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Phylogenetic Signal and Bias in Paleontology

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What this work says

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

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Distinguishing heat from light in debate over controversial fossils
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The new framework for understanding placental mammal evolution
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Corroboration among Data Sets in Simultaneous Analysis: Hidden Support for Phylogenetic Relationships among Higher Level Artiodactyl Taxa
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What Does Palaeontology Contribute to Systematics in a Molecular World?
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Analysis of Phylogenetics and Evolution with R
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Genetic Structure and Extinction of the Woolly Mammoth, Mammuthus primigenius
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Morphological Phylogenetics in the Genomic Age
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Phylogenomics and Morphology of Extinct Paleognaths Reveal the Origin and Evolution of the Ratites
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Ancient Mitogenomes Reveal the Evolutionary History and Biogeography of Sloths
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Molecular timescales and the fossil record: a paleontological perspective
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Post-molecular systematics and the future of phylogenetics
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Effects of missing data on topological inference using a Total Evidence approach
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Deciphering whale origins with molecules and fossils
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Using experimental decay of modern forms to reconstruct the early evolution and morphology of fossil enteropneusts
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Relationships of Endemic African Mammals and Their Fossil Relatives Based on Morphological and Molecular Evidence
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Convergent evolution of anthropoid-like adaptations in Eocene adapiform primates
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A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
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A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
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A new hypothesis of dinosaur relationships and early dinosaur evolution
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Late-surviving stem mammal links the lowermost Cretaceous of North America and Gondwana
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The genome of the offspring of a Neanderthal mother and a Denisovan father
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Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny
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Skeleton of a Cretaceous mammal from Madagascar reflects long-term insularity
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Fossilization causes organisms to appear erroneously primitive by distorting evolutionary trees
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Preservation and phylogeny of Cambrian ecdysozoans tested by experimental decay of Priapulus
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Neuronal networks provide rapid neuroprotection against spreading toxicity
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Graphical Methods for Data Analysis
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Bias in Phylogenetic Estimation and Its Relevance to the Choice between Parsimony and Likelihood Methods
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Accepting Partnership by Submission? Morphological Phylogenetics in a Molecular Millennium
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Tenrec Phylogeny and the Noninvasive Extraction of Nuclear DNA
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The Adequacy of Morphology for Reconstructing the Early History of Placental Mammals
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Morphology, Paleontology, and Placental Mammal Phylogeny
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phangorn: phylogenetic analysis in R
inferredcites →https://doi.org/10.1093/bioinformatics/btu157openalex-snapshot
tqDist: a library for computing the quartet and triplet distances between binary or general trees
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The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference
inferredcites →https://doi.org/10.1093/gbe/evx168openalex-snapshot
Investigating Difficult Nodes in the Placental Mammal Tree with Expanded Taxon Sampling and Thousands of Ultraconserved Elements
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Calibrating And Constraining Molecular Clocks
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040071openalex-snapshot
Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules, and morphology.
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Cases in which Parsimony or Compatibility Methods will be Positively Misleading
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/syaa023openalex-snapshot
Death is on Our Side: Paleontological Data Drastically Modify Phylogenetic Hypotheses
inferredcites →https://doi.org/10.1093/sysbio/syp012openalex-snapshot
Paleontology, Genomics, and Combined-Data Phylogenetics: Can Molecular Data Improve Phylogeny Estimation for Fossil Taxa?
inferredcites →https://doi.org/10.1093/sysbio/syq048openalex-snapshot
Combining Phylogenomics and Fossils in Higher-Level Squamate Reptile Phylogeny: Molecular Data Change the Placement of Fossil Taxa
inferredcites →https://doi.org/10.1093/sysbio/sys029openalex-snapshot
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
inferredcites →https://doi.org/10.1093/sysbio/sys058openalex-snapshot
A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera
inferredcites →https://doi.org/10.1093/sysbio/syu044openalex-snapshot
Maximum Likelihood Inference of Small Trees in the Presence of Long Branches
inferredcites →https://doi.org/10.1093/sysbio/syu077openalex-snapshot
