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Genomic Distortion of Jawed Vertebrate Phylogeny

https://doi.org/10.64898/2026.06.28.735080

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

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The first record of a pterothrissin (Albuliformes, Albulidae) from the Muhi Quarry, mid-Cretaceous (Albian-Cenomanian) of Hidalgo, central Mexico

inferredcites →https://doi.org/10.1016/j.palaeo.2016.12.051openalex-snapshot

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inferredcites →https://doi.org/10.1016/j.ympev.2015.04.004openalex-snapshot

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Pliocene fossils support a New Zealand origin for the smallest extant penguins

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Facies characterisation and stratigraphy of the upper Maastrichtian to lower Danian Maastricht Formation, South Limburg, the Netherlands

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Batfishes from the Eocene of Monte Bolca

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Quantitative Analysis of the Timing of the Origin and Diversification of Extant Placental Orders

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A primitive sarcopterygian fish with an eyestalk

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Cretaceous eutherians and Laurasian origin for placental mammals near the K/T boundary

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The oldest known primate skeleton and early haplorhine evolution

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A Silurian placoderm with osteichthyan-like marginal jaw bones

inferredcites →https://doi.org/10.1038/nature13414openalex-snapshot

A primitive fish from the Cambrian of North America

inferredcites →https://doi.org/10.1038/nature14065openalex-snapshot

Osteichthyan-like cranial conditions in an Early Devonian stem gnathostome

inferredcites →https://doi.org/10.1038/nature14900openalex-snapshot

Evolutionary origin of the turtle skull

inferredcites →https://doi.org/10.1038/nature15697openalex-snapshot

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inferredcites →https://doi.org/10.1038/nature23654openalex-snapshot

Early members of ‘living fossil’ lineage imply later origin of modern ray-finned fishes

inferredcites →https://doi.org/10.1038/nature24483openalex-snapshot

A Jurassic gliding euharamiyidan mammal with an ear of five auditory bones

inferredcites →https://doi.org/10.1038/ncomms6996openalex-snapshot

The oldest known snakes from the Middle Jurassic-Lower Cretaceous provide insights on snake evolution

inferredcites →https://doi.org/10.1038/ng.2568openalex-snapshot

Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution

inferredcites →https://doi.org/10.1038/ng.2615openalex-snapshot

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inferredcites →https://doi.org/10.1038/ng.3526openalex-snapshot

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons

inferredcites →https://doi.org/10.1038/nmeth.4285openalex-snapshot

ModelFinder: fast model selection for accurate phylogenetic estimates

inferredcites →https://doi.org/10.1038/s41467-017-01801-zopenalex-snapshot

A new stem sarcopterygian illuminates patterns of character evolution in early bony fishes

inferredcites →https://doi.org/10.1038/s41467-021-23665-0openalex-snapshot

Whole-genome microsynteny-based phylogeny of angiosperms

inferredcites →https://doi.org/10.1038/s41467-021-25136-yopenalex-snapshot

Evolution and dispersal of snakes across the Cretaceous-Paleogene mass extinction

inferredcites →https://doi.org/10.1038/s41467-022-30091-3openalex-snapshot

The rapid evolution of lungfish durophagy

inferredcites →https://doi.org/10.1038/s41467-022-31508-9openalex-snapshot

Genomic insights into the secondary aquatic transition of penguins

inferredcites →https://doi.org/10.1038/s41467-022-34217-5openalex-snapshot

Evolutionary origins of the prolonged extant squamate radiation

inferredcites →https://doi.org/10.1038/s41467-023-42606-7openalex-snapshot

Middle ear innovation in Early Cretaceous eutherian mammals

inferredcites →https://doi.org/10.1038/s41467-023-43557-9openalex-snapshot

Bony-fish-like scales in a Silurian maxillate placoderm

inferredcites →https://doi.org/10.1038/s41559-017-0120openalex-snapshot

Scallop genome provides insights into evolution of bilaterian karyotype and development

inferredcites →https://doi.org/10.1038/s41559-018-0494-6openalex-snapshot

Explosive diversification of marine fishes at the Cretaceous–Palaeogene boundary

inferredcites →https://doi.org/10.1038/s41559-024-02586-3openalex-snapshot

Reduced evolutionary constraint accompanies ongoing radiation in deep-sea anglerfishes

