inferredcites →https://doi.org/10.1038/nrg1770openalex-snapshot

Hearing silence: non-neutral evolution at synonymous sites in mammals

inferredcites →https://doi.org/10.1073/pnas.0604065103openalex-snapshot

Early evolution of animal cell signaling and adhesion genes

inferredcites →https://doi.org/10.1073/pnas.191248498openalex-snapshot

Incomplete taxon sampling is not a problem for phylogenetic inference

inferredcites →https://doi.org/10.1073/pnas.201415598openalex-snapshot

Molecular synapomorphies resolve evolutionary relationships of extant jawed vertebrates

inferredcites →https://doi.org/10.1073/pnas.2133766100openalex-snapshot

Alu elements and hominid phylogenetics

inferredcites →https://doi.org/10.1073/pnas.82.14.4753openalex-snapshot

Ancient origin for Hawaiian Drosophilinae inferred from protein comparisons.

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The notion of the Cambrian pananimalia genome.

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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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Is It Better to Add Taxa or Characters to a Difficult Phylogenetic Problem?

inferredcites →https://doi.org/10.1080/106351598261021openalex-snapshot

Large-Scale Phylogenies and Measuring the Performance of Phylogenetic Estimators

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Genomic Divergences between Humans and Other Hominoids and the Effective Population Size of the Common Ancestor of Humans and Chimpanzees

inferredcites →https://doi.org/10.1086/383584openalex-snapshot

Inferring Phylogenies.

inferredcites →https://doi.org/10.1093/auk/105.3.565openalex-snapshot

The Stochastic Mode of Molecular Evolution: What Consequences for Systematic Investigations?

inferredcites →https://doi.org/10.1093/genetics/147.4.1497openalex-snapshot

Exceptional Convergent Evolution in a Virus

inferredcites →https://doi.org/10.1093/molbev/msh150openalex-snapshot

The Phylogenetic Relationship of Tetrapod, Coelacanth, and Lungfish Revealed by the Sequences of Forty-Four Nuclear Genes

inferredcites →https://doi.org/10.1093/molbev/msi102openalex-snapshot

The Opisthokonta and the Ecdysozoa May Not Be Clades: Stronger Support for the Grouping of Plant and Animal than for Animal and Fungi and Stronger Support for the Coelomata than Ecdysozoa

inferredcites →https://doi.org/10.1093/molbev/msi111openalex-snapshot

Multigene Analyses of Bilaterian Animals Corroborate the Monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia

inferredcites →https://doi.org/10.1093/molbev/msi121openalex-snapshot

More Genes or More Taxa? The Relative Contribution of Gene Number and Taxon Number to Phylogenetic Accuracy

inferredcites →https://doi.org/10.1093/molbev/msi179openalex-snapshot

A Retroposon Analysis of Afrotherian Phylogeny

inferredcites →https://doi.org/10.1093/oso/9780195068832.001.0001openalex-snapshot

The Causes of Molecular Evolution

inferredcites →https://doi.org/10.1093/oso/9780195099744.001.0001openalex-snapshot

Natural Hybridization and Evolution

inferredcites →https://doi.org/10.1093/oso/9780198566106.003.0014openalex-snapshot

How Much Can Evolved Characters Tell us about the Tree that Generated Them?

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a004213openalex-snapshot

Contribution of Homoplasy and of Ancestral Polymorphism to the Evolution of Genes in Anthropoid Primates

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025789openalex-snapshot

Detection of convergent and parallel evolution at the amino acid sequence level

inferredcites →https://doi.org/10.1093/sysbio/27.4.401openalex-snapshot

Cases in which Parsimony or Compatibility Methods will be Positively Misleading

inferredcites →https://doi.org/10.1093/sysbio/44.1.17openalex-snapshot

Performance of Phylogenetic Methods in Simulation

inferredcites →https://doi.org/10.1098/rspb.1996.0060openalex-snapshot

Excessive homoplasy in an evolutionarily constrained protein

inferredcites →https://doi.org/10.1098/rspb.2002.2025openalex-snapshot

A covarion-based method for detecting molecular adaptation: application to the evolution of primate mitochondrial genomes

inferredcites →https://doi.org/10.1101/gr.1347404openalex-snapshot

Coelomata and Not Ecdysozoa: Evidence From Genome-Wide Phylogenetic Analysis

inferredcites →https://doi.org/10.1111/j.0014-3820.2005.tb01072.xopenalex-snapshot

SPECIATIONAL HISTORY OF AUSTRALIAN GRASS FINCHES (POEPHILA) INFERRED FROM THIRTY GENE TREES

inferredcites →https://doi.org/10.1111/j.1558-5646.1985.tb00398.xopenalex-snapshot

