Megaphylogeny resolves global patterns of mushroom evolution

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

Explosive diversification of marine fishes at the Cretaceous–Palaeogene boundary

(2018) Michael E. Alfaro et al.   Nature Ecology & Evolution

Evolutionary dynamics of host specialization in wood-decay fungi

(2018) Franz-Sebastian Krah et al.   BMC EVOLUTIONARY BIOLOGY

Contemporaneous radiations of fungi and plants linked to symbiosis

(2018) François Lutzoni et al.   Nature Communications

Biotic and environmental dynamics through the Late Jurassic-Early Cretaceous transition: evidence for protracted faunal and ecological turnover

(2016) Jonathan P. Tennant et al.   BIOLOGICAL REVIEWS

Is the switch to an ectomycorrhizal state an evolutionary key innovation in mushroom-forming fungi? A case study in the Tricholomatineae (Agaricales)

(2016) Marisol Sánchez-García et al.   EVOLUTION

Into and out of the tropics: global diversification patterns in a hyperdiverse clade of ectomycorrhizal fungi

(2016) Brian P. Looney et al.   MOLECULAR ECOLOGY

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

Dimensions of biodiversity in the Earth mycobiome

(2016) Kabir G. Peay et al.   NATURE REVIEWS MICROBIOLOGY

Evolution of ectomycorrhizas as a driver of diversification and biogeographic patterns in the model mycorrhizal mushroom genus Laccaria

(2016) Andrew W. Wilson et al.   NEW PHYTOLOGIST

Critically evaluating the theory and performance of Bayesian analysis of macroevolutionary mixtures

(2016) Brian R. Moore et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2016) Michael R. May et al.   Methods in Ecology and Evolution

FinisherSC: a repeat-aware tool for upgradingde novoassembly using long reads

(2015) Ka-Kit Lam et al.   BIOINFORMATICS

Challenges in the estimation of extinction from molecular phylogenies: A response to Beaulieu and O'Meara

(2015) Daniel L. Rabosky   EVOLUTION

High speciation rate at temperate latitudes explains unusual diversity gradients in a clade of ectomycorrhizal fungi

(2015) Santiago Sánchez-Ramírez et al.   EVOLUTION

Extinction can be estimated from moderately sized molecular phylogenies

(2015) Jeremy M. Beaulieu et al.   EVOLUTION

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

(2015) Sebastian Höhna   JOURNAL OF THEORETICAL BIOLOGY

Comparative Genomics of Early-Diverging Mushroom-Forming Fungi Provides Insights into the Origins of Lignocellulose Decay Capabilities

(2015) László G. Nagy et al.   MOLECULAR BIOLOGY AND EVOLUTION

Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists

(2015) Annegret Kohler et al.   NATURE GENETICS

Adaptive radiation versus ‘radiation’ and ‘explosive diversification’: why conceptual distinctions are fundamental to understanding evolution

(2015) Thomas J. Givnish   NEW PHYTOLOGIST

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Bird's nest fungi (Nidulariales: Nidulariaceae) in Baltic and Dominican amber

(2014) George Poinar   Fungal Biology

Palaeotropical origins, boreotropical distribution and increased rates of diversification in a clade of edible ectomycorrhizal mushrooms (AmanitasectionCaesareae)

(2014) Santiago Sánchez-Ramírez et al.   JOURNAL OF BIOGEOGRAPHY

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

(2014) Daniel L. Rabosky   PLoS One

Global diversity and geography of soil fungi

(2014) L. Tedersoo et al.   SCIENCE

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

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

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

(2013) Sebastian Höhna   BIOINFORMATICS

Variation in forest soil fungal diversity along a latitudinal gradient

(2013) Ling-Ling Shi et al.   FUNGAL DIVERSITY

Iteratively Refined Guide Trees Help Improving Alignment and Phylogenetic Inference in the Mushroom Family Bolbitiaceae

(2013) Annamária Tóth et al.   PLoS One

Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation

(2013) Daniel L. Rabosky et al.   Nature Communications

The global diversity of birds in space and time

(2012) W. Jetz et al.   NATURE

Diversity and evolution of ectomycorrhizal host associations in the Sclerodermatineae (Boletales, Basidiomycota)

(2012) Andrew W. Wilson et al.   NEW PHYTOLOGIST

The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes

(2012) D. Floudas et al.   SCIENCE

An Update of Wallace's Zoogeographic Regions of the World

(2012) B. G. Holt et al.   SCIENCE

The Evolution of Defense Mechanisms Correlate with the Explosive Diversification of Autodigesting Coprinellus Mushrooms (Agaricales, Fungi)

(2012) László G. Nagy et al.   SYSTEMATIC BIOLOGY

Diversitree: comparative phylogenetic analyses of diversification in R

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

Fungi and the Rise of Mammals

(2012) Arturo Casadevall   PLoS Pathogens

Phylogenetic Inference of Reciprocal Effects between Geographic Range Evolution and Diversification

(2011) Emma E. Goldberg 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

Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads

(2010) Jeffrey Martin et al.   BMC GENOMICS

EFFECTS OF GASTEROID FRUITING BODY MORPHOLOGY ON DIVERSIFICATION RATES IN THREE INDEPENDENT CLADES OF FUNGI ESTIMATED USING BINARY STATE SPECIATION AND EXTINCTION ANALYSIS

(2010) Andrew W. Wilson et al.   EVOLUTION

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre 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

Improving Marginal Likelihood Estimation for Bayesian Phylogenetic Model Selection

(2010) Wangang Xie et al.   SYSTEMATIC BIOLOGY

Phanerozoic atmospheric oxygen: New results using the GEOCARBSULF model

(2009) R. A. Berner   AMERICAN JOURNAL OF SCIENCE

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The angiosperm radiation revisited, an ecological explanation for Darwin’s ‘abominable mystery’

(2009) Frank Berendse et al.   ECOLOGY LETTERS

EXTINCTION RATES SHOULD NOT BE ESTIMATED FROM MOLECULAR PHYLOGENIES

(2009) Daniel L. Rabosky   EVOLUTION

Temporal lags and overlap in the diversification of weevils and flowering plants

(2009) D. D. McKenna 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

Adaptive Radiation: Contrasting Theory with Data

(2009) S. Gavrilets et al.   SCIENCE

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

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

Birth-death prior on phylogeny and speed dating

(2008) Orjan Akerborg et al.   BMC EVOLUTIONARY BIOLOGY

Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis

(2008) A. Loytynoja et al.   SCIENCE