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The Impact of Fossils and Taxon Sampling on Ancient Molecular Dating Analyses

https://doi.org/10.1093/molbev/msm115
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What this work says

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

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Ancient Phylogenetic Relationships
inferredcites →https://doi.org/10.1007/s00239-004-2624-9openalex-snapshot
Error in Estimation of Rate and Time Inferred from the Early Amniote Fossil Record and Avian Molecular Clocks
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Molecules as documents of evolutionary history
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Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision
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Precision of molecular time estimates
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The comparative method for evaluating fossil calibration dates: a reply to Hedges and Kumar
inferredcites →https://doi.org/10.1016/j.tig.2004.12.006openalex-snapshot
Molecular dating: ape bones agree with chicken entrails
inferredcites →https://doi.org/10.1016/j.tree.2005.02.007openalex-snapshot
Molecular dating when rates vary
inferredcites →https://doi.org/10.1016/s0168-9525(04)00072-1openalex-snapshot
Precision of molecular time estimates
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A molecular timescale for vertebrate evolution
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Phylogenomics and the reconstruction of the tree of life
inferredcites →https://doi.org/10.1073/pnas.0401670101openalex-snapshot
Estimating metazoan divergence times with a molecular clock
inferredcites →https://doi.org/10.1073/pnas.0403984101openalex-snapshot
The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils?
inferredcites →https://doi.org/10.1073/pnas.0503660102openalex-snapshot
Origin of the Eumetazoa: Testing ecological predictions of molecular clocks against the Proterozoic fossil record
inferredcites →https://doi.org/10.1080/10635150290102456openalex-snapshot
Divergence Time and Evolutionary Rate Estimation with Multilocus Data
inferredcites →https://doi.org/10.1080/10635150390235557openalex-snapshot
Comparison of Likelihood and Bayesian Methods for Estimating Divergence Times Using Multiple Gene Loci and Calibration Points, with Application to a Radiation of Cute-Looking Mouse Lemur Species
inferredcites →https://doi.org/10.1080/10635150600697358openalex-snapshot
Resolution of Phylogenetic Conflict in Large Data Sets by Increased Taxon Sampling
inferredcites →https://doi.org/10.1086/427734openalex-snapshot
Assessing Concordance of Fossil Calibration Points in Molecular Clock Studies: An Example Using Turtles
inferredcites →https://doi.org/10.1093/acprof:oso/9780198567028.001.0001openalex-snapshot
Computational Molecular Evolution
inferredcites →https://doi.org/10.1093/bioinformatics/13.5.555openalex-snapshot
PAML: a program package for phylogenetic analysis by maximum likelihood
inferredcites →https://doi.org/10.1093/bioinformatics/18.3.502openalex-snapshot
TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing
inferredcites →https://doi.org/10.1093/bioinformatics/19.2.301openalex-snapshot
r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock
inferredcites →https://doi.org/10.1093/molbev/msg226openalex-snapshot
Bayesian Models of Episodic Evolution Support a Late Precambrian Explosive Diversification of the Metazoa
inferredcites →https://doi.org/10.1093/molbev/msh176openalex-snapshot
IQPNNI: Moving Fast Through Tree Space and Stopping in Time
inferredcites →https://doi.org/10.1093/molbev/msi039openalex-snapshot
Molecular Clocks Do Not Support the Cambrian Explosion
inferredcites →https://doi.org/10.1093/molbev/msj024openalex-snapshot
Bayesian Estimation of Species Divergence Times Under a Molecular Clock Using Multiple Fossil Calibrations with Soft Bounds
inferredcites →https://doi.org/10.1093/molbev/msl150openalex-snapshot
Paleontological Evidence to Date the Tree of Life
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a003811openalex-snapshot
Performance of a Divergence Time Estimation Method under a Probabilistic Model of Rate Evolution
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/oxfordjournals.molbev.a025731openalex-snapshot
A Nonparametric Approach to Estimating Divergence Times in the Absence of Rate Constancy
inferredcites →https://doi.org/10.1098/rspb.2006.3537openalex-snapshot
A molecular time-scale for eukaryote evolution recalibrated with the continuous microfossil record
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Assessing the quality of molecular divergence time estimates by fossil calibrations and fossil–based model selection
inferredcites →https://doi.org/10.1098/rstb.2006.1845openalex-snapshot
The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation
inferredcites →https://doi.org/10.1126/science.1077795openalex-snapshot
Dating the Tree of Life
inferredcites →https://doi.org/10.1186/1471-2148-4-2openalex-snapshot
A molecular timescale of eukaryote evolution and the rise of complex multicellular life