FACTORS DETERMINING THE ACCURACY OF CLADOGRAM ESTIMATION: EVALUATION USING COMPUTER SIMULATION

inferredcites →https://doi.org/10.1126/science.1065889openalex-snapshot

Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology

inferredcites →https://doi.org/10.1126/science.1116759openalex-snapshot

Animal Evolution and the Molecular Signature of Radiations Compressed in Time

inferredcites →https://doi.org/10.1126/science.1122033openalex-snapshot

Population Size Does Not Influence Mitochondrial Genetic Diversity in Animals

inferredcites →https://doi.org/10.1126/science.276.5310.227openalex-snapshot

Phylogenetic Methods Come of Age: Testing Hypotheses in an Evolutionary Context

inferredcites →https://doi.org/10.1126/science.284.5423.2124openalex-snapshot

Phylogenetic Classification and the Universal Tree

inferredcites →https://doi.org/10.1126/science.287.5456.1283openalex-snapshot

Evidence for a High Frequency of Simultaneous Double-Nucleotide Substitutions

inferredcites →https://doi.org/10.1146/annurev.ecolsys.33.010802.150509openalex-snapshot

Troubleshooting Molecular Phylogenetic Analyses

inferredcites →https://doi.org/10.1186/gb-2004-5-10-117openalex-snapshot

Genomic and proteomic adaptations to growth at high temperature.

inferredcites →https://doi.org/10.1186/gb-2005-6-5-r41openalex-snapshot

Genome-scale evidence of the nematode-arthropod clade

inferredcites →https://doi.org/10.1371/journal.pgen.0020068openalex-snapshot

Discordance of Species Trees with Their Most Likely Gene Trees

inferredcites →https://doi.org/10.1554/br05-7.1openalex-snapshot

WHERE HAVE ALL THE CLADES GONE? A SYSTEMATIST'S TAKE ON INFERRING PHYLOGENIES1

inferredcites →https://doi.org/10.2307/1375605openalex-snapshot

The Major Features of Evolution

inferredcites →https://doi.org/10.2307/2405671openalex-snapshot

THE MAJOR FEATURES OF EVOLUTION

inferredcites →https://doi.org/10.5860/choice.30-2064openalex-snapshot

The causes of molecular evolution

inferredcites →https://doi.org/10.5860/choice.35-0883openalex-snapshot

Natural hybridization and evolution

inferredcites →https://doi.org/10.5860/choice.40-2180openalex-snapshot

Gaining ground: the origin and evolution of tetrapods

inferredcites →https://doi.org/10.5860/choice.42-4627openalex-snapshot

Assembling the tree of life

inferredcites →https://doi.org/10.5860/choice.50-3274openalex-snapshot

Gaining ground: the origin and evolution of tetrapods

What points at this work

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

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Phylogenomics of the tropical plant family Ochnaceae using targeted enrichment of nuclear genes and 250+ taxa

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Advances in Legume Systematics 14. Classification of Caesalpinioideae. Part 2: Higher-level classification

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Genome reduction as the dominant mode of evolution

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Explosive radiation and spatial expansion across the cold environments of the Old World in an avian family

inferred← citeshttps://doi.org/10.1002/sae2.70187openalex-snapshot

Complete Chloroplast Genome of Indonesian Sugarcane ( Saccharum ‘Bululawang’): Comparative, Structural, and Evolutionary Analysis of Photosystem I‐Encoding Genes

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Molecular‐based phylogenetic placement and revision of Micrasepalum ( Spermacoceae‐Rubiaceae )

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Paganuccia icatuensis (Rubiaceae), a new genus and species from Bahia, Brazil, with a key to all the genera of the tribe Spermacoceae in the Americas

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The phylogenetic position of milkweeds (Apocynaceae subfamilies Secamonoideae and Asclepiadoideae): Evidence from the nucleus and chloroplast

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Gene Transfer and the Reconstruction of Life’s Early History from Genomic Data

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A Guide to Phylogenomic Inference

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Phylogenomics

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Bayesian Phylogenomic Dating

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Mayr Versus Woese: Akaryotes and Eukaryotes

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An Optimization-Based Sampling Scheme for Phylogenetic Trees

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Developmental gene expression as a phylogenetic data class: support for the monophyly of Arachnopulmonata

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Phylogenetic relationships and divergence time of Hydrangea sect. Macrophyllae (Hydrangeaceae) revealed by genome-wide SNPs

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Satellite-DNA diversification and the evolution of major lineages in Cardueae (Carduoideae Asteraceae)