inferredcites →https://doi.org/10.1038/s41586-018-0093-3openalex-snapshot

The origin of squamates revealed by a Middle Triassic lizard from the Italian Alps

inferredcites →https://doi.org/10.1038/s41586-018-0126-yopenalex-snapshot

Late-surviving stem mammal links the lowermost Cretaceous of North America and Gondwana

inferredcites →https://doi.org/10.1038/s41586-020-2096-0openalex-snapshot

Late Cretaceous neornithine from Europe illuminates the origins of crown birds

inferredcites →https://doi.org/10.1038/s41586-020-2100-8openalex-snapshot

Elpistostege and the origin of the vertebrate hand

inferredcites →https://doi.org/10.1038/s41586-020-2234-8openalex-snapshot

Skeleton of a Cretaceous mammal from Madagascar reflects long-term insularity

inferredcites →https://doi.org/10.1038/s41586-020-3011-4openalex-snapshot

Enigmatic dinosaur precursors bridge the gap to the origin of Pterosauria

inferredcites →https://doi.org/10.1038/s41586-021-03198-8openalex-snapshot

Giant lungfish genome elucidates the conquest of land by vertebrates

inferredcites →https://doi.org/10.1038/s41586-021-03834-3openalex-snapshot

A Triassic stem lepidosaur illuminates the origin of lizard-like reptiles

inferredcites →https://doi.org/10.1038/s41586-021-04341-1openalex-snapshot

A species-level timeline of mammal evolution integrating phylogenomic data

inferredcites →https://doi.org/10.1038/s41586-022-05233-8openalex-snapshot

Spiny chondrichthyan from the lower Silurian of South China

inferredcites →https://doi.org/10.1038/s41586-022-05332-6openalex-snapshot

Synchrotron tomography of a stem lizard elucidates early squamate anatomy

inferredcites →https://doi.org/10.1038/s41586-022-05646-5openalex-snapshot

Triassic stem caecilian supports dissorophoid origin of living amphibians

inferredcites →https://doi.org/10.1038/s41586-023-05936-6openalex-snapshot

Ancient gene linkages support ctenophores as sister to other animals

inferredcites →https://doi.org/10.1038/s41586-023-06434-5openalex-snapshot

Palaeospondylus and the early evolution of gnathostomes

inferredcites →https://doi.org/10.1038/s41586-024-07070-3openalex-snapshot

The hagfish genome and the evolution of vertebrates

inferredcites →https://doi.org/10.1038/s41586-024-07323-1openalex-snapshot

Complexity of avian evolution revealed by family-level genomes

inferredcites →https://doi.org/10.1038/s41586-024-07324-0openalex-snapshot

Phylogenomics and the rise of the angiosperms

inferredcites →https://doi.org/10.1038/s41586-024-07830-1openalex-snapshot

The genomes of all lungfish inform on genome expansion and tetrapod evolution

inferredcites →https://doi.org/10.1038/s41588-021-00914-yopenalex-snapshot

The bowfin genome illuminates the developmental evolution of ray-finned fishes

inferredcites →https://doi.org/10.1038/s41598-016-0001-8openalex-snapshot

Ultrastructural Characterization of the Lower Motor System in a Mouse Model of Krabbe Disease

inferredcites →https://doi.org/10.1038/s41598-017-17984-wopenalex-snapshot

Earliest known lepisosteoid extends the range of anatomically modern gars to the Late Jurassic

inferredcites →https://doi.org/10.1038/s41598-019-40845-7openalex-snapshot

Scale morphology and squamation pattern of Guiyu oneiros provide new insights into early osteichthyan body plan

inferredcites →https://doi.org/10.1038/s41598-020-58883-xopenalex-snapshot

A tiny new Middle Triassic stem-lepidosauromorph from Germany: implications for the early evolution of lepidosauromorphs and the Vellberg fauna

inferredcites →https://doi.org/10.1038/s42003-020-0953-xopenalex-snapshot

Parameter tuning differentiates granule cell subtypes enriching transmission properties at the cerebellum input stage

inferredcites →https://doi.org/10.1073/pnas.0334222100openalex-snapshot

Placental mammal diversification and the Cretaceous–Tertiary boundary

inferredcites →https://doi.org/10.1073/pnas.0400609101openalex-snapshot

Nuclear protein-coding genes support lungfish and not the coelacanth as the closest living relatives of land vertebrates

