Inferring the Total-Evidence Timescale of Marattialean Fern Evolution in the Face of Model Sensitivity

Exploring the phylogeny of the marattialean ferns

(2020) Samuli Lehtonen et al.   CLADISTICS

Death is on Our Side: Paleontological Data Drastically Modify Phylogenetic Hypotheses

(2020) Nicolás Mongiardino Koch et al.   SYSTEMATIC BIOLOGY

Integration of Anatomy Ontologies and Evo-Devo Using Structured Markov Models Suggests a New Framework for Modeling Discrete Phenotypic Traits

(2019) Sergei Tarasov   SYSTEMATIC BIOLOGY

Simultaneous Bayesian inference of phylogeny and molecular coevolution

(2019) Xavier Meyer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ignoring stratigraphic age uncertainty leads to erroneous estimates of species divergence times under the fossilized birth–death process

(2019) Joëlle Barido-Sottani et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A New Marattialean Fern from the Lower Permian of Patagonia (Argentina) with Cautionary Tales on Synangial Morphology and Pinnule Base Characters

(2019) Kolby R. Lundgren et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

One thousand plant transcriptomes and the phylogenomics of green plants

(2019)   NATURE

Selective Sampling of Species and Fossils Influences Age Estimates Under the Fossilized Birth–Death Model

(2019) Michael Matschiner   Frontiers in Genetics

Using the Fossil Record to Evaluate Timetree Timescales

(2019) Charles R. Marshall   Frontiers in Genetics

Resolving the overall pattern of marattialean fern phylogeny

(2018) Gar W. Rothwell et al.   AMERICAN JOURNAL OF BOTANY

A well-resolved fern nuclear phylogeny reveals the evolution history of numerous transcription factor families

(2018) Xinping Qi et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Tip-dating and homoplasy: reconciling the shallow molecular divergences of modern gharials with their long fossil record

(2018) Michael S. Y. Lee et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Order-level fern plastome phylogenomics: new insights from Hymenophyllales

(2018) Li-Yaung Kuo et al.   AMERICAN JOURNAL OF BOTANY

P3: Phylogenetic Posterior Prediction in RevBayes

(2017) Sebastian Höhna et al.   MOLECULAR BIOLOGY AND EVOLUTION

Large-scale phylogenomic analysis resolves a backbone phylogeny in ferns

(2017) Hui Shen et al.   GigaScience

Environmentally driven extinction and opportunistic origination explain fern diversification patterns

(2017) Samuli Lehtonen et al.   Scientific Reports

Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data

(2016) Denise Kühnert et al.   MOLECULAR BIOLOGY AND EVOLUTION

A 4000-species dataset provides new insight into the evolution of ferns

(2016) Weston Testo 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

A mixed relaxed clock model

(2016) Nicolas Lartillot et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Marattiaceae synangia from the Lower Cretaceous of Antarctica

(2016) Ezequiel I. Vera et al.   REVIEW OF PALAEOBOTANY AND PALYNOLOGY

RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language

(2016) Sebastian Höhna et al.   SYSTEMATIC BIOLOGY

The evolutionary history of ferns inferred from 25 low-copy nuclear genes

(2015) C. J. Rothfels et al.   AMERICAN JOURNAL OF BOTANY

Natural Hybridization between Genera That Diverged from Each Other Approximately 60 Million Years Ago

(2015) Carl J. Rothfels et al.   AMERICAN NATURALIST

Origin and diversification of living cycads: a cautionary tale on the impact of the branching process prior in Bayesian molecular dating

(2015) Fabien L Condamine et al.   BMC EVOLUTIONARY BIOLOGY

An evaluation of fossil tip-dating versus node-age calibrations in tetraodontiform fishes (Teleostei: Percomorphaceae)

(2015) Dahiana Arcila et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Horsetails are the sister group to all other monilophytes and Marattiales are sister to leptosporangiate ferns

(2015) Nils Knie et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Molecular dates require geologic testing

(2015) Peter Wilf et al.   NEW PHYTOLOGIST

Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds"

(2015) J. Cracraft et al.   SCIENCE

Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds"

(2015) K. J. Mitchell et al.   SCIENCE

Total-Evidence Dating under the Fossilized Birth–Death Process

(2015) Chi Zhang et al.   SYSTEMATIC BIOLOGY

Modeling Character Change Heterogeneity in Phylogenetic Analyses of Morphology through the Use of Priors

(2015) April M. Wright et al.   SYSTEMATIC BIOLOGY

Multidimensional Scaling Using Majorization: SMACOF inR

(2015) Jan de Leeuw et al.   Journal of Statistical Software

Clock model makes a large difference to age estimates of long-stemmed clades with no internal calibration: a test using Australian grasstrees

(2014) Michael D Crisp et al.   BMC EVOLUTIONARY BIOLOGY

A new marattiaceous fern from the Lower Jurassic of Patagonia (Argentina): the renaissance ofMarattiopsis

(2014) Ignacio H. Escapa et al.   JOURNAL OF SYSTEMATIC PALAEONTOLOGY

Green Web or megabiased clock? Plant fossils from Gondwanan Patagonia speak on evolutionary radiations

(2014) Peter Wilf et al.   NEW PHYTOLOGIST

Phylotranscriptomic analysis of the origin and early diversification of land plants

(2014) Norman J. Wickett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The fossilized birth-death process for coherent calibration of divergence-time estimates

(2014) T. A. Heath et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatiotemporal relationships among Late Pennsylvanian plant assemblages: Palynological evidence from the Markley Formation, West Texas, U.S.A.