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Revisiting the Darwinian shortfall in biodiversity conservation

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Establishing the foundation for an applied molecular taxonomy of otters in Southeast Asia

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Multilocus phylogeography and phylogenetics using sequence-based markers

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Gene Transfer and the Reconstruction of Life’s Early History from Genomic Data

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Phylogenetic relationships in Betula (Betulaceae) based on AFLP markers

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Summary of phylogeny in subfamily Colobinae (Primate: Cercopithecidae)

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A densely sampled molecular phylogeny of Tachigali (Leguminosae), an evolutionarily successful lineage of neotropical ant-housing canopy trees

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Deep Phylogeny and Evolution of Sponges (Phylum Porifera)

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Characterisation, evolution and expression analysis of heat shock protein 20 genes from Japanese flounder (Paralichthys olivaceus) in response to Edwardsiella tarda infection

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Placozoa and the evolution of Metazoa and intrasomatic cell differentiation

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Rooted phylogeny of the three superkingdoms

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Toward next-generation sequencing of mitochondrial genomes — Focus on parasitic worms of animals and biotechnological implications

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Evolution of Gene Regulatory Networks Controlling Body Plan Development

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Whole-Body Acoel Regeneration Is Controlled by Wnt and Bmp-Admp Signaling

inferred← citeshttps://doi.org/10.1016/j.cub.2017.08.054openalex-snapshot

Embracing Uncertainty in Reconstructing Early Animal Evolution

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The evolution of insect biodiversity

inferred← citeshttps://doi.org/10.1016/j.cub.2022.11.014openalex-snapshot

Genome-level analyses resolve an ancient lineage of symbiotic ascomycetes

inferred← citeshttps://doi.org/10.1016/j.cub.2025.10.019openalex-snapshot

Robust termite phylogenies built using transposable element composition and insertion events

inferred← citeshttps://doi.org/10.1016/j.dsr2.2009.05.016openalex-snapshot

Cryptic species, phenotypic plasticity, and complex life histories: Assessing deep-sea faunal diversity with molecular markers

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Sequence length bounds for resolving a deep phylogenetic divergence

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Three highly variable genome regions of the four dengue virus serotypes can accurately recapitulate the CDS phylogeny

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Histories of molecules: Reconciling the past

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When integration fails: Prokaryote phylogeny and the tree of life

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Deciphering ancient rapid radiations

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Post-molecular systematics and the future of phylogenetics

inferred← citeshttps://doi.org/10.1016/j.ympev.2007.03.005openalex-snapshot

Multiple nuclear loci reveal patterns of incomplete lineage sorting and complex species history within western mouse lemurs (Microcebus)

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Mitochondrial DNA reveals the genealogical history of the snake-eyed lizards (Ophisops elegans and O. occidentalis) (Sauria: Lacertidae)

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Working through polytomies: Auklets revisited

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Phylogeny and biogeography of the rice tribe (Oryzeae): Evidence from combined analysis of 20 chloroplast fragments

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Phylogenetics of Coenonymphina (Nymphalidae: Satyrinae) and the problem of rooting rapid radiations

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Phylogenetic studies of sinipercid fish (Perciformes: Sinipercidae) based on multiple genes, with first application of an immune-related gene, the virus-induced protein (viperin) gene

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Analyzing the relationship between sequence divergence and nodal support using Bayesian phylogenetic analyses

inferred← citeshttps://doi.org/10.1016/j.ympev.2012.07.010openalex-snapshot

Molecular phylogeny of extant equids and effects of ancestral polymorphism in resolving species-level phylogenies

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Deep metazoan phylogeny: When different genes tell different stories

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Unexpected phylogenetic positions of the genera Rupirana and Crossodactylodes reveal insights into the biogeography and reproductive evolution of leptodactylid frogs

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A multi-locus phylogeny suggests an ancient hybridization event between Campephilus and melanerpine woodpeckers (Aves: Picidae)

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Phylogenetic relationships and genome divergence among the AA- genome species of the genus Oryza as revealed by 53 nuclear genes and 16 intergenic regions

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Molecular evidence for the monophyly of flatfishes (Carangimorpharia: Pleuronectiformes)

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Molecular systematics of the deep-sea bamboo corals (Octocorallia: Isididae: Keratoisidinae) from New Zealand with descriptions of two new species of Keratoisis

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Phylogenetic signal detection from an ancient rapid radiation: Effects of noise reduction, long-branch attraction, and model selection in crown clade Apocynaceae

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Effectiveness of phylogenomic data and coalescent species-tree methods for resolving difficult nodes in the phylogeny of advanced snakes (Serpentes: Caenophidia)