inferredcites →https://doi.org/10.1371/journal.pbio.0040088openalex-snapshot
Relaxed Phylogenetics and Dating with Confidence
inferredcites →https://doi.org/10.2307/3473141openalex-snapshot
Assessing Concordance of Fossil Calibration Points in Molecular Clock Studies: An Example Using Turtles

What points at this work

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

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Reconstructing the history of Campanulaceae with a Bayesian approach to molecular dating and dispersal–vicariance analyses
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The impact of calibration and clock-model choice on molecular estimates of divergence times
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Molecular phylogenetics and diversification of trap-jaw ants in the genera Anochetus and Odontomachus (Hymenoptera: Formicidae)
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A 4000-species dataset provides new insight into the evolution of ferns
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Phylogenomic analyses based on genome-skimming data reveal cyto-nuclear discordance in the evolutionary history of Cotoneaster (Rosaceae)
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Fossil-calibrated time tree of Podarcis wall lizards provides limited support for biogeographic calibration models
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Extant diversity of bryophytes emerged from successive post-Mesozoic diversification bursts
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Copyright Page
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Foreword
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Contributors
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.002.0008openalex-snapshot
Introduction
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0001openalex-snapshot
The earliest fossil record of the animals and its significance
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
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Genomic, phylogenetic, and cell biological insights into metazoan origins
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The mouth, the anus, and the blastopore—open questions about questionable openings
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Origins of metazoan body plans: the larval revolution
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Assembling the spiralian tree of life
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The evolution of nervous system centralization
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The origins and evolution of the Ecdysozoa
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Deciphering deuterostome phylogeny: molecular, morphological, and palaeontological perspectives
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Molecular genetic insights into deuterostome evolution from the direct-developing hemichordateSaccoglossus kowalevskii
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Invertebrate Problematica: kinds, causes, and solutions
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Improvement of molecular phylogenetic inference and the phylogeny of Bilateria
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Beyond linear sequence comparisons: the use of genome-level characters for phylogenetic reconstruction
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The animal in the genome: comparative genomics and evolution
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MicroRNAs and metazoan phylogeny: big trees from little genes
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The evolution of developmental gene networks: lessons from comparative studies on holometabolous insects
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Conserved developmental processes and the evolution of novel traits: wounds, embryos, veins, and butterfly eyespots
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Reassembling animal evolution: a four-dimensional puzzle
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Genome-Wide Phylogenetic Comparative Analysis of Plant Transcriptional Regulation: A Timeline of Loss, Gain, Expansion, and Correlation with Complexity
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RelTime Relaxes the Strict Molecular Clock throughout the Phylogeny
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Global Rate Variation in Bony Vertebrates
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Performance of Relaxed-Clock Methods in Estimating Evolutionary Divergence Times and Their Credibility Intervals
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The Diversity of Class II Transposable Elements in Mammalian Genomes Has Arisen from Ancestral Phylogenetic Splits during Ancient Waves of Proliferation through the Genome
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Global Diversification Dynamics Since the Jurassic: Low Dispersal and Habitat-Dependent Evolution Explain Hotspots of Diversity and Shell Disparity in River Snails (Viviparidae)