(2014) Cindy V. Looy et al.   REVIEW OF PALAEOBOTANY AND PALYNOLOGY

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

(2014) Tianqi Zhu et al.   SYSTEMATIC BIOLOGY

Revision of the fern family Marattiaceae in the Seychelles with two new species and a discussion of the African Ptisana fraxinea complex.

(2014) Bruno Senterre et al.   Phytotaxa

Molecular dating of phylogenies by likelihood methods: A comparison of models and a new information criterion

(2013) Emmanuel Paradis   MOLECULAR PHYLOGENETICS AND EVOLUTION

Identifying Hidden Rate Changes in the Evolution of a Binary Morphological Character: The Evolution of Plant Habit in Campanulid Angiosperms

(2013) Jeremy M. Beaulieu et al.   SYSTEMATIC BIOLOGY

Dating Phylogenies with Sequentially Sampled Tips

(2013) Tanja Stadler et al.   SYSTEMATIC BIOLOGY

Accelerated Rate of Molecular Evolution for Vittarioid Ferns is Strong and Not Driven by Selection

(2013) Carl J. Rothfels et al.   SYSTEMATIC BIOLOGY

(2151) Proposal to conserve the name Marattiopsis (fossil Marattiaceae) with a conserved type

(2013) Benjamin Bomfleur et al.   TAXON

Critiquing blind dating: the dangers of over-confident date estimates in comparative genomics

(2013) Christopher W. Wheat et al.   TRENDS IN ECOLOGY & EVOLUTION

Phylogenetic evidence for a shift in the mode of mammalian body size evolution at the Cretaceous-Palaeogene boundary

(2013) Graham J. Slater   Methods in Ecology and Evolution

Incorporating phylogenetic uncertainty on phylogeny-based palaeontological dating and the timing of turtle diversification

(2012) Juliana Sterli et al.   CLADISTICS

Overcoming Deep Roots, Fast Rates, and Short Internodes to Resolve the Ancient Rapid Radiation of Eupolypod II Ferns

(2012) Carl J. Rothfels et al.   SYSTEMATIC BIOLOGY

A Hierarchical Bayesian Model for Calibrating Estimates of Species Divergence Times

(2012) Tracy A. Heath   SYSTEMATIC BIOLOGY

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

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Treating Fossils as Terminal Taxa in Divergence Time Estimation Reveals Ancient Vicariance Patterns in the Palpimanoid Spiders

(2012) Hannah Marie Wood et al.   SYSTEMATIC BIOLOGY

The unbearable uncertainty of Bayesian divergence time estimation

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

First insights into fern matK phylogeny

(2011) Li-Yaung Kuo et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Towards Resolving the Complete Fern Tree of Life

(2011) Samuli Lehtonen   PLoS One

Recent Synchronous Radiation of a Living Fossil

(2011) N. S. Nagalingum et al.   SCIENCE

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

(2011) R. Alexander Pyron   SYSTEMATIC BIOLOGY

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

Utility of a large, multigene plastid data set in inferring higher-order relationships in ferns and relatives (monilophytes)

(2010) Hardeep S. Rai et al.   AMERICAN JOURNAL OF BOTANY

Early Middle Ordovician evidence for land plants in Argentina (eastern Gondwana)

(2010) C. V. Rubinstein et al.   NEW PHYTOLOGIST

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

Improving Marginal Likelihood Estimation for Bayesian Phylogenetic Model Selection

(2010) Wangang Xie et al.   SYSTEMATIC BIOLOGY

Effects of Substitution Models on Divergence Time Estimates: Simulations and an Empirical Study of Model Uncertainty Using Cornales

(2010) John J. Schenk et al.   SYSTEMATIC BOTANY

Accounting for Calibration Uncertainty in Phylogenetic Estimation of Evolutionary Divergence Times

(2009) Simon Y. W. Ho et al.   SYSTEMATIC BIOLOGY

Phylogeny of marattioid ferns (Marattiaceae): inferring a root in the absence of a closely related outgroup

(2008) Andrew G. Murdock   AMERICAN JOURNAL OF BOTANY

A Simple Method for Bracketing Absolute Divergence Times on Molecular Phylogenies Using Multiple Fossil Calibration Points

(2008) Charles R. Marshall   AMERICAN NATURALIST

Phylogenetic uncertainty and molecular clock calibrations: A case study of legless lizards (Pygopodidae, Gekkota)

(2008) M.S.Y. Lee et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION