A Bayesian approach for detecting the impact of mass-extinction events on molecular phylogenies when rates of lineage diversification may vary

RPANDA: an R package for macroevolutionary analyses on phylogenetic trees

(2016) Hélène Morlon et al.   Methods in Ecology and Evolution

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

(2015) Sebastian Höhna et al.   BIOINFORMATICS

Detecting patterns of species diversification in the presence of both rate shifts and mass extinctions

(2015) Sacha Laurent et al.   BMC EVOLUTIONARY BIOLOGY

The time-dependent reconstructed evolutionary process with a key-role for mass-extinction events

(2015) Sebastian Höhna   JOURNAL OF THEORETICAL BIOLOGY

Revisiting the origin and diversification of vascular plants through a comprehensive Bayesian analysis of the fossil record

(2015) Daniele Silvestro et al.   NEW PHYTOLOGIST

Phylogenetic approaches for studying diversification

(2014) Hélène Morlon   ECOLOGY LETTERS

Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth-death SIR model

(2014) D. Kuhnert et al.   Journal of the Royal Society Interface

Phylogenetic analysis accounting for age-dependent death and sampling with applications to epidemics

(2014) Amaury Lambert et al.   JOURNAL OF THEORETICAL BIOLOGY

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

(2014) Daniel L. Rabosky   PLoS One

Likelihood Inference of Non-Constant Diversification Rates with Incomplete Taxon Sampling

(2014) Sebastian Höhna   PLoS One

Bayesian Estimation of Speciation and Extinction from Incomplete Fossil Occurrence Data

(2014) Daniele Silvestro et al.   SYSTEMATIC BIOLOGY

Why does diversification slow down?

(2014) Daniel Moen et al.   TRENDS IN ECOLOGY & EVOLUTION

Fast simulation of reconstructed phylogenies under global time-dependent birth–death processes

(2013) Sebastian Höhna   BIOINFORMATICS

Macroevolutionary perspectives to environmental change

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

Searching for efficient Markov chain Monte Carlo proposal kernels

(2013) Z. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The plant fossil record reflects just two great extinction events

(2013) Borja Cascales-Miñana et al.   TERRA NOVA

Birth–death models and coalescent point processes: The shape and probability of reconstructed phylogenies

(2013) Amaury Lambert et al.   THEORETICAL POPULATION BIOLOGY

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

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

Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV)

(2012) T. Stadler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hemisphere-scale differences in conifer evolutionary dynamics

(2012) A. B. Leslie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Bayesian framework to estimate diversification rates and their variation through time and space

(2011) Daniele Silvestro et al.   BMC EVOLUTIONARY BIOLOGY

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

Mammalian phylogeny reveals recent diversification rate shifts

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

Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record

(2011) R. S. Etienne et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

The contour of splitting trees is a Lévy process

(2010) Amaury Lambert   ANNALS OF PROBABILITY

TIME-DEPENDENT SPECIATION AND EXTINCTION FROM PHYLOGENIES: A LEAST SQUARES APPROACH

(2010) Emmanuel Paradis   EVOLUTION

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

EXPLOSIVE RADIATION OR CRYPTIC MASS EXTINCTION? INTERPRETING SIGNATURES IN MOLECULAR PHYLOGENIES

(2009) Michael D. Crisp et al.   EVOLUTION

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

(2009) Tanja Stadler   JOURNAL OF THEORETICAL BIOLOGY

A Bayesian approach for evaluating the impact of historical events on rates of diversification

(2009) B. R. Moore et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

EXPLOSIVE EVOLUTIONARY RADIATIONS: DECREASING SPECIATION OR INCREASING EXTINCTION THROUGH TIME?

(2008) Daniel L. Rabosky et al.   EVOLUTION