inferredcites →https://doi.org/10.1073/pnas.0900251106openalex-snapshot

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

inferredcites →https://doi.org/10.1073/pnas.101092598openalex-snapshot

Lessons from the past: Evolutionary impacts of mass extinctions

inferredcites →https://doi.org/10.1073/pnas.1206625109openalex-snapshot

Resolution of ray-finned fish phylogeny and timing of diversification

inferredcites →https://doi.org/10.1073/pnas.1211526110openalex-snapshot

Mass extinction of lizards and snakes at the Cretaceous–Paleogene boundary

inferredcites →https://doi.org/10.1073/pnas.1211733109openalex-snapshot

Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

inferredcites →https://doi.org/10.1073/pnas.1304661110openalex-snapshot

Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes

inferredcites →https://doi.org/10.1073/pnas.1403666111openalex-snapshot

Iterative adaptive radiations of fossil canids show no evidence for diversity-dependent trait evolution

inferredcites →https://doi.org/10.1073/pnas.1421707112openalex-snapshot

Oldest known euarchontan tarsals and affinities of Paleocene Purgatorius to Primates

inferredcites →https://doi.org/10.1073/pnas.1519387112openalex-snapshot

Mandibular and dental characteristics of Late Triassic mammaliaform Haramiyavia and their ramifications for basal mammal evolution

inferredcites →https://doi.org/10.1073/pnas.1607237113openalex-snapshot

Little evidence for enhanced phenotypic evolution in early teleosts relative to their living fossil sister group

inferredcites →https://doi.org/10.1073/pnas.1700188114openalex-snapshot

Early Paleocene landbird supports rapid phylogenetic and morphological diversification of crown birds after the K–Pg mass extinction

inferredcites →https://doi.org/10.1073/pnas.1704632114openalex-snapshot

Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous–Paleogene boundary

inferredcites →https://doi.org/10.1073/pnas.1719358115openalex-snapshot

Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data

inferredcites →https://doi.org/10.1073/pnas.2001424117openalex-snapshot

A Triassic stem-salamander from Kyrgyzstan and the origin of salamanders

inferredcites →https://doi.org/10.1073/pnas.2101780118openalex-snapshot

Fossilized cell structures identify an ancient origin for the teleost whole-genome duplication

inferredcites →https://doi.org/10.1073/pnas.2114100119openalex-snapshot

Middle Jurassic fossils document an early stage in salamander evolution

inferredcites →https://doi.org/10.1073/pnas.2123544119openalex-snapshot

Alternating regimes of shallow and deep-sea diversification explain a species-richness paradox in marine fishes

inferredcites →https://doi.org/10.1073/pnas.2319506121openalex-snapshot

A region of suppressed recombination misleads neoavian phylogenomics

inferredcites →https://doi.org/10.1073/pnas.2319696121openalex-snapshot

Genomes, fossils, and the concurrent rise of modern birds and flowering plants in the Late Cretaceous

inferredcites →https://doi.org/10.1073/pnas.72.2.646openalex-snapshot

A theory of evolution above the species level.

inferredcites →https://doi.org/10.1080/02724634.1984.10012024openalex-snapshot

The skull and pectoral girdle of the parasemionotid fishWatsonulus eugnathoidesfrom the Early Triassic Sakamena Group of Madagascar, with comments on the relationships of the holostean fishes

inferredcites →https://doi.org/10.1080/02724634.1994.10011566openalex-snapshot

New primitive carnivorans (Mammalia) from the Paleocene of western Canada, and their bearing on relationships of the order

inferredcites →https://doi.org/10.1080/02724634.1995.10011207openalex-snapshot

Iguanians From the Upper Cretaceous Djadochta Formation, Gobi Desert, China

inferredcites →https://doi.org/10.1080/02724634.1998.10011060openalex-snapshot

A new pipoid anuran from the Late Jurassic Morrison Formation at Dinosaur National Monument, Utah

inferredcites →https://doi.org/10.1080/02724634.2017.1278606openalex-snapshot

Morphological and histological evidence for the oldest known softshell turtles from Japan