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Filling in the gaps of the papilionoid legume phylogeny: The enigmatic Amazonian genus Petaladenium is a new branch of the early-diverging Amburaneae clade

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Multilocus species tree analyses resolve the ancient radiation of the subtribe Zizaniinae (Poaceae)

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Explosive radiation or uninformative genes? Origin and early diversification of tachinid flies (Diptera: Tachinidae)

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Utilizing next-generation sequencing to resolve the backbone of the Core Goodeniaceae and inform future taxonomic and floral form studies

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Molecular systematics of the Amazonian genus Aldina, a phylogenetically enigmatic ectomycorrhizal lineage of papilionoid legumes

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Phylogenomic analysis of yellowjackets and hornets (Hymenoptera: Vespidae, Vespinae)

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A pilot study applying the plant Anchored Hybrid Enrichment method to New World sages (Salvia subgenus Calosphace; Lamiaceae)

inferred← citeshttps://doi.org/10.1016/j.ympev.2017.10.004openalex-snapshot

Assessing the utility of transcriptome data for inferring phylogenetic relationships among coleoid cephalopods

inferred← citeshttps://doi.org/10.1016/j.ympev.2017.11.008openalex-snapshot

Resolving taxonomic turbulence and uncovering cryptic diversity in the musk turtles (Sternotherus) using robust demographic modeling

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Discordance between genomic divergence and phenotypic variation in a rapidly evolving avian genus (Motacilla)

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Combining high-throughput sequencing and targeted loci data to infer the phylogeny of the “Adenocalymma-Neojobertia” clade (Bignonieae, Bignoniaceae)

inferred← citeshttps://doi.org/10.1016/j.ympev.2018.03.023openalex-snapshot

Phylogenomic evidence for a recent and rapid radiation of lizards in the Patagonian Liolaemus fitzingerii species group

inferred← citeshttps://doi.org/10.1016/j.ympev.2018.06.006openalex-snapshot

Improving phylogenetic inference of core Chlorophyta using chloroplast sequences with strong phylogenetic signals and heterogeneous models

inferred← citeshttps://doi.org/10.1016/j.ympev.2018.07.012openalex-snapshot

Exploring data processing strategies in NGS target enrichment to disentangle radiations in the tribe Cardueae (Compositae)

inferred← citeshttps://doi.org/10.1016/j.ympev.2020.106779openalex-snapshot

Investigating the utility of traditional and genomic multi-locus datasets to resolve relationships in Lipaugus and Tijuca (Cotingidae)

inferred← citeshttps://doi.org/10.1016/j.ympev.2020.107012openalex-snapshot

Swimming through the sands of the Sahara and Arabian deserts: Phylogeny of sandfish skinks (Scincidae, Scincus) reveals a recent and rapid diversification

inferred← citeshttps://doi.org/10.1016/j.ympev.2022.107700openalex-snapshot

Ultraconserved elements-based phylogenomic systematics of the snake superfamily Elapoidea, with the description of a new Afro-Asian family

inferred← citeshttps://doi.org/10.1016/j.ympev.2024.108197openalex-snapshot

Reticulate evolution: Detection and utility in the phylogenomics era

inferred← citeshttps://doi.org/10.1016/j.ympev.2024.108246openalex-snapshot

Gondwanan relic or recent arrival? The biogeographic origins and systematics of Australian tarantulas

inferred← citeshttps://doi.org/10.1017/9781108938891.013openalex-snapshot

Genomic Perspectives

inferred← citeshttps://doi.org/10.1017/9781108938891.014openalex-snapshot

Using Comparative Genomics to Resolve the Origin and Early Evolution of Snakes

inferred← citeshttps://doi.org/10.1017/s0094837300026403openalex-snapshot

The ecology of invasion: acquisition and loss of the siphonal canal in gastropods

inferred← citeshttps://doi.org/10.1038/hdy.2012.100openalex-snapshot

Reconstruction of phylogenetic relationships in a highly reticulate group with deep coalescence and recent speciation (Hieracium, Asteraceae)

inferred← citeshttps://doi.org/10.1038/nature12130openalex-snapshot

Inferring ancient divergences requires genes with strong phylogenetic signals

inferred← citeshttps://doi.org/10.1038/ncomms5956openalex-snapshot

Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times

inferred← citeshttps://doi.org/10.1038/nrg2062openalex-snapshot

The choice of model organisms in evo–devo

inferred← citeshttps://doi.org/10.1038/nrg2226openalex-snapshot

Evolutionary developmental biology and genomics

inferred← citeshttps://doi.org/10.1038/s41467-023-36139-2openalex-snapshot

Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces

inferred← citeshttps://doi.org/10.1038/s41477-021-00990-2openalex-snapshot

Insights into angiosperm evolution, floral development and chemical biosynthesis from the Aristolochia fimbriata genome