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Accounting for Calibration Uncertainty in Phylogenetic Estimation of Evolutionary Divergence Times
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Divergence Time Estimation Using Fossils as Terminal Taxa and the Origins of Lissamphibia
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A Hierarchical Bayesian Model for Calibrating Estimates of Species Divergence Times
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Phylogenomic Insights into the Cambrian Explosion, the Colonization of Land and the Evolution of Flight in Arthropoda
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Molecular Dating, Evolutionary Rates, and the Age of the Grasses
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A Rich Fossil Record Yields Calibrated Phylogeny for Acanthaceae (Lamiales) and Evidence for Marked Biases in Timing and Directionality of Intercontinental Disjunctions
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Methods for the Quantitative Comparison of Molecular Estimates of Clade Age and the Fossil Record
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Geomolecular Dating and the Origin of Placental Mammals
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A Simulation-Based Evaluation of Tip-Dating Under the Fossilized Birth–Death Process
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The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records
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On the Age of Eukaryotes: Evaluating Evidence from Fossils and Molecular Clocks
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Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary
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Phylogenetic divergences of the true bugs (Insecta: Hemiptera: Heteroptera), with emphasis on the aquatic lineages: the last piece of the aquatic insect jigsaw originated in the Late Permian/Early Triassic
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Fine‐scale biogeographical and temporal diversification processes of peacock swallowtails (Papilio subgenus Achillides) in the Indo‐Australian Archipelago
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Evidence from mitochondrial genomics supports the lower Mesozoic of South Asia as the time and place of basal divergence of cypriniform fishes (Actinopterygii: Ostariophysi)
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Not so old Archaea – the antiquity of biogeochemical processes in the archaeal domain of life
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Timing of morphological and ecological innovations in the cyanobacteria – a key to understanding the rise in atmospheric oxygen
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Evolution of sympatric species: a case study of the coral reef fish genus P omacanthus ( P omacanthidae)
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inferred← citeshttps://doi.org/10.1111/jpy.12111openalex-snapshot
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A tale of worldwide success: Behind the scenes of Carex (Cyperaceae) biogeography and diversification
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Assessing the sensitivity of divergence time estimates to locus sampling, calibration points, and model priors in a RAD‐seq phylogeny of Carex section Schoenoxiphium
inferred← citeshttps://doi.org/10.1111/jse.13194openalex-snapshot
Phylogeny and biogeography of the fern genus Hymenasplenium (Aspleniaceae), with special reference to island speciation
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Inconsistent performance of multi‐type genomic data in phylogenomics of neuropteridan insects, with solutions toward conflicting results
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Ediacaran origin and Ediacaran-Cambrian diversification of Metazoa
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Evolutionary divergence times in the Annonaceae: evidence of a late Miocene origin of Pseuduvaria in Sundaland with subsequent diversification in New Guinea
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Multigene phylogeny of the Mustelidae: Resolving relationships, tempo and biogeographic history of a mammalian adaptive radiation
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Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages
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A Molecular Genetic Timescale for the Diversification of Autotrophic Stramenopiles (Ochrophyta): Substantive Underestimation of Putative Fossil Ages
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A New Basal Caniform (Mammalia: Carnivora) from the Middle Eocene of North America and Remarks on the Phylogeny of Early Carnivorans
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Are characiform Fishes Gondwanan in Origin? Insights from a Time-Scaled Molecular Phylogeny of the Citharinoidei (Ostariophysi: Characiformes)
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In or Out-of-Madagascar?—Colonization Patterns for Large-Bodied Diving Beetles (Coleoptera: Dytiscidae)
inferred← citeshttps://doi.org/10.1371/journal.pone.0210269openalex-snapshot
