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Bayesian Tip-dated Phylogenetics: Topological Effects, Stratigraphic Fit and the Early Evolution of Mammals
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Stratigraphy and phylogeny
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Ear ossicle morphology of the Jurassic euharamiyidan Arboroharamiya and evolution of mammalian middle ear
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Forum. Stratigraphic Fit to Phylogenies: A Proposed Solution,
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Recent Advances in Methods of Phylogenetic Inference
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The Phylogenetic Affinities of the Enigmatic Mammalian Clade Gondwanatheria
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Comparison of phylogenetic trees
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Evidence for a Mid-Jurassic Adaptive Radiation in Mammals
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Morphological Phylogenetics in the Genomic Age
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The evolutionary relationships and age of Homo naledi: An assessment using dated Bayesian phylogenetic methods
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Sampling-through-time in birth–death trees
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New chronostratigraphic constraints on the Yixian Formation with implications for the Jehol Biota
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STRATIGRAPHY IN PHYLOGENY RECONSTRUCTION—REPLY TO SMITH (2000)
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Comparing the stratigraphic record to estimates of phylogeny
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Stratigraphic tests of cladistic hypotheses
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A likelihood approach for evaluating estimates of phylogenetic relationships among fossil taxa
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Bayesian statistical inference for psychological research.
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Quality of the fossil record through time
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Haramiyids and Triassic mammalian evolution
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Transformation and diversification in early mammal evolution
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A Jurassic eutherian mammal and divergence of marsupials and placentals
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A new arboreal haramiyid shows the diversity of crown mammals in the Jurassic period
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Three new Jurassic euharamiyidan species reinforce early divergence of mammals
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First cranial remains of a gondwanatherian mammal reveal remarkable mosaicism
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New evidence for mammaliaform ear evolution and feeding adaptation in a Jurassic ecosystem
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The oldest record of ornithuromorpha from the early cretaceous of China
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Late-surviving stem mammal links the lowermost Cretaceous of North America and Gondwana
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An Early Cretaceous eutherian and the placental–marsupial dichotomy
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New Australian sauropods shed light on Cretaceous dinosaur palaeobiogeography
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Birth–death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV)
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The fossilized birth–death process for coherent calibration of divergence-time estimates
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Mandibular and dental characteristics of Late Triassic mammaliaform Haramiyavia and their ramifications for basal mammal evolution
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Phylogeny of the Ichthyopterygia
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The vertebrates of the Jurassic Daohugou Biota of northeastern China
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Tacuarembemys kusterae , gen. et sp. nov., a new Late Jurassic–?earliest Cretaceous continental turtle from western Gondwana
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Phylogeny of the Ichthyopterygia incorporating recent discoveries from South China
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A Likelihood Approach to Estimating Phylogeny from Discrete Morphological Character Data
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Congruence Between Phylogeny and Stratigraphy: Randomization Tests and the Gap Excess Ratio
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APE: Analyses of Phylogenetics and Evolution in R language
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phangorn: phylogenetic analysis in R
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RWTY (R We There Yet): An R package for examining convergence of Bayesian phylogenetic analyses
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Mesozoic mammals of China: implications for phylogeny and early evolution of mammals
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The Origin and Evolution of Mammals
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MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
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A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera
inferredcites →https://doi.org/10.1093/sysbio/syt110openalex-snapshot
Morphological Clocks in Paleontology, and a Mid-Cretaceous Origin of Crown Aves
inferredcites →https://doi.org/10.1093/sysbio/syw039openalex-snapshot
Measuring Stratigraphic Congruence Across Trees, Higher Taxa, and Time
inferredcites →https://doi.org/10.1093/sysbio/syw060openalex-snapshot
Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins
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Bayesian Morphological Clock Methods Resurrect Placoderm Monophyly and Reveal Rapid Early Evolution in Jawed Vertebrates
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Dental data perform relatively poorly in reconstructing mammal phylogenies: Morphological partitions evaluated with molecular benchmarks
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Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data
inferredcites →https://doi.org/10.1098/rsbl.2016.0237openalex-snapshot
Topology, divergence dates, and macroevolutionary inferences vary between different tip-dating approaches applied to fossil theropods (Dinosauria)
inferredcites →https://doi.org/10.1098/rsbl.2016.0328openalex-snapshot
Inferring node dates from tip dates in fossil Canidae: the importance of tree priors
inferredcites →https://doi.org/10.1098/rsbl.2018.0263openalex-snapshot
Parsimony, not Bayesian analysis, recovers more stratigraphically congruent phylogenetic trees
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Baleen boom and bust: a synthesis of mysticete phylogeny, diversity and disparity
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The evolution of giant flightless birds and novel phylogenetic relationships for extinct fowl (Aves, Galloanseres)
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Congruence between phylogenetic and stratigraphic data on the history of life
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A new developmental mechanism for the separation of the mammalian middle ear ossicles from the jaw
inferredcites →https://doi.org/10.1098/rspb.2017.0986openalex-snapshot
Bayesian and likelihood phylogenetic reconstructions of morphological traits are not discordant when taking uncertainty into consideration: a comment on Puttick et al .