inferred← citeshttps://doi.org/10.1038/s41559-017-0126openalex-snapshot

Contentious relationships in phylogenomic studies can be driven by a handful of genes

inferred← citeshttps://doi.org/10.1038/s41576-018-0043-9openalex-snapshot

Understanding explosive diversification through cichlid fish genomics

inferred← citeshttps://doi.org/10.1038/s41576-023-00620-xopenalex-snapshot

Incongruence in the phylogenomics era

inferred← citeshttps://doi.org/10.1038/srep41005openalex-snapshot

Multiple measures could alleviate long-branch attraction in phylogenomic reconstruction of Cupressoideae (Cupressaceae)

inferred← citeshttps://doi.org/10.1071/is11002openalex-snapshot

The evolutionary and biogeographic history of the armoured harvestmen – Laniatores phylogeny based on ten molecular markers, with the description of two new families of Opiliones (Arachnida)

inferred← citeshttps://doi.org/10.1073/pnas.0800884105openalex-snapshot

Stable isotope evidence for an amphibious phase in early proboscidean evolution

inferred← citeshttps://doi.org/10.1073/pnas.0900251106openalex-snapshot

Paleocene emergence of elephant relatives and the rapid radiation of African ungulates

inferred← citeshttps://doi.org/10.1073/pnas.0901808106openalex-snapshot

The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages

inferred← citeshttps://doi.org/10.1073/pnas.0909377106openalex-snapshot

Whole-genome phylogeny of mammals: Evolutionary information in genic and nongenic regions

inferred← citeshttps://doi.org/10.1073/pnas.2000388117openalex-snapshot

Triad hybridization via a conduit species

inferred← citeshttps://doi.org/10.1073/pnas.2107434118openalex-snapshot

Morphological ghosts of introgression in Darwin’s finch populations

inferred← citeshttps://doi.org/10.1073/pnas.2116841119openalex-snapshot

Diploid-dominant life cycles characterize the early evolution of Fungi

inferred← citeshttps://doi.org/10.1075/jhl.17009.veropenalex-snapshot

Detecting non-tree-like signal using multiple tree topologies

inferred← citeshttps://doi.org/10.1080/10635150802166053openalex-snapshot

Branch Lengths, Support, and Congruence: Testing the Phylogenomic Approach with 20 Nuclear Loci in Snakes

inferred← citeshttps://doi.org/10.1080/10635150802306527openalex-snapshot

Assessing the Performance of Single-Copy Genes for Recovering Robust Phylogenies

inferred← citeshttps://doi.org/10.1080/14772000.2012.699477openalex-snapshot

A standardized reanalysis of molecular phylogenetic hypotheses of Gobioidei

inferred← citeshttps://doi.org/10.1089/cmb.2011.0164openalex-snapshot

An Optimization-Based Sampling Scheme for Phylogenetic Trees

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.001.0001openalex-snapshot

Animal Evolution

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.002.0003openalex-snapshot

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.002.0004openalex-snapshot

Foreword

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.002.0007openalex-snapshot

Contributors

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.002.0008openalex-snapshot

Introduction

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0002openalex-snapshot

The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0003openalex-snapshot

Genomic, phylogenetic, and cell biological insights into metazoan origins

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0004openalex-snapshot

The mouth, the anus, and the blastopore—open questions about questionable openings

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0005openalex-snapshot

Origins of metazoan body plans: the larval revolution

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0006openalex-snapshot

Assembling the spiralian tree of life

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0007openalex-snapshot

The evolution of nervous system centralization

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0008openalex-snapshot

The origins and evolution of the Ecdysozoa

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0009openalex-snapshot

Deciphering deuterostome phylogeny: molecular, morphological, and palaeontological perspectives

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0010openalex-snapshot

Molecular genetic insights into deuterostome evolution from the direct-developing hemichordateSaccoglossus kowalevskii

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0012openalex-snapshot

Improvement of molecular phylogenetic inference and the phylogeny of Bilateria

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0014openalex-snapshot

The animal in the genome: comparative genomics and evolution

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0015openalex-snapshot

MicroRNAs and metazoan phylogeny: big trees from little genes

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0016openalex-snapshot

The evolution of developmental gene networks: lessons from comparative studies on holometabolous insects