Phylogeny, Paleontology, and Primates: Do Incomplete Fossils Bias the Tree of Life?
inferredcites →https://doi.org/10.1093/sysbio/syv052openalex-snapshot
A Nonstationary Markov Model Detects Directional Evolution in Hymenopteran Morphology
inferredcites →https://doi.org/10.1093/sysbio/syw116openalex-snapshot
Dental data perform relatively poorly in reconstructing mammal phylogenies: Morphological partitions evaluated with molecular benchmarks
inferredcites →https://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
inferredcites →https://doi.org/10.1098/rsbl.2015.1003openalex-snapshot
Assessment of available anatomical characters for linking living mammals to fossil taxa in phylogenetic analyses
inferredcites →https://doi.org/10.1098/rsbl.2018.0632openalex-snapshot
Bayesian and parsimony approaches reconstruct informative trees from simulated morphological datasets
inferredcites →https://doi.org/10.1098/rsos.190387openalex-snapshot
Congruence, fossils and the evolutionary tree of rodents and lagomorphs
inferredcites →https://doi.org/10.1098/rspb.2012.0683openalex-snapshot
Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny
inferredcites →https://doi.org/10.1098/rspb.2014.1278openalex-snapshot
Ancient dates or accelerated rates? Morphological clocks and the antiquity of placental mammals
inferredcites →https://doi.org/10.1098/rspb.2018.1632openalex-snapshot
Improvements in the fossil record may largely resolve current conflicts between morphological and molecular estimates of mammal phylogeny
inferredcites →https://doi.org/10.1098/rspb.2018.2418openalex-snapshot
Rapid morphological evolution in placental mammals post-dates the origin of the crown group
inferredcites →https://doi.org/10.1098/rspb.2019.0091openalex-snapshot
Does exceptional preservation distort our view of disparity in the fossil record?
inferredcites →https://doi.org/10.1098/rstb.2015.0140openalex-snapshot
Mammal madness: is the mammal tree of life not yet resolved?
inferredcites →https://doi.org/10.1111/cla.12160openalex-snapshot
TNT version 1.5, including a full implementation of phylogenetic morphometrics
inferredcites →https://doi.org/10.1111/cla.12170openalex-snapshot
Resolution of a concatenation/coalescence kerfuffle: partitioned coalescence support and a robust family‐level tree for Mammalia
inferredcites →https://doi.org/10.1111/j.1096-0031.2008.00209.xopenalex-snapshot
Weighting against homoplasy improves phylogenetic analysis of morphological data sets
inferredcites →https://doi.org/10.1111/j.1096-3642.2006.00293.xopenalex-snapshot
Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion
inferredcites →https://doi.org/10.1111/j.1420-9101.2009.01843.xopenalex-snapshot
Strong morphological support for the molecular evolutionary tree of placental mammals
inferredcites →https://doi.org/10.1111/j.1439-0469.2007.00433.xopenalex-snapshot
Avian higher-level phylogeny: well-supported clades and what we can learn from a phylogenetic analysis of 2954 morphological characters
inferredcites →https://doi.org/10.1111/j.1439-0469.2012.00670.xopenalex-snapshot
The interpretation of hidden support in combined data phylogenetics
inferredcites →https://doi.org/10.1111/pala.12314openalex-snapshot
Comparative experimental taphonomy of eight marine arthropods indicates distinct differences in preservation potential
inferredcites →https://doi.org/10.1111/pala.12353openalex-snapshot
Parsimony and model‐based phylogenetic methods for morphological data: comments on O'Reilly et al.
inferredcites →https://doi.org/10.1126/science.1229237openalex-snapshot
The Placental Mammal Ancestor and the Post–K-Pg Radiation of Placentals
inferredcites →https://doi.org/10.1126/science.aau9345openalex-snapshot
New Jurassic mammaliaform sheds light on early evolution of mammal-like hyoid bones
inferredcites →https://doi.org/10.1146/annurev.earth.31.100901.141308openalex-snapshot
Phylogenetic Approaches Toward Crocodylian History
inferredcites →https://doi.org/10.1163/18759866-07001001openalex-snapshot
Molecules, morphology, and the monophyly of diapsid reptiles
inferredcites →https://doi.org/10.1186/1471-2148-14-9openalex-snapshot
Caves as microrefugia: Pleistocene phylogeography of the troglophilic North American scorpion Pseudouroctonus reddelli
inferredcites →https://doi.org/10.1186/1471-2148-7-108openalex-snapshot
A web-database of mammalian morphology and a reanalysis of placental phylogeny
inferredcites →https://doi.org/10.1186/s12862-014-0222-zopenalex-snapshot
Decay of velvet worms (Onychophora), and bias in the fossil record of lobopodians
inferredcites →https://doi.org/10.1371/journal.pbio.3000494openalex-snapshot
Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation
inferredcites →https://doi.org/10.1371/journal.pone.0049521openalex-snapshot
Macroevolutionary Dynamics and Historical Biogeography of Primate Diversification Inferred from a Species Supermatrix
inferredcites →https://doi.org/10.1671/0272-4634(2005)025[0911:nmocml]2.0.co;2openalex-snapshot
New material ofCentetodon(Mammalia, Lipotyphla) and the importance of (missing) DNA sequences in systematic paleontology
inferredcites →https://doi.org/10.21105/joss.01686openalex-snapshot
Welcome to the Tidyverse
inferredcites →https://doi.org/10.2307/2412923openalex-snapshot
Cases in which Parsimony or Compatibility Methods Will be Positively Misleading
inferredcites →https://doi.org/10.2307/3515093openalex-snapshot
Experimental taphonomy
inferredcites →https://doi.org/10.26879/424openalex-snapshot
Constraints on the timescale of animal evolutionary history
inferredcites →https://doi.org/10.2992/0145-9058(2006)37[1:pon]2.0.co;2openalex-snapshot
PHYLOGENY OF NEORNITHES
inferredcites →https://doi.org/10.3389/fgene.2019.01241openalex-snapshot
Evolutionary Models for the Diversification of Placental Mammals Across the KPg Boundary
inferredcites →https://doi.org/10.5281/zenodo.2536318openalex-snapshot
Quartet: Comparison of Phylogenetic Trees Using Quartet and Bipartition Measures
inferredcites →https://doi.org/10.5281/zenodo.3522725openalex-snapshot
TreeTools: Create, modify and analyse phylogenetic trees
inferredcites →https://doi.org/10.5281/zenodo.3528123openalex-snapshot
TreeDist: Distances Between Phylogenetic Trees
inferredcites →https://doi.org/10.7554/elife.46205openalex-snapshot
Cretaceous dinosaur bone contains recent organic material and provides an environment conducive to microbial communities