inferredcites →https://doi.org/10.1098/rspb.2018.1071openalex-snapshot
Tip-dating and homoplasy: reconciling the shallow molecular divergences of modern gharials with their long fossil record
inferredcites →https://doi.org/10.1098/rstb.2015.0129openalex-snapshot
Bayesian phylogenetic estimation of fossil ages
inferredcites →https://doi.org/10.1111/1755-6724.13033openalex-snapshot
An Updated Review of the Middle‐Late Jurassic Yanliao Biota: Chronology, Taphonomy, Paleontology and Paleoecology
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ggtree : an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data
inferredcites →https://doi.org/10.1111/cla.12205openalex-snapshot
Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology
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From success to persistence: Identifying an evolutionary regime shift in the diverse Paleozoic aquatic arthropod group Eurypterida, driven by the Devonian biotic crisis
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AMNIOTE PHYLOGENY AND THE IMPORTANCE OF FOSSILS
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TNT, a free program for phylogenetic analysis
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PHYLOGENETIC INFERENCE FROM RESTRICTION ENDONUCLEASE CLEAVAGE SITE MAPS WITH PARTICULAR REFERENCE TO THE EVOLUTION OF HUMANS AND THE APES
inferredcites →https://doi.org/10.1111/pala.12142openalex-snapshot
strap: an R package for plotting phylogenies against stratigraphy and assessing their stratigraphic congruence
inferredcites →https://doi.org/10.1111/pala.12220openalex-snapshot
Horseshoe crab phylogeny and independent colonizations of fresh water: ecological invasion as a driver for morphological innovation
inferredcites →https://doi.org/10.1111/pala.12245openalex-snapshot
Mosaicism in a new E ocene pufferfish highlights rapid morphological innovation near the origin of crown tetraodontiforms
inferredcites →https://doi.org/10.1111/pala.12361openalex-snapshot
Empirical realism of simulated data is more important than the model used to generate it: a reply to Goloboff et al.
inferredcites →https://doi.org/10.1126/science.1252243openalex-snapshot
Sustained miniaturization and anatomical innovation in the dinosaurian ancestors of birds
inferredcites →https://doi.org/10.1126/science.255.5052.1690openalex-snapshot
The Fossil Record and Evolution: Comparing Cladistic and Paleontologic Evidence for Vertebrate History
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Reconstructing Phylogeny with and without Temporal Data
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Phylogenies, Temporal Data, and Negative Evidence
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Testing the quality of the fossil record: Paleontological knowledge is improving
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Developmental Patterns in Mesozoic Evolution of Mammal Ears
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Stratocladistics: Integrating Temporal Data and Character Data in Phylogenetic Inference
inferredcites →https://doi.org/10.1186/s12983-016-0171-zopenalex-snapshot
Resolving the evolution of the mammalian middle ear using Bayesian inference
inferredcites →https://doi.org/10.1206/3874.1openalex-snapshot
Two New Tritylodontids (Synapsida, Cynodontia, Mammaliamorpha) from the Upper Jurassic, Southwestern Mongolia
inferredcites →https://doi.org/10.1371/journal.pbio.0040088openalex-snapshot
Relaxed Phylogenetics and Dating with Confidence
inferredcites →https://doi.org/10.1371/journal.pcbi.1003537openalex-snapshot
BEAST 2: A Software Platform for Bayesian Evolutionary Analysis
inferredcites →https://doi.org/10.1371/journal.pcbi.1003919openalex-snapshot
Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration
inferredcites →https://doi.org/10.1371/journal.pone.0109210openalex-snapshot
Bayesian Analysis Using a Simple Likelihood Model Outperforms Parsimony for Estimation of Phylogeny from Discrete Morphological Data
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Empirical and Bayesian approaches to fossil-only divergence times: A study across three reptile clades
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STRATIGRAPHY IN PHYLOGENY RECONSTRUCTION
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Timeless characters: a response to Vermeij (1999)
inferredcites →https://doi.org/10.2307/2413376openalex-snapshot
Mammal-Like Reptiles and the Origin of Mammals.
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Notice of Jurassic mammals representing two new orders
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EVOLUTION OF DENTAL REPLACEMENT IN MAMMALS
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Highly derived eutherian mammals from the earliest Cretaceous of southern Britain
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The age of Homo naledi and associated sediments in the Rising Star Cave, South Africa
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Skeleton of a Cretaceous mammal from Madagascar reflects long-term insularity
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Untangling the Multiple Ecological Radiations of Early Mammals
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Molecular evolutionary insights from PRLR in mammals
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Phylogenetic placement of Adalatherium hui (Mammalia, Gondwanatheria) from the Late Cretaceous of Madagascar: implications for allotherian relationships
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Bayesian Morphological Clock versus Parsimony: An Insight into the Relationships and Dispersal Events of Postvacuum Cricetidae (Rodentia, Mammalia)
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A Total-Evidence Dated Phylogeny of Echinoids and the Evolution of Body Size across Adaptive Landscape
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Relative performance of Bayesian morphological clock and parsimony methods for phylogenetic reconstructions: Insights from the case of Myomiminae and Dryomyinae glirid rodents
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Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation
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Can We Reliably Calibrate Deep Nodes in the Tetrapod Tree? Case Studies in Deep Tetrapod Divergences
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Integrative Phylogenetics: Tools for Palaeontologists to Explore the Tree of Life
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