A Total-Group Phylogenetic Metatree for Cetacea and the Importance of Fossil Data in Diversification Analyses

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ecologically diverse clades dominate the oceans via extinction resistance

(2020) Matthew L. Knope et al.   SCIENCE

Extant timetrees are consistent with a myriad of diversification histories

(2020) Stilianos Louca et al.   NATURE

Norisdelphis annakaensis, A new Miocene delphinid from Japan

(2020) Toshiyuki Kimura et al.   JOURNAL OF VERTEBRATE PALEONTOLOGY

Evolution and Diversification of Delphinid Skull Shapes

(2020) Anders Galatius et al.   iScience

Hierarchy in adaptive radiation: A case study using the Carnivora (Mammalia)

(2019) Graham J. Slater et al.   EVOLUTION

Megaphylogeny resolves global patterns of mushroom evolution

(2019) Torda Varga et al.   Nature Ecology & Evolution

Diversity and skepticism are vital for comparative biology: a response to Donoghue and Edwards (2019)

(2019) Jeremy M. Beaulieu et al.   AMERICAN JOURNAL OF BOTANY

The Paradox Behind the Pattern of Rapid Adaptive Radiation: How Can the Speciation Process Sustain Itself Through an Early Burst?

(2019) Christopher H. Martin et al.   Annual Review of Ecology Evolution and Systematics

A Laurasian origin for a pantropical bird radiation is supported by genomic and fossil data (Aves: Coraciiformes)

(2019) Jenna M. McCullough et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Phylogenomic Resolution of the Cetacean Tree of Life Using Target Sequence Capture

(2019) Michael R McGowen et al.   SYSTEMATIC BIOLOGY

Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation

(2019) Nathan S. Upham et al.   PLOS BIOLOGY

The complete mitochondrial genome of the critically endangered Atlantic humpback dolphin, Sousa teuszii (Kükenthal, 1892)

(2019) Michael R. McGowen et al.   Mitochondrial DNA Part B-Resources

Constructing a broadly inclusive seed plant phylogeny

(2018) Stephen A. Smith et al.   AMERICAN JOURNAL OF BOTANY

Can we build it? Yes we can, but should we use it? Assessing the quality and value of a very large phylogeny of campanulid angiosperms

(2018) Jeremy M. Beaulieu et al.   AMERICAN JOURNAL OF BOTANY

Out of the Antilles: Fossil phylogenies support reverse colonization of bats to South America

(2018) Valéria da C. Tavares et al.   JOURNAL OF BIOGEOGRAPHY

The interplay of past diversification and evolutionary isolation with present imperilment across the amphibian tree of life

(2018) Walter Jetz et al.   Nature Ecology & Evolution

Global priorities for conserving the evolutionary history of sharks, rays and chimaeras

(2018) R. William Stein et al.   Nature Ecology & Evolution

An overview of extant conifer evolution from the perspective of the fossil record

(2018) Andrew B. Leslie et al.   AMERICAN JOURNAL OF BOTANY

An inverse latitudinal gradient in speciation rate for marine fishes

(2018) Daniel L. Rabosky et al.   NATURE

Fossil lemurs from Egypt and Kenya suggest an African origin for Madagascar’s aye-aye

(2018) Gregg F. Gunnell et al.   Nature Communications

Bad Clade Deletion Supertrees: A Fast and Accurate Supertree Algorithm

(2017) Markus Fleischauer et al.   MOLECULAR BIOLOGY AND EVOLUTION

treespace : Statistical exploration of landscapes of phylogenetic trees

(2017) Thibaut Jombart et al.   Molecular Ecology Resources

Mega-evolutionary dynamics of the adaptive radiation of birds

(2017) Christopher R. Cooney et al.   NATURE

Estimating Age-Dependent Extinction: Contrasting Evidence from Fossils and Phylogenies

(2017) Oskar Hagen et al.   SYSTEMATIC BIOLOGY

Lineage Diversity and Size Disparity in Musteloidea: Testing Patterns of Adaptive Radiation Using Molecular and Fossil-Based Methods

(2017) Chris J. Law et al.   SYSTEMATIC BIOLOGY

A new fossil dolphin Dilophodelphis fordycei provides insight into the evolution of supraorbital crests in Platanistoidea (Mammalia, Cetacea)

(2017) Alexandra T. Boersma et al.   Royal Society Open Science

Five palaeobiological laws needed to understand the evolution of the living biota

