Phylogenomic and Macroevolutionary Evidence for an Explosive Radiation of a Plant Genus in the Miocene

Gene Tree Discord, Simplex Plots, and Statistical Tests under the Coalescent

(2021) Elizabeth S Allman et al.   SYSTEMATIC BIOLOGY

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

The role of evolutionary time, diversification rates and dispersal in determining the global diversity of a large radiation of passerine birds

(2020) Tianlong Cai et al.   JOURNAL OF BIOGEOGRAPHY

The genome of a cave plant, Primulina huaijiensis , provides insights into adaptation to limestone karst habitats

(2020) Chao Feng et al.   NEW PHYTOLOGIST

Why the ‘Uplift of the Tibetan Plateau’ is a myth

(2020) Robert A Spicer et al.   National Science Review

The early Eocene rise of the Gonjo Basin, SE Tibet: From low desert to high forest

(2020) Zhongyu Xiong et al.   EARTH AND PLANETARY SCIENCE LETTERS

Ancient orogenic and monsoon-driven assembly of the world’s richest temperate alpine flora

(2020) Wen-Na Ding et al.   SCIENCE

MSCquartets 1.0: Quartet methods for species trees and networks under the multispecies coalescent model in R

(2020) John A Rhodes et al.   BIOINFORMATICS

Parallel ddRAD and Genome Skimming Analyses Reveal a Radiative and Reticulate Evolutionary History of the Temperate Bamboos

(2020) Cen Guo et al.   SYSTEMATIC BIOLOGY

Mountains as Evolutionary Arenas: Patterns, Emerging Approaches, Paradigm Shifts, and Their Implications for Plant Phylogeographic Research in the Tibeto-Himalayan Region

(2019) Alexandra N. Muellner-Riehl   Frontiers in Plant Science

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

(2019) Remco Bouckaert et al.   PLoS Computational Biology

Phylogenomic conflict resulting from ancient introgression following species diversification in Stewartia s.l. (Theaceae)

(2019) Han-Yang Lin et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenomics Uncovers Confidence and Conflict in the Rapid Radiation of Australo-Papuan Rodents

(2019) Emily J Roycroft et al.   SYSTEMATIC BIOLOGY

Assessing the causes of diversification slowdowns: temperature‐dependent and diversity‐dependent models receive equivalent support

(2019) Fabien L. Condamine et al.   ECOLOGY LETTERS

Rapid diversification of alpine bamboos associated with the uplift of the Hengduan Mountains

(2019) Xia‐Ying Ye et al.   JOURNAL OF BIOGEOGRAPHY

Building mountain biodiversity: Geological and evolutionary processes

(2019) Carsten Rahbek et al.   SCIENCE

RASP 4: ancestral state reconstruction tool for multiple genes and characters

(2019) Yan Yu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Past East Asian monsoon evolution controlled by paleogeography, not CO2

(2019) Alex Farnsworth et al.   Science Advances

Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life

(2018) James B. Pease et al.   AMERICAN JOURNAL OF BOTANY

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

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

Phylogenomics of a rapid radiation: the Australian rainbow skinks

(2018) Jason G. Bragg et al.   BMC EVOLUTIONARY BIOLOGY

Conceptual and statistical problems with the DEC+J model of founder-event speciation and its comparison with DEC via model selection

(2018) Richard H. Ree et al.   JOURNAL OF BIOGEOGRAPHY

Phylogenomic Analysis of the Explosive Adaptive Radiation of the Espeletia Complex (Asteraceae) in the Tropical Andes

(2018) Charles Pouchon et al.   SYSTEMATIC BIOLOGY

Testing the Role of the Red Queen and Court Jester as Drivers of the Macroevolution of Apollo Butterflies

(2018) Fabien L. Condamine et al.   SYSTEMATIC BIOLOGY

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

(2018) Andrew Rambaut et al.   SYSTEMATIC BIOLOGY

Phylogenetics and dispersal patterns of Brassicaceae around the Qinghai-Tibet Plateau

(2018) Chaoju Qian et al.   Journal of Systematics and Evolution

BAMM at the court of false equivalency: A response to Meyer and Wiens

(2018) Daniel L. Rabosky   EVOLUTION

Resolving the rapid plant radiation of early diverging lineages in the tropical Zingiberales: Pushing the limits of genomic data

(2018) Mónica M. Carlsen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogeny and evolutionary history of Pinaceae updated by transcriptomic analysis

(2018) Jin-Hua Ran et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Geological and climatic influences on mountain biodiversity

(2018) Alexandre Antonelli et al.   Nature Geoscience

How mountains shape biodiversity: the role of the Andes in biogeography, diversification and reproductive biology in South America's most species rich lizard radiation (Squamata: Liolaemidae)

(2018) Damien Esquerré et al.   EVOLUTION

Global Cooling Contributed to the Establishment of a Modern-Like East Asian Monsoon Climate by the Early Miocene

(2018) Ran Zhang et al.   GEOPHYSICAL RESEARCH LETTERS

Rapid incision of the Mekong River in the middle Miocene linked to monsoonal precipitation

(2018) Junsheng Nie et al.   Nature Geoscience

The rise of the Andes promoted rapid diversification in Neotropical Phlegmariurus (Lycopodiaceae)

(2018) Weston L. Testo et al.   NEW PHYTOLOGIST

Estimating diversification rates for higher taxa: BAMM can give problematic estimates of rates and rate shifts

(2017) Andreas L. S. Meyer et al.   EVOLUTION

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Both temperature fluctuations and East Asian monsoons have driven plant diversification in the karst ecosystems from southern China