What points at this work

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

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Did some extinct South American native ungulates arise from an afrothere ancestor? A critical appraisal of Avilla and Mothé’s (2021) Sudamericungulata – Panameridiungulata hypothesis
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The effects of ordered multistate morphological characters on phylogenetic analyses of eutherian mammals
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Life-position succulent Euphorbia L. fossils buried in Pleistocene explosive volcanic deposits from Tenerife, Canary Islands, Spain
inferred← citeshttps://doi.org/10.1080/03115518.2023.2184492openalex-snapshot
The evolutionary relationships of Diprotodontia and improving the accuracy of phylogenetic inference from morphological data
inferred← citeshttps://doi.org/10.1093/iob/obaf029openalex-snapshot
Toward a Comprehensive Anatomical Matrix for Crown Birds: Phylogenetic Insights from the Pectoral Girdle and Forelimb Skeleton
inferred← citeshttps://doi.org/10.1093/sysbio/syad031openalex-snapshot
Online Phylogenetics with matOptimize Produces Equivalent Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Implementations
inferred← citeshttps://doi.org/10.1098/rspb.2022.2014openalex-snapshot
The Cambrian cirratuliform Iotuba denotes an early annelid radiation
inferred← citeshttps://doi.org/10.1098/rspb.2024.1856openalex-snapshot
The origin and evolution of shrews (Soricidae, Mammalia)
inferred← citeshttps://doi.org/10.1098/rspb.2025.0856openalex-snapshot
Collagen fingerprinting and sequence analysis provides a molecular phylogeny of extinct Australian megafauna
inferred← citeshttps://doi.org/10.1111/cla.12581openalex-snapshot
Exploring the effects of weighting against homoplasy in genealogies of palaeontological phylogenetic matrices
inferred← citeshttps://doi.org/10.1111/jse.70039openalex-snapshot
Why are Magnoliaceae so diverse in the tropics? Disentangling the roles of diversification and time‐for‐speciation effects
inferred← citeshttps://doi.org/10.2139/ssrn.6019356openalex-snapshot
Life-Position Succulent Euphorbia L. Fossils Buried in Pleistocene Explosive Volcanic Deposits from Tenerife, Canary Islands, Spain
inferred← citeshttps://doi.org/10.2139/ssrn.6036422openalex-snapshot
Life-Position Succulent Euphorbia L. Fossils Buried in Pleistocene Explosive Volcanic Deposits from Tenerife, Canary Islands, Spain
inferred← citeshttps://doi.org/10.32614/cran.package.quartetopenalex-snapshot
Quartet: Comparison of Phylogenetic Trees Using Quartet and Split Measures
inferred← citeshttps://doi.org/10.32614/cran.package.treetoolsopenalex-snapshot
TreeTools: Create, Modify and Analyse Phylogenetic Trees
inferred← citeshttps://doi.org/10.32614/rj-2023-019openalex-snapshot
TreeSearch: Morphological Phylogenetic Analysis in R
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The Avian Acetabulum: Small Structure, but Rich with Illumination and Questions
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Concatenated ScaA and TSA56 Surface Antigen Sequences Reflect Genome-Scale Phylogeny of Orientia tsutsugamushi: An Analysis Including Two Genomes from Taiwan
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Low-Coverage Genome Sequencing Outperforms Target Enrichment Phylogenomics
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