(2017) Charles R. Marshall   Nature Ecology & Evolution

Ecological Opportunity and Adaptive Radiation

(2016) James T. Stroud et al.   Annual Review of Ecology Evolution and Systematics

Fully-sampled phylogenies of squamates reveal evolutionary patterns in threat status

(2016) João Filipe Riva Tonini et al.   BIOLOGICAL CONSERVATION

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

Probabilistic divergence time estimation without branch lengths: dating the origins of dinosaurs, avian flight and crown birds

(2016) G. T. Lloyd et al.   Biology Letters

The Origin of High-Frequency Hearing in Whales

(2016) Morgan Churchill et al.   CURRENT BIOLOGY

Historical Biogeography of Delphininae Dolphins and Related Taxa (Artiodactyla: Delphinidae)

(2016) Karina Bohrer do Amaral et al.   JOURNAL OF MAMMALIAN EVOLUTION

Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution

(2016) Michelle Kendall et al.   MOLECULAR BIOLOGY AND EVOLUTION

Little evidence for enhanced phenotypic evolution in early teleosts relative to their living fossil sister group

(2016) John T. Clarke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fossil-based comparative analyses reveal ancient marine ancestry erased by extinction in ray-finned fishes

(2015) Ricardo Betancur-R et al.   ECOLOGY LETTERS

Extinction can be estimated from moderately sized molecular phylogenies

(2015) Jeremy M. Beaulieu et al.   EVOLUTION

C ongruent phylogenetic and fossil signatures of mammalian diversification dynamics driven by Tertiary abiotic change

(2015) Juan L. Cantalapiedra et al.   EVOLUTION

Mitochondrial genome of theNeophocaena asiaeorientalis asiaeorientalis(Phocaenidae: Neophocaena)

(2015) Xinyang Liu et al.   Mitochondrial DNA

Reconstructing (Super)Trees from Data Sets with Missing Distances: Not All Is Lost

(2015) George Kettleborough et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Paleobiology Database application programming interface

(2015) Shanan E. Peters et al.   PALEOBIOLOGY

Iterative adaptive radiations of fossil canids show no evidence for diversity-dependent trait evolution

(2015) Graham J. Slater   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Taxonomy and Phylogeny Can Yield Comparable Results in Comparative Paleontological Analyses

(2015) Laura C. Soul et al.   SYSTEMATIC BIOLOGY

Model Inadequacy and Mistaken Inferences of Trait-Dependent Speciation

(2015) Daniel L. Rabosky et al.   SYSTEMATIC BIOLOGY

Implementing and testing Bayesian and maximum-likelihood supertree methods in phylogenetics

(2015) Wasiu A. Akanni et al.   Royal Society Open Science

Baleen boom and bust: a synthesis of mysticete phylogeny, diversity and disparity

(2015) F. G. Marx et al.   Royal Society Open Science

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Eodelphis kabatensis, a new name for the oldest true dolphinStenella kabatensisHorikawa, 1977 (Cetacea, Odontoceti, Delphinidae), from the upper Miocene of Japan, and the phylogeny and paleobiogeography of Delphinoidea

(2014) Mizuki Murakami et al.   JOURNAL OF VERTEBRATE PALEONTOLOGY

Huaridelphis raimondii, a new early Miocene Squalodelphinidae (Cetacea, Odontoceti) from the Chilcatay Formation, Peru

(2014) Olivier Lambert et al.   JOURNAL OF VERTEBRATE PALEONTOLOGY

Resurrection ofMesoplodon hotaulaDeraniyagala 1963: A new species of beaked whale in the tropical Indo-Pacific

(2014) Merel L. Dalebout et al.   MARINE MAMMAL SCIENCE

ExaBayes: Massively Parallel Bayesian Tree Inference for the Whole-Genome Era

(2014) Andre J. Aberer et al.   MOLECULAR BIOLOGY AND EVOLUTION

strap: an R package for plotting phylogenies against stratigraphy and assessing their stratigraphic congruence

(2014) Mark A. Bell et al.   PALAEONTOLOGY

Automatic Detection of Key Innovations, Rate Shifts, and Diversity-Dependence on Phylogenetic Trees

(2014) Daniel L. Rabosky   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

Integrating Fossils, Phylogenies, and Niche Models into Biogeography to Reveal Ancient Evolutionary History: The Case of Hypericum (Hypericaceae)

(2014) Andrea S. Meseguer et al.   SYSTEMATIC BIOLOGY

BAMMtools: an R package for the analysis of evolutionary dynamics on phylogenetic trees