inferredcites →https://doi.org/10.1080/02724634.2017.1398169openalex-snapshot

A well-preserved new mid-paleocene penguin (Aves, Sphenisciformes) from the Waipara Greensand in New Zealand

inferredcites →https://doi.org/10.1080/02724634.2018.1444619openalex-snapshot

A new lepidosauromorph reptile from the Middle Triassic (Ladinian) of Germany and its phylogenetic relationships

inferredcites →https://doi.org/10.1080/02724634.2018.1488137openalex-snapshot

A rare, articulated sturgeon (Chondrostei: Acipenseriformes) from the Upper Cretaceous of Dinosaur Provincial Park, Alberta, Canada

inferredcites →https://doi.org/10.1080/02724634.2020.1767638openalex-snapshot

A systematic review of the giant alligatoroidDeinosuchusfrom the Campanian of North America and its implications for the relationships at the root of Crocodylia

inferredcites →https://doi.org/10.1080/02724634.2020.1775091openalex-snapshot

Paddlefish and sturgeon (Chondrostei: Acipenseriformes: Polyodontidae and Acipenseridae) from lower Paleocene deposits of Montana, U.S.A.

inferredcites →https://doi.org/10.1080/02724634.2020.1801706openalex-snapshot

Phylogenetic placement of Adalatherium hui (Mammalia, Gondwanatheria) from the Late Cretaceous of Madagascar: implications for allotherian relationships

inferredcites →https://doi.org/10.1080/02755947.2016.1265030openalex-snapshot

Natural Hybridization of Lepisosteids: Implications for Managing the Alligator Gar

inferredcites →https://doi.org/10.1080/08912963.2024.2308212openalex-snapshot

Skull morphology of the enigmatic Genyornis newtoni Stirling and Zeitz, 1896 (Aves, Dromornithidae), with implications for functional morphology, ecology, and evolution in the context of Galloanserae

inferredcites →https://doi.org/10.1080/08912963.2024.2370015openalex-snapshot

Oldest record of a crown anomaluroid rodent from sub-Saharan Africa: a new genus and species from the early Oligocene Topernawi Formation of northern Kenya

inferredcites →https://doi.org/10.1080/10635150490522278openalex-snapshot

Explosive Radiations and the Reliability of Molecular Clocks: Island Endemic Radiations as a Test Case

inferredcites →https://doi.org/10.1080/10635150490522340openalex-snapshot

Molecular Phylogenetics of Squamata: The Position of Snakes, Amphisbaenians, and Dibamids, and the Root of the Squamate Tree

inferredcites →https://doi.org/10.1080/10635150701397635openalex-snapshot

Fossils, Molecules, Divergence Times, and the Origin of Lissamphibians

inferredcites →https://doi.org/10.1080/106351599260472openalex-snapshot

The Fossil Record of North American Mammals: Evidence for a Paleocene Evolutionary Radiation

inferredcites →https://doi.org/10.1080/14772019.2021.1968966openalex-snapshot

Redescription of ‘Amyzon’ brevipinne and remarks on North American Eocene catostomids (Cypriniformes: Catostomidae)

inferredcites →https://doi.org/10.1080/14772019.2022.2068386openalex-snapshot

Redescription, taxonomy and phylogenetic relationships ofBoavusMarsh, 1871 (Serpentes: Booidea) from the early–middle Eocene of the USA

inferredcites →https://doi.org/10.1080/14772019.2023.2168571openalex-snapshot

An earliest Paleocene squirrelfish (Teleostei: Beryciformes: Holocentroidea) and its bearing on the timescale of holocentroid evolution

inferredcites →https://doi.org/10.1080/14772019.2023.2223797openalex-snapshot

A new Mesozoic teleost of the subfamily Albulinae (Albuliformes: Albulidae) highlights the proto-Gulf of Mexico in the early diversification of extant bonefishes

inferredcites →https://doi.org/10.1093/bioinformatics/btt403openalex-snapshot

nhmmer: DNA homology search with profile HMMs

inferredcites →https://doi.org/10.1093/biosci/biy084openalex-snapshot

Rethinking Living Fossils

inferredcites →https://doi.org/10.1093/evolut/qpae028openalex-snapshot

The genomic signatures of evolutionary stasis

inferredcites →https://doi.org/10.1093/evolut/qpaf040openalex-snapshot

Cenozoic evolutionary history obscures the Mesozoic origins of acanthopterygian fishes