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0018openalex-snapshot

Reassembling animal evolution: a four-dimensional puzzle

inferred← citeshttps://doi.org/10.1093/bioinformatics/btab096openalex-snapshot

PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data

inferred← citeshttps://doi.org/10.1093/gbe/evac129openalex-snapshot

A Practical Guide to Design and Assess a Phylogenomic Study

inferred← citeshttps://doi.org/10.1093/gbe/evp011openalex-snapshot

Analysis of Rare Genomic Changes Does Not Support the Unikont–Bikont Phylogeny and Suggests Cyanobacterial Symbiosis as the Point of Primary Radiation of Eukaryotes

inferred← citeshttps://doi.org/10.1093/gbe/evr121openalex-snapshot

Random Addition Concatenation Analysis: A Novel Approach to the Exploration of Phylogenomic Signal Reveals Strong Agreement between Core and Shell Genomic Partitions in the Cyanobacteria

inferred← citeshttps://doi.org/10.1093/gbe/evw053openalex-snapshot

Maintenance of Species Boundaries Despite Ongoing Gene Flow in Ragworts

inferred← citeshttps://doi.org/10.1093/icb/icm040openalex-snapshot

Can we ever identify the Urmetazoan?

inferred← citeshttps://doi.org/10.1093/icb/icz006openalex-snapshot

Evolution of the Gekkotan Adhesive System: Does Digit Anatomy Point to One or More Origins?

inferred← citeshttps://doi.org/10.1093/jambio/lxag056openalex-snapshot

Tracing ancient life through the genomic record

inferred← citeshttps://doi.org/10.1093/molbev/msab038openalex-snapshot

Taxonomic Sampling and Rare Genomic Changes Overcome Long-Branch Attraction in the Phylogenetic Placement of Pseudoscorpions

inferred← citeshttps://doi.org/10.1093/molbev/msad175openalex-snapshot

Major Revisions in Pancrustacean Phylogeny and Evidence of Sensitivity to Taxon Sampling

inferred← citeshttps://doi.org/10.1093/molbev/msag182openalex-snapshot

Improved gene tree inference from removing alignment errors both from focal genes and when training substitution models

inferred← citeshttps://doi.org/10.1093/molbev/msm218openalex-snapshot

Analysis of Rare Amino Acid Replacements Supports the Coelomata Clade

inferred← citeshttps://doi.org/10.1093/molbev/msn108openalex-snapshot

The Deep Archaeal Roots of Eukaryotes

inferred← citeshttps://doi.org/10.1093/molbev/msn143openalex-snapshot

Frequent and Widespread Parallel Evolution of Protein Sequences

inferred← citeshttps://doi.org/10.1093/molbev/msp202openalex-snapshot

Molecular Phylogenetics, Temporal Diversification, and Principles of Evolution in the Mustard Family (Brassicaceae)

inferred← citeshttps://doi.org/10.1093/molbev/msr285openalex-snapshot

A Consistent Phylogenetic Backbone for the Fungi

inferred← citeshttps://doi.org/10.1093/molbev/msr297openalex-snapshot

Corolla Monosymmetry: Evolution of a Morphological Novelty in the Brassicaceae Family

inferred← citeshttps://doi.org/10.1093/molbev/msu061openalex-snapshot

Novel Information Theory-Based Measures for Quantifying Incongruence among Phylogenetic Trees

inferred← citeshttps://doi.org/10.1093/molbev/msu235openalex-snapshot

Phylogenomic Interrogation of Arachnida Reveals Systemic Conflicts in Phylogenetic Signal

inferred← citeshttps://doi.org/10.1093/nar/gkp089openalex-snapshot

Darwinian evolution in the light of genomics

inferred← citeshttps://doi.org/10.1093/nar/gkv1248openalex-snapshot

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

inferred← citeshttps://doi.org/10.1093/sysbio/syaa034openalex-snapshot

Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life

inferred← citeshttps://doi.org/10.1093/sysbio/syaa041openalex-snapshot

The Origin of the Legumes is a Complex Paleopolyploid Phylogenomic Tangle Closely Associated with the Cretaceous–Paleogene (K–Pg) Mass Extinction Event

inferred← citeshttps://doi.org/10.1093/sysbio/syaa054openalex-snapshot

Congruence and Conflict in the Higher-Level Phylogenetics of Squamate Reptiles: An Expanded Phylogenomic Perspective

inferred← citeshttps://doi.org/10.1093/sysbio/syab018openalex-snapshot

Testing the Utility of Alternative Metrics of Branch Support to Address the Ancient Evolutionary Radiation of Tunas, Stromateoids, and Allies (Teleostei: Pelagiaria)