(2014) Daniel L. Rabosky et al.   Methods in Ecology and Evolution

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration

(2014) Alexandra Gavryushkina et al.   PLoS Computational Biology

Three keys to the radiation of angiosperms into freezing environments

(2013) Amy E. Zanne et al.   NATURE

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 phylogenetic blueprint for a modern whale

(2012) John Gatesy et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The global diversity of birds in space and time

(2012) W. Jetz et al.   NATURE

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

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Mitogenomic phylogenetic analyses of the Delphinidae with an emphasis on the Globicephalinae

(2011) Julia T Vilstrup et al.   BMC EVOLUTIONARY BIOLOGY

MorphoBank: phylophenomics in the “cloud”

(2011) Maureen A. O’Leary et al.   CLADISTICS

EVOLUTIONARY DIVERSIFICATION OF REEF CORALS: A COMPARISON OF THE MOLECULAR AND FOSSIL RECORDS

(2011) Carl Simpson et al.   EVOLUTION

The extinct baleen whale fauna from the Miocene-Pliocene of Belgium and the diagnostic cetacean ear bones

(2011) Mette Elstrup Steeman   JOURNAL OF SYSTEMATIC PALAEONTOLOGY

Inferring Speciation and Extinction Rates under Different Sampling Schemes

(2011) S. Hohna et al.   MOLECULAR BIOLOGY AND EVOLUTION

Reconciling molecular phylogenies with the fossil record

(2011) H. Morlon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SuperFine: Fast and Accurate Supertree Estimation

(2011) M. Shel Swenson et al.   SYSTEMATIC BIOLOGY

A simple polytomy resolver for dated phylogenies

(2011) Tyler S. Kuhn et al.   Methods in Ecology and Evolution

Phylogenetic Insights on Adaptive Radiation

(2010) Richard E. Glor   Annual Review of Ecology Evolution and Systematics

SUPERTRIPLETS: a triplet-based supertree approach to phylogenomics

(2010) V. Ranwez et al.   BIOINFORMATICS

Diversity versus disparity and the radiation of modern cetaceans

(2010) G. J. Slater et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

When Can Decreasing Diversification Rates Be Detected with Molecular Phylogenies and the Fossil Record?

(2010) Lee Hsiang Liow et al.   SYSTEMATIC BIOLOGY

Diversity dynamics: molecular phylogenies need the fossil record

(2010) Tiago B. Quental et al.   TRENDS IN ECOLOGY & EVOLUTION

Fossils provide better estimates of ancestral body size than do extant taxa in fishes

(2009) James S. Albert et al.   ACTA ZOOLOGICA

Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches

(2009) Stephen A Smith et al.   BMC EVOLUTIONARY BIOLOGY

EXTINCTION RATES SHOULD NOT BE ESTIMATED FROM MOLECULAR PHYLOGENIES

(2009) Daniel L. Rabosky   EVOLUTION

Divergence date estimation and a comprehensive molecular tree of extant cetaceans

(2009) Michael R. McGowen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Estimating Trait-Dependent Speciation and Extinction Rates from Incompletely Resolved Phylogenies

(2009) Richard G. FitzJohn et al.   SYSTEMATIC BIOLOGY

Radiation of Extant Cetaceans Driven by Restructuring of the Oceans

(2009) Mette E. Steeman et al.   SYSTEMATIC BIOLOGY

Species Selection: Theory and Data

(2008) David Jablonski   Annual Review of Ecology Evolution and Systematics

TNT, a free program for phylogenetic analysis

(2008) Pablo A. Goloboff et al.   CLADISTICS

New protocetid whales from Alabama and Mississippi, and a new Cetacean clade, Pelagiceti

(2008) Mark D. Uhen   JOURNAL OF VERTEBRATE PALEONTOLOGY

Dinosaurs and the Cretaceous Terrestrial Revolution

(2008) G. T Lloyd et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Phylogeny of the Beaked Whale Genus Mesoplodon (Ziphiidae: Cetacea) Revealed by Nuclear Introns: Implications for the Evolution of Male Tusks

(2008) Merel L. Dalebout et al.   SYSTEMATIC BIOLOGY

Maximum Likelihood Supertrees

(2008) Mike Steel et al.   SYSTEMATIC BIOLOGY

Maximum Likelihood Inference of Geographic Range Evolution by Dispersal, Local Extinction, and Cladogenesis

(2008) Richard H. Ree et al.   SYSTEMATIC BIOLOGY