inferredcites →https://doi.org/10.1093/gbe/evab052openalex-snapshot

Resolving the Early Divergence Pattern of Teleost Fish Using Genome-Scale Data

inferredcites →https://doi.org/10.1093/gbe/evab161openalex-snapshot

Comparing Ultraconserved Elements and Exons for Phylogenomic Analyses of Middle American Cichlids: When Data Agree to Disagree

inferredcites →https://doi.org/10.1093/gbe/evab200openalex-snapshot

Taxonomic Uncertainty and the Anomaly Zone: Phylogenomics Disentangle a Rapid Radiation to Resolve Contentious Species ( Gila robusta Complex) in the Colorado River

inferredcites →https://doi.org/10.1093/gbe/evae189openalex-snapshot

Arthropod Phylotranscriptomics With a Special Focus on the Basal Phylogeny of the Myriapoda

inferredcites →https://doi.org/10.1093/gbe/evae272openalex-snapshot

Investigating the Impact of Whole-Genome Duplication on Transposable Element Evolution in Teleost Fishes

inferredcites →https://doi.org/10.1093/gbe/evv261openalex-snapshot

The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference

inferredcites →https://doi.org/10.1093/gbe/evy125openalex-snapshot

Global Rate Variation in Bony Vertebrates

inferredcites →https://doi.org/10.1093/iob/obad011openalex-snapshot

Syngnathoid Evolutionary History and the Conundrum of Fossil Misplacement

inferredcites →https://doi.org/10.1093/molbev/msaa015openalex-snapshot

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

inferredcites →https://doi.org/10.1093/molbev/msaa106openalex-snapshot

New Methods to Calculate Concordance Factors for Phylogenomic Datasets

inferredcites →https://doi.org/10.1093/molbev/msaa191openalex-snapshot

An Unbiased Molecular Approach Using 3′-UTRs Resolves the Avian Family-Level Tree of Life

inferredcites →https://doi.org/10.1093/molbev/msi075openalex-snapshot

Sister Group Relationship of Turtles to the Bird-Crocodilian Clade Revealed by Nuclear DNA–Coded Proteins

inferredcites →https://doi.org/10.1093/molbev/msj124openalex-snapshot

Early Penguin Fossils, Plus Mitochondrial Genomes, Calibrate Avian Evolution

inferredcites →https://doi.org/10.1093/molbev/msl150openalex-snapshot

Paleontological Evidence to Date the Tree of Life

inferredcites →https://doi.org/10.1093/molbev/msm193openalex-snapshot

A General Comparison of Relaxed Molecular Clock Models

inferredcites →https://doi.org/10.1093/molbev/msr228openalex-snapshot

Relaxed Clocks and Inferences of Heterogeneous Patterns of Nucleotide Substitution and Divergence Time Estimates across Whales and Dolphins (Mammalia: Cetacea)

inferredcites →https://doi.org/10.1093/molbev/mst010openalex-snapshot

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

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/msz067openalex-snapshot

Inadvertent Paralog Inclusion Drives Artifactual Topologies and Timetree Estimates in Phylogenomics

inferredcites →https://doi.org/10.1093/nargab/lqac064openalex-snapshot

Pitfalls of the site-concordance factor (sCF) as measure of phylogenetic branch support

inferredcites →https://doi.org/10.1093/ornithology/ukab048openalex-snapshot

Extinct crane-like birds (Eogruidae and Ergilornithidae) from the Cenozoic of Central Asia are indeed ostrich precursors

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a003974openalex-snapshot

Estimating Absolute Rates of Molecular Evolution and Divergence Times: A Penalized Likelihood Approach

inferredcites →https://doi.org/10.1093/sysbio/46.3.479openalex-snapshot

Morphology, Fossils, Divergence Timing, and the Phylogenetic Relationships of Gavialis

inferredcites →https://doi.org/10.1093/sysbio/syaa054openalex-snapshot

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

inferredcites →https://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)

inferredcites →https://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

inferredcites →https://doi.org/10.1093/sysbio/syac080openalex-snapshot

Phylogenomics of the Ancient and Species-Depauperate Gars Tracks 150 Million Years of Continental Fragmentation in the Northern Hemisphere

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