A General and Efficient Algorithm for the Likelihood of Diversification and Discrete-Trait Evolutionary Models

Macroevolutionary diversification rates show time dependency

(2019) L. Francisco Henao Diaz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

AnnoTree: visualization and exploration of a functionally annotated microbial tree of life

(2019) Kerrin Mendler et al.   NUCLEIC ACIDS RESEARCH

Swapping Birth and Death: Symmetries and Transformations in Phylodynamic Models

(2019) Tanja Stadler et al.   SYSTEMATIC BIOLOGY

What we (don't) know about global plant diversity

(2019) William K. Cornwell et al.   ECOGRAPHY

Constructing a broadly inclusive seed plant phylogeny

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

Bacterial diversification through geological time

(2018) Stilianos Louca et al.   Nature Ecology & Evolution

Hidden state models improve state-dependent diversification approaches, including biogeographical models

(2018) Daniel S. Caetano et al.   EVOLUTION

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Detecting the Dependence of Diversification on Multiple Traits from Phylogenetic Trees and Trait Data

(2018) Leonel Herrera-Alsina et al.   SYSTEMATIC BIOLOGY

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Speciation gradients and the distribution of biodiversity

(2017) Dolph Schluter et al.   NATURE

Inordinate Fondness Multiplied and Redistributed: the Number of Species on Earth and the New Pie of Life

(2017) Brendan B. Larsen et al.   QUARTERLY REVIEW OF BIOLOGY

Rapid maximum likelihood ancestral state reconstruction of continuous characters: A rerooting-free algorithm

(2017) Eric W. Goolsby   Ecology and Evolution

Detecting Hidden Diversification Shifts in Models of Trait-Dependent Speciation and Extinction

(2016) Jeremy M. Beaulieu et al.   SYSTEMATIC BIOLOGY

Adaptive radiation by waves of gene transfer leads to fine-scale resource partitioning in marine microbes

(2016) Jan-Hendrik Hehemann et al.   Nature Communications

TESS: an R package for efficiently simulating phylogenetic trees and performing Bayesian inference of lineage diversification rates

(2015) Sebastian Höhna et al.   BIOINFORMATICS

Synthesis of phylogeny and taxonomy into a comprehensive tree of life

(2015) Cody E. Hinchliff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenetic approaches for studying diversification

(2014) Hélène Morlon   ECOLOGY LETTERS

How traits shape trees: new approaches for detecting character state-dependent lineage diversification

(2014) J. Ng et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

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

(2014) Daniel L. Rabosky   PLoS One

A Linear-Time Algorithm for Gaussian and Non-Gaussian Trait Evolution Models

(2014) Lam si Tung Ho et al.   SYSTEMATIC BIOLOGY

An integrative view of phylogenetic comparative methods: connections to population genetics, community ecology, and paleobiology

(2013) Matthew W. Pennell et al.   Annals of the New York Academy of Sciences

Macroevolutionary perspectives to environmental change

(2013) Fabien L. Condamine et al.   ECOLOGY LETTERS

Three keys to the radiation of angiosperms into freezing environments

(2013) Amy E. Zanne et al.   NATURE

Dietary innovations spurred the diversification of ruminants during the Caenozoic

(2013) J. L. Cantalapiedra et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Horizontal gene transfer and the evolution of bacterial and archaeal population structure

(2013) Martin F. Polz et al.   TRENDS IN GENETICS

Linking the Investigations of Character Evolution and Species Diversification

(2012) Karen Magnuson-Ford et al.   AMERICAN NATURALIST

A Conceptual and Statistical Framework for Adaptive Radiations with a Key Role for Diversity Dependence

(2012) Rampal S. Etienne et al.   AMERICAN NATURALIST

Evolutionary Inferences from Phylogenies: A Review of Methods

(2012) Brian C. O'Meara   Annual Review of Ecology Evolution and Systematics

The evolution of nitrogen fixation in cyanobacteria

(2012) Natasha Latysheva et al.   BIOINFORMATICS

TEMPO AND MODE IN PLANT BREEDING SYSTEM EVOLUTION

(2012) Emma E. Goldberg et al.   EVOLUTION

The global diversity of birds in space and time

(2012) W. Jetz et al.   NATURE

Diversitree: comparative phylogenetic analyses of diversification in R

(2012) Richard G. FitzJohn   Methods in Ecology and Evolution

Fast likelihood calculations for comparative analyses

(2012) Robert P. Freckleton   Methods in Ecology and Evolution

Cenozoic extinctions account for the low diversity of extant gymnosperms compared with angiosperms

(2011) Michael D. Crisp et al.   NEW PHYTOLOGIST

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

Mammalian phylogeny reveals recent diversification rate shifts

(2011) T. Stadler   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenetic Inference of Reciprocal Effects between Geographic Range Evolution and Diversification

(2011) Emma E. Goldberg et al.   SYSTEMATIC BIOLOGY

Simulating Trees with a Fixed Number of Extant Species

(2011) Tanja Stadler   SYSTEMATIC BIOLOGY

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

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

How Many Species Are There on Earth and in the Ocean?

(2011) Camilo Mora et al.   PLOS BIOLOGY

Rapid evolutionary innovation during an Archaean genetic expansion

(2010) Lawrence A. David et al.   NATURE

Equilibrium speciation dynamics in a model adaptive radiation of island lizards

(2010) D. L. Rabosky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantitative Traits and Diversification

(2010) Richard G. FitzJohn   SYSTEMATIC BIOLOGY

Inferring the Dynamics of Diversification: A Coalescent Approach

(2010) Hélène Morlon et al.   PLOS BIOLOGY

On incomplete sampling under birth–death models and connections to the sampling-based coalescent

(2009) Tanja Stadler   JOURNAL OF THEORETICAL BIOLOGY

Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates

(2009) M. E. Alfaro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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