Molecular phylogeny and diversification timing of the Nemouridae family (Insecta, Plecoptera) in the Japanese Archipelago
inferred← citeshttps://doi.org/10.1371/journal.pone.0227525openalex-snapshot
Phylogenomics indicates the “living fossil” Isoetes diversified in the Cenozoic
inferred← citeshttps://doi.org/10.15835/buasvmcn-asb:69:1-2:8503openalex-snapshot
Analysis of Genetic Diversity of Mulberry Silkworm ( Bombyx mori L.) Using RAPD Molecular Markers
inferred← citeshttps://doi.org/10.1600/036364410792495809openalex-snapshot
Effects of Substitution Models on Divergence Time Estimates: Simulations and an Empirical Study of Model Uncertainty Using Cornales
inferred← citeshttps://doi.org/10.1600/036364417x696438openalex-snapshot
The Emergence of Earliest Angiosperms May be Earlier than Fossil Evidence Indicates
inferred← citeshttps://doi.org/10.1664/10-ra-012.1openalex-snapshot
Fossil Cross-Validation of the Dated Ant Phylogeny (Hymenoptera: Formicidae)
inferred← citeshttps://doi.org/10.1664/11-ra-013.1openalex-snapshot
Fossil Cross-validation of the Dated Ant Phylogeny (Hymenoptera: Formicidae)
inferred← citeshttps://doi.org/10.1666/09041.1openalex-snapshot
Integrating phylogeny, molecular clocks, and the fossil record in the evolution of coralline algae (Corallinales and Sporolithales, Rhodophyta)
inferred← citeshttps://doi.org/10.33338/ef.79904openalex-snapshot
Taxonomic separateness of the subspecies of Noctua interjecta Hübner (Lepidoptera: Noctuidae) inhabiting central Europe
inferred← citeshttps://doi.org/10.3389/fgene.2012.00130openalex-snapshot
Recent progress in paleontological methods for dating the Tree of Life
inferred← citeshttps://doi.org/10.3389/fgene.2014.00138openalex-snapshot
Beyond fossil calibrations: realities of molecular clock practices in evolutionary biology
inferred← citeshttps://doi.org/10.3389/fgene.2020.00252openalex-snapshot
Quantifying the Error of Secondary vs. Distant Primary Calibrations in a Simulated Environment
inferred← citeshttps://doi.org/10.3390/d17010061openalex-snapshot
Resolving Rapid Radiation of Voles and Lemmings (Arvicolinae: Cricetinae, Rodentia) with QuaddRAD Sequencing and Transcriptome Analysis
inferred← citeshttps://doi.org/10.3390/plants14071061openalex-snapshot
Multiple Dataset-Based Insights into the Phylogeny and Phylogeography of the Genus Exbucklandia (Hamamelidaceae): Additional Evidence on the Evolutionary History of Tropical Plants
inferred← citeshttps://doi.org/10.3724/sp.j.1002.2008.08016openalex-snapshot
Taxon sampling and the accuracy of phylogenetic analyses
inferred← citeshttps://doi.org/10.3732/ajb.1600083openalex-snapshot
Molecular evidence supports ancient long‐distance dispersal for the amphi‐Atlantic disjunction in the giant yellow shrimp plant (Barleria oenotheroides)
inferred← citeshttps://doi.org/10.4137/bbi.s9677openalex-snapshot
The Influence of Taxon Sampling and Tree Shape on Molecular Dating: An Empirical Example from Mammalian Mitochondrial Genomes
inferred← citeshttps://doi.org/10.4137/ebo.s13908openalex-snapshot
Assignment of Calibration Information to Deeper Phylogenetic Nodes is More Effective in Obtaining Precise and Accurate Divergence Time Estimates
inferred← citeshttps://doi.org/10.4137/ebo.s9627openalex-snapshot
Impact of the Partitioning Scheme on Divergence Times Inferred from Mammalian Genomic Data Sets
inferred← citeshttps://doi.org/10.4236/abb.2012.31004openalex-snapshot
Genetic diversity of Persea bombycina from goalpara district of Assam, India
inferred← citeshttps://doi.org/10.4238/2012.february.3.1openalex-snapshot
Genetic and biochemical differentiation in Vitis vinifera (Kabarcik) populations grown at different altitudes in Coruh Valley
inferred← citeshttps://doi.org/10.47023/ea.bilim.9426openalex-snapshot
Fosil Nedir, Nasıl Oluşur? Bir Canlının Fosilleşmesi İçin Hangi Şartlar Gerekir? Fosilleşme Basamakları Nelerdir?
inferred← citeshttps://doi.org/10.5897/ajb.9000455openalex-snapshot
Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and random amplified polymorphic DNA (RAPD) based genetic variation studies in eri silkworm (Samia cynthia ricini Lepidoptera: Saturniidae)
inferred← citeshttps://doi.org/10.5897/ajb10.1745openalex-snapshot
Analysis of genetic diversity of muga silkworm (Antheraea assamensis, Helfer; Lepidoptera : Saturniidae) using RAPD-based molecular markers
inferred← citeshttps://doi.org/10.5943/mycosphere/14/1/5openalex-snapshot
Phylogenomics and diversification of Sordariomycetes
inferred← citeshttps://doi.org/10.5943/mycosphere/7/11/9openalex-snapshot
Evolution of Xylariomycetidae (Ascomycota: Sordariomycetes)
inferred← citeshttps://doi.org/10.70675/0f12a13fz7e1az4402z99a7z9c8028bf13fdopenalex-snapshot
Diversité et évolution des algues vertes Udoteaceae et Rhipiliaceae (Bryopsidales, Chlorophyta)
inferred← citeshttps://doi.org/10.70675/ac7907fbz1356z461azb759z5770743b3e29openalex-snapshot
Towards a chronology of life using Lateral Gene Transfers
inferred← citeshttps://doi.org/10.7150/ijbs.3982openalex-snapshot
A Comparative Study of Mammalian Diversification Pattern
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