inferred← citeshttps://doi.org/10.1093/sysbio/syab028openalex-snapshot

Phylogenomics and Historical Biogeography of Seahorses, Dragonets, Goatfishes, and Allies (Teleostei: Syngnatharia): Assessing Factors Driving Uncertainty in Biogeographic Inferences

inferred← citeshttps://doi.org/10.1093/sysbio/syac006openalex-snapshot

Between a Rock and a Hard Polytomy: Phylogenomics of the Rock-Dwelling Mbuna Cichlids of Lake Malaŵi

inferred← citeshttps://doi.org/10.1093/sysbio/syae010openalex-snapshot

Phylogenomics of Neogastropoda: The Backbone Hidden in the Bush

inferred← citeshttps://doi.org/10.1093/sysbio/syaf043openalex-snapshot

Accelerating Maximum Likelihood Phylogenetic Inference via Early Stopping to Evade (Over-)optimization

inferred← citeshttps://doi.org/10.1093/sysbio/syp012openalex-snapshot

Paleontology, Genomics, and Combined-Data Phylogenetics: Can Molecular Data Improve Phylogeny Estimation for Fossil Taxa?

inferred← citeshttps://doi.org/10.1093/sysbio/sys036openalex-snapshot

Phylogenetic Signal and Noise: Predicting the Power of a Data Set to Resolve Phylogeny

inferred← citeshttps://doi.org/10.1093/sysbio/sys049openalex-snapshot

Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

inferred← citeshttps://doi.org/10.1093/sysbio/sys093openalex-snapshot

Relaxed Phylogenetics and the Palaeoptera Problem: Resolving Deep Ancestral Splits in the Insect Phylogeny

inferred← citeshttps://doi.org/10.1093/sysbio/syt039openalex-snapshot

Addressing Gene Tree Discordance and Non-Stationarity to Resolve a Multi-Locus Phylogeny of the Flatfishes (Teleostei: Pleuronectiformes)

inferred← citeshttps://doi.org/10.1093/sysbio/syu054openalex-snapshot

Chloroplast Phylogenomic Analyses Resolve Deep-Level Relationships of an Intractable Bamboo Tribe Arundinarieae (Poaceae)

inferred← citeshttps://doi.org/10.1093/sysbio/syv053openalex-snapshot

Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies

inferred← citeshttps://doi.org/10.1093/sysbio/syw014openalex-snapshot

Analysis of a Rapid Evolutionary Radiation Using Ultraconserved Elements: Evidence for a Bias in Some Multispecies Coalescent Methods

inferred← citeshttps://doi.org/10.1093/sysbio/syw069openalex-snapshot

Disentangling Incomplete Lineage Sorting and Introgression to Refine Species-Tree Estimates for Lake Tanganyika Cichlid Fishes

inferred← citeshttps://doi.org/10.1093/sysbio/syw084openalex-snapshot

Who Let the CAT Out of the Bag? Accurately Dealing with Substitutional Heterogeneity in Phylogenomic Analyses

inferred← citeshttps://doi.org/10.1093/sysbio/syx041openalex-snapshot

Why Do Phylogenomic Data Sets Yield Conflicting Trees? Data Type Influences the Avian Tree of Life more than Taxon Sampling

inferred← citeshttps://doi.org/10.1093/sysbio/syz011openalex-snapshot

A Critical Appraisal of the Placement of Xiphosura (Chelicerata) with Account of Known Sources of Phylogenetic Error

inferred← citeshttps://doi.org/10.1093/sysbio/syz044openalex-snapshot

Phylogenomics Uncovers Confidence and Conflict in the Rapid Radiation of Australo-Papuan Rodents

inferred← citeshttps://doi.org/10.1098/rsbl.2012.0703openalex-snapshot

Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species

inferred← citeshttps://doi.org/10.1098/rspb.2011.1430openalex-snapshot

Cretaceous origin and repeated tertiary diversification of the redefined butterflies

inferred← citeshttps://doi.org/10.1098/rspb.2012.0744openalex-snapshot

Insect phylogenomics: results, problems and the impact of matrix composition

inferred← citeshttps://doi.org/10.1098/rspb.2012.1630openalex-snapshot

Multiple nuclear genes and retroposons support vicariance and dispersal of the palaeognaths, and an Early Cretaceous origin of modern birds

