Fossils improve phylogenetic analyses of morphological characters

Morphological phylogenetics evaluated using novel evolutionary simulations

(2020) Joseph N Keating et al.   SYSTEMATIC BIOLOGY

Extant timetrees are consistent with a myriad of diversification histories

(2020) Stilianos Louca et al.   NATURE

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

(2020) Nicolás Mongiardino Koch et al.   SYSTEMATIC BIOLOGY

Morphological characters can strongly influence early animal relationships inferred from phylogenomic datasets

(2020) Johannes S Neumann et al.   SYSTEMATIC BIOLOGY

Bayesian Tip-dated Phylogenetics in Paleontology: Topological Effects and Stratigraphic Fit

(2020) Benedict King   SYSTEMATIC BIOLOGY

Ignoring Fossil Age Uncertainty Leads to Inaccurate Topology and Divergence Time Estimates in Time Calibrated Tree Inference

(2020) Joëlle Barido-Sottani et al.   Frontiers in Ecology and Evolution

Seven rules for simulations in paleobiology

(2020) Joëlle Barido-Sottani et al.   PALEOBIOLOGY

A Total-Evidence Dated Phylogeny of Echinoidea Combining Phylogenomic and Paleontological Data

(2020) Nicolás Mongiardino Koch et al.   SYSTEMATIC BIOLOGY

Hagfish from the Cretaceous Tethys Sea and a reconciliation of the morphological–molecular conflict in early vertebrate phylogeny

(2019) Tetsuto Miyashita et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Trilobite evolutionary rates constrain the duration of the Cambrian explosion

(2019) John R. Paterson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bayesian and parsimony approaches reconstruct informative trees from simulated morphological datasets

(2019) Martin R. Smith   Biology Letters

A Simulation-Based Evaluation of Tip-Dating Under the Fossilized Birth-Death Process

(2019) Arong Luo et al.   SYSTEMATIC BIOLOGY

Which morphological characters are influential in a Bayesian phylogenetic analysis? Examples from the earliest osteichthyans

(2019) Benedict King   Biology Letters

Congruence, fossils and the evolutionary tree of rodents and lagomorphs

(2019) Robert J. Asher et al.   Royal Society Open Science

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

Parsimony, not Bayesian analysis, recovers more stratigraphically congruent phylogenetic trees

(2018) Robert S. Sansom et al.   Biology Letters

The origin of squamates revealed by a Middle Triassic lizard from the Italian Alps

(2018) Tiago R. Simões et al.   NATURE

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

Probabilistic methods outperform parsimony in the phylogenetic analysis of data simulated without a probabilistic model

(2018) Mark N. Puttick et al.   PALAEONTOLOGY

Reconstructing the Evolution of Giant Extinct Kangaroos: Comparing the Utility of DNA, Morphology, and Total Evidence

(2018) Manuela Cascini et al.   SYSTEMATIC BIOLOGY

Ancestral morphology of crown-group molluscs revealed by a new Ordovician stem aculiferan

(2017) Jakob Vinther et al.   NATURE

Empirical and Bayesian approaches to fossil-only divergence times: A study across three reptile clades

(2017) Alan H. Turner et al.   PLoS One

Estimating morphological diversity and tempo with discrete character-taxon matrices: implementation, challenges, progress, and future directions

(2016) Graeme T. Lloyd   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Partially incorrect fossil data augment analyses of discrete trait evolution in living species

(2016) Mark N. Puttick   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

TNT version 1.5, including a full implementation of phylogenetic morphometrics

(2016) Pablo A. Goloboff et al.   CLADISTICS

The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference

(2016) James E. Tarver et al.   Genome Biology and Evolution

Closing the gap between rocks and clocks using total-evidence dating

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

The non-uniformity of fossil preservation

(2016) Steven M. Holland   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The impact of fossil data on annelid phylogeny inferred from discrete morphological characters

(2016) Luke A. Parry et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Morphological Phylogenetics in the Genomic Age

(2015) Michael S.Y. Lee et al.   CURRENT BIOLOGY

The Fossil Calibration Database—A New Resource for Divergence Dating

(2015) Daniel T. Ksepka et al.   SYSTEMATIC BIOLOGY

Dating Tips for Divergence-Time Estimation

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

tqDist: a library for computing the quartet and triplet distances between binary or general trees

(2014) Andreas Sand et al.   BIOINFORMATICS

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

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

Ancient dates or accelerated rates? Morphological clocks and the antiquity of placental mammals

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

Rates of Phenotypic and Genomic Evolution during the Cambrian Explosion

(2013) Michael S.Y. Lee et al.   CURRENT BIOLOGY

Arthropod fossil data increase congruence of morphological and molecular phylogenies

(2013) David A. Legg et al.   Nature Communications

Unifying fossils and phylogenies for comparative analyses of diversification and trait evolution

(2013) Graham J. Slater et al.   Methods in Ecology and 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

INTEGRATING FOSSILS WITH MOLECULAR PHYLOGENIES IMPROVES INFERENCE OF TRAIT EVOLUTION

(2012) Graham J. Slater et al.   EVOLUTION

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

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

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

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

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Stratocladistics: Integrating Temporal Data and Character Data in Phylogenetic Inference

(2008) Daniel C. Fisher   Annual Review of Ecology Evolution and Systematics