Constraining uncertainty in the timescale of angiosperm evolution and the veracity of a Cretaceous Terrestrial Revolution

Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case

(2018) Mario Dos Reis et al.   SYSTEMATIC BIOLOGY

Reconstructing the genome of the most recent common ancestor of flowering plants

(2017) Florent Murat et al.   NATURE GENETICS

Probabilistic methods surpass parsimony when assessing clade support in phylogenetic analyses of discrete morphological data

(2017) Joseph E. O'Reilly et al.   PALAEONTOLOGY

Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution

(2017) Rachel C. M. Warnock et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data

(2017) Mark N. Puttick et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Past Sure is Tense: On Interpreting Phylogenetic Divergence Time Estimates

(2017) Joseph W Brown et al.   SYSTEMATIC BIOLOGY

Tips and nodes are complementary not competing approaches to the calibration of molecular clocks

(2016) Joseph E. O'Reilly et al.   Biology Letters

Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data

(2016) Joseph E. O'Reilly et al.   Biology Letters

Is Darwin's ‘Abominable Mystery’ still a mystery today?

(2016) Borja Cascales-Miñana et al.   CRETACEOUS RESEARCH

Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species

(2016) Yuchi Zheng et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The evolution of methods for establishing evolutionary timescales

(2016) Philip C. J. Donoghue et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Yuhania: a unique angiosperm from the Middle Jurassic of Inner Mongolia, China

(2016) Zhong-Jian Liu et al.   HISTORICAL BIOLOGY

Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales

(2015) Mario dos Reis et al.   CURRENT BIOLOGY

Bayesian molecular clock dating of species divergences in the genomics era

(2015) Mario dos Reis et al.   NATURE REVIEWS GENETICS

A metacalibrated time-tree documents the early rise of flowering plant phylogenetic diversity

(2015) Susana Magallón et al.   NEW PHYTOLOGIST

Montsechia, an ancient aquatic angiosperm

(2015) Bernard Gomez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Total-Evidence Dating under the Fossilized Birth–Death Process

(2015) Chi Zhang et al.   SYSTEMATIC BIOLOGY

Heterogeneous Rates of Molecular Evolution and Diversification Could Explain the Triassic Age Estimate for Angiosperms

(2015) Jeremy M. Beaulieu et al.   SYSTEMATIC BIOLOGY

Dating Tips for Divergence-Time Estimation

(2015) Joseph E. O’Reilly et al.   TRENDS IN GENETICS

A perfect flower from the Jurassic of China

(2015) Zhong-Jian Liu et al.   HISTORICAL BIOLOGY

A Review of the Effect of Relaxed Clock Method, Long Branches, Genes, and Calibrations in the Estimation of Angiosperm Age

(2015) Susana Magallón   Botanical Sciences

From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes

(2014) Brad R Ruhfel et al.   BMC EVOLUTIONARY BIOLOGY

The enigma of the rise of angiosperms: can we untie the knot?

(2014) L. Augusto et al.   ECOLOGY LETTERS

Bayesian Analysis Using a Simple Likelihood Model Outperforms Parsimony for Estimation of Phylogeny from Discrete Morphological Data

(2014) April M. Wright et al.   PLoS One

Calibration uncertainty in molecular dating analyses: there is no substitute for the prior evaluation of time priors

(2014) R. C. M. Warnock et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Phylogenomics resolves the timing and pattern of insect evolution

(2014) B. Misof et al.   SCIENCE

Characterization of the Uncertainty of Divergence Time Estimation under Relaxed Molecular Clock Models Using Multiple Loci

(2014) Tianqi Zhu et al.   SYSTEMATIC BIOLOGY

Extant diversity of bryophytes emerged from successive post-Mesozoic diversification bursts

(2014) B. Laenen et al.   Nature Communications

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

(2014) Liping Zeng et al.   Nature Communications

Land plant evolutionary timeline: Gene effects are secondary to fossil constraints in relaxed clock estimation of age and substitution rates

(2013) Susana Magallón et al.   AMERICAN JOURNAL OF BOTANY

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

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Three keys to the radiation of angiosperms into freezing environments

(2013) Amy E. Zanne et al.   NATURE

Bees diversified in the age of eudicots

(2013) S. Cardinal et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Fossilization causes organisms to appear erroneously primitive by distorting evolutionary trees

(2013) Robert S. Sansom et al.   Scientific Reports

Angiosperm-like pollen and Afropollis from the Middle Triassic (Anisian) of the Germanic Basin (Northern Switzerland)

(2013) Peter A. Hochuli et al.   Frontiers in Plant Science

Molecular and Fossil Evidence on the Origin of Angiosperms

(2012) James A. Doyle   Annual Review of Earth and Planetary Sciences

Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic Uncertainty

(2012) Guy Baele et al.   MOLECULAR BIOLOGY AND EVOLUTION

Impact of Missing Data on Phylogenies Inferred from Empirical Phylogenomic Data Sets

(2012) Béatrice Roure et al.   MOLECULAR BIOLOGY AND EVOLUTION

Cretaceous tetrapod fossil record sampling and faunal turnover: Implications for biogeography and the rise of modern clades

(2012) Roger B.J. Benson et al.   PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY

Rise to dominance of angiosperm pioneers in European Cretaceous environments

(2012) C. Coiffard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny

(2012) M. dos Reis et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

The unbearable uncertainty of Bayesian divergence time estimation

(2012) Mario DOS REIS et al.   Journal of Systematics and Evolution

Angiosperm phylogeny: 17 genes, 640 taxa

(2011) Douglas E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

Approximate Likelihood Calculation on a Phylogeny for Bayesian Estimation of Divergence Times

(2011) M. d. Reis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Establishing a time-scale for plant evolution

(2011) John T. Clarke et al.   NEW PHYTOLOGIST

Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification

(2011) R. W. Meredith et al.   SCIENCE

Divergence Time Estimation Using Fossils as Terminal Taxa and the Origins of Lissamphibia

(2011) R. Alexander Pyron   SYSTEMATIC BIOLOGY

Testing the Impact of Calibration on Molecular Divergence Times Using a Fossil-Rich Group: The Case of Nothofagus (Fagales)

(2011) Hervé Sauquet et al.   SYSTEMATIC BIOLOGY

Best Practices for Justifying Fossil Calibrations

(2011) James F. Parham et al.   SYSTEMATIC BIOLOGY

Evaluation of Bayesian Models of Substitution Rate Evolution—Parental Guidance versus Mutual Independence

(2011) Martin Linder et al.   SYSTEMATIC BIOLOGY

The age and diversification of the angiosperms re-revisited

(2010) Charles D. Bell et al.   AMERICAN JOURNAL OF BOTANY

Non-random decay of chordate characters causes bias in fossil interpretation

(2010) Robert S. Sansom et al.   NATURE

TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations

(2010) Federico Abascal et al.   NUCLEIC ACIDS RESEARCH

Diversity in obscurity: fossil flowers and the early history of angiosperms

(2010) E. M. Friis et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The origins of modern biodiversity on land

(2010) M. J. Benton   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

An uncorrelated relaxed-clock analysis suggests an earlier origin for flowering plants

(2010) S. A. Smith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Using Fossils to Break Long Branches in Molecular Dating: A Comparison of Relaxed Clocks Applied to the Origin of Angiosperms

(2010) Susana Magallón   SYSTEMATIC BIOLOGY

Improving Marginal Likelihood Estimation for Bayesian Phylogenetic Model Selection

(2010) Wangang Xie et al.   SYSTEMATIC BIOLOGY

An examination of phylogenetic models of substitution rate variation among lineages

(2009) S. Y.W. Ho   Biology Letters

Ancestral xerophobia: a hypothesis on the whole plant ecophysiology of early angiosperms

(2009) T. S FEILD et al.   Geobiology

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

(2009) M. Gouy et al.   MOLECULAR BIOLOGY AND EVOLUTION

High-precision 40Ar/39Ar age for the Jehol Biota

(2009) Su-chin Chang et al.   PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY

The Impact of the Representation of Fossil Calibrations on Bayesian Estimation of Species Divergence Times

(2009) Jun Inoue et al.   SYSTEMATIC BIOLOGY

Angiosperm diversification through time

(2008) Susana Magallón et al.   AMERICAN JOURNAL OF BOTANY

The meaning of Darwin's “abominable mystery”

(2008) William E. Friedman   AMERICAN JOURNAL OF BOTANY

Seed ferns from the late Paleozoic and Mesozoic: Any angiosperm ancestors lurking there?

(2008) Edith L. Taylor et al.   AMERICAN JOURNAL OF BOTANY

Integrating Molecular Phylogenetic and Paleobotanical Evidence on Origin of the Flower

(2008) James A. Doyle   INTERNATIONAL JOURNAL OF PLANT SCIENCES