inferred← citeshttps://doi.org/10.1098/rstb.2007.2238openalex-snapshot

Back in time: a new systematic proposal for the Bilateria

inferred← citeshttps://doi.org/10.1098/rstb.2007.2240openalex-snapshot

Problematica old and new

inferred← citeshttps://doi.org/10.1098/rstb.2008.0171openalex-snapshot

The genetic code can cause systematic bias in simple phylogenetic models

inferred← citeshttps://doi.org/10.1098/rstb.2009.0033openalex-snapshot

Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life

inferred← citeshttps://doi.org/10.1098/rstb.2012.0430openalex-snapshot

A world of cytochrome P450s

inferred← citeshttps://doi.org/10.1099/ijs.0.000090openalex-snapshot

Taxogenomics of the order Chlamydiales

inferred← citeshttps://doi.org/10.1099/vir.0.014423-0openalex-snapshot

Sequence diversity, population genetics and potential recombination events in grapevine rupestris stem pitting-associated virus in Pacific North-West vineyards

inferred← citeshttps://doi.org/10.1101/164459openalex-snapshot

Using mitochondrial genomes to infer phylogenetic relationships among the oldest extant winged insects (Palaeoptera)

inferred← citeshttps://doi.org/10.1101/2020.04.20.049999openalex-snapshot

Disentangling biological and analytical factors that give rise to outlier genes in phylogenomic matrices

inferred← citeshttps://doi.org/10.1101/2021.07.27.453752openalex-snapshot

Substitution Rate Variation in a Robust Procellariiform Seabird Phylogeny is not Solely Explained by Body Mass, Flight Efficiency, Population Size or Life History Traits

inferred← citeshttps://doi.org/10.1101/2023.09.20.556338openalex-snapshot

A genome-scale Opisthokonta tree of life: toward phylogenomic resolution of ancient divergences

inferred← citeshttps://doi.org/10.1101/2024.07.04.602058openalex-snapshot

Much Ado About Nothing: Accelerating Maximum Likelihood Phylogenetic Inference via Early Stopping to evade (Over-)optimization

inferred← citeshttps://doi.org/10.1101/cshperspect.a016188openalex-snapshot

The Dispersed Archaeal Eukaryome and the Complex Archaeal Ancestor of Eukaryotes

inferred← citeshttps://doi.org/10.1101/gr.5918807openalex-snapshot

Using genomic data to unravel the root of the placental mammal phylogeny

inferred← citeshttps://doi.org/10.1101/sqb.2009.74.006openalex-snapshot

The Phylogenetic Forest and the Quest for the Elusive Tree of Life

inferred← citeshttps://doi.org/10.1109/csci58124.2022.00110openalex-snapshot

Data-Mining with Three Genome-Scale Approaches Supports that Lungfish is the Closest Living Relative of Land Vertebrate, but not Coelacanth

inferred← citeshttps://doi.org/10.1109/csci62032.2023.00101openalex-snapshot

The Most Frequent Gene Tree Based on Phylogenomic Data Reveals Insights into the Origins of Land Vertebrates

inferred← citeshttps://doi.org/10.1111/1755-0998.12248openalex-snapshot

Identification of putative orthologous genes for the phylogenetic reconstruction of temperate woody bamboos ( P oaceae: B ambusoideae)

inferred← citeshttps://doi.org/10.1111/bij.12667openalex-snapshot

Phylogeography of the micro-endemicPedicia staryigroup (Insecta: Diptera): evidence of relict biodiversity in the Carpathians

inferred← citeshttps://doi.org/10.1111/cla.12191openalex-snapshot

Optimal data partitioning, multispecies coalescent and Bayesian concordance analyses resolve early divergences of the grape family (Vitaceae)

inferred← citeshttps://doi.org/10.1111/cla.12570openalex-snapshot

Introgression and incomplete lineage sorting blurred phylogenetic relationships across the genomes of sclerophyllous oaks from southwest China

inferred← citeshttps://doi.org/10.1111/j.1096-0031.2007.00178.xopenalex-snapshot

Molecular phylogeny of songbirds (Aves: Passeriformes) and the relative utility of common nuclear marker loci

inferred← citeshttps://doi.org/10.1111/j.1096-0031.2008.00213.xopenalex-snapshot

Finding an upper limit for gap costs in direct optimization parsimony

inferred← citeshttps://doi.org/10.1111/j.1096-0031.2010.00337.xopenalex-snapshot

The mega-matrix tree of life: using genome-scale horizontal gene transfer and sequence evolution data as information about the vertical history of life

inferred← citeshttps://doi.org/10.1111/j.1096-0031.2012.00405.xopenalex-snapshot

Revival of Palaeoptera—head characters support a monophyletic origin of Odonata and Ephemeroptera (Insecta)

inferred← citeshttps://doi.org/10.1111/j.1096-3642.2011.00752.xopenalex-snapshot

Molecular phylogeny and evolution of the Perissodactyla

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