(2017) Hanghui Kong et al.   MOLECULAR ECOLOGY

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Recent origin and rapid speciation of Neotropical orchids in the world's richest plant biodiversity hotspot

(2017) Oscar Alejandro Pérez-Escobar et al.   NEW PHYTOLOGIST

Accelerated body size evolution during cold climatic periods in the Cenozoic

(2017) Julien Clavel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Uplift-driven diversification in the Hengduan Mountains, a temperate biodiversity hotspot

(2017) Yaowu Xing et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analysis of Phylogenomic Tree Space Resolves Relationships Among Marsupial Families

(2017) David A Duchêne et al.   SYSTEMATIC BIOLOGY

Genomic data reveals potential for hybridization, introgression, and incomplete lineage sorting to confound phylogenetic relationships in an adaptive radiation of narrow-mouth frogs

(2016) Alana M. Alexander et al.   EVOLUTION

Late Cenozoic genus Fupingopollenites development and its implications for the Asian summer monsoon evolution

(2016) Yunfa Miao et al.   GONDWANA RESEARCH

Available data point to a 4-km-high Tibetan Plateau by 40 Ma, but 100 molecular-clock papers have linked supposed recent uplift to young node ages

(2016) Susanne S. Renner   JOURNAL OF BIOGEOGRAPHY

Out-of-Tibet: the spatio-temporal evolution ofGentiana(Gentianaceae)

(2016) Adrien Favre et al.   JOURNAL OF BIOGEOGRAPHY

Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies

(2016) Erfan Sayyari et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenetic relationships, character evolution and biogeographic diversification of Pogostemon s.l. (Lamiaceae)

(2016) Gang Yao et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The abiotic and biotic drivers of rapid diversification in Andean bellflowers (Campanulaceae)

(2016) Laura P. Lagomarsino 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

Distinct Processes Drive Diversification in Different Clades of Gesneriaceae

(2016) Eric H. Roalson et al.   SYSTEMATIC BIOLOGY

The Evolving Theory of Evolutionary Radiations

(2016) M. Simões et al.   TRENDS IN ECOLOGY & EVOLUTION

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

RPANDA: an R package for macroevolutionary analyses on phylogenetic trees

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

Diversity distribution patterns of Chinese endemic seed plant species and their implications for conservation planning

(2016) Jihong Huang et al.   Scientific Reports

A new delineation for Oreocharis incorporating an additional ten genera of Chinese Gesneriaceae

(2016) M. Moller et al.   Phytotaxa

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

(2015) Sebastian Höhna et al.   BIOINFORMATICS

Origin and diversification of living cycads: a cautionary tale on the impact of the branching process prior in Bayesian molecular dating

(2015) Fabien L Condamine et al.   BMC EVOLUTIONARY BIOLOGY

Cenozoic paleoaltimetry of the SE margin of the Tibetan Plateau: Constraints on the tectonic evolution of the region

(2015) Shanying Li et al.   EARTH AND PLANETARY SCIENCE LETTERS

Dissecting Molecular Evolution in the Highly Diverse Plant Clade Caryophyllales Using Transcriptome Sequencing

(2015) Ya Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2015) Thomas J. Givnish   NEW PHYTOLOGIST

Model Inadequacy and Mistaken Inferences of Trait-Dependent Speciation

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

The Challenges of Resolving a Rapid, Recent Radiation: Empirical and Simulated Phylogenomics of Philippine Shrews

(2015) Thomas C. Giarla et al.   SYSTEMATIC BIOLOGY

Quartet Inference from SNP Data Under the Coalescent Model

(2014) Julia Chifman et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

The role of the uplift of the Qinghai-Tibetan Plateau for the evolution of Tibetan biotas

(2014) Adrien Favre et al.   BIOLOGICAL REVIEWS

Stable isotopes reveal high southeast Tibetan Plateau margin since the Paleogene

(2014) Gregory D. Hoke et al.   EARTH AND PLANETARY SCIENCE LETTERS

Reconstructing chemical weathering, physical erosion and monsoon intensity since 25Ma in the northern South China Sea: A review of competing proxies

(2014) Peter D. Clift et al.   EARTH-SCIENCE REVIEWS

Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics

(2014) Ya Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Taxonomic Status, Phylogenetic Affinities and Genetic Diversity of a Presumed Extinct Genus, Paraisometrum W.T. Wang (Gesneriaceae) from the Karst Regions of Southwest China

(2014) Wen-Hong Chen et al.   PLoS One

Why does diversification slow down?

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

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

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

Diversity-Dependence, Ecological Speciation, and the Role of Competition in Macroevolution

(2013) Daniel L. Rabosky   Annual Review of Ecology Evolution and Systematics

Influence of the Tibetan Plateau uplift on the Asian monsoon-arid environment evolution

(2013) XiaoDong Liu et al.   CHINESE SCIENCE BULLETIN

Macroevolutionary perspectives to environmental change

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

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Biodiversity from mountain building

(2013) Carina Hoorn et al.   Nature Geoscience

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Evolution of the monsoon and dry climate in East Asia during late Cenozoic: A review

(2013) HuaYu Lu et al.   Science China-Earth Sciences

Inferring the biogeographic origins of inter-continental disjunct endemics using a Bayes-DIVA approach

(2013) AJ HARRIS et al.   Journal of Systematics and Evolution

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

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

Páramo is the world's fastest evolving and coolest biodiversity hotspot

(2013) Santiago Madriñán et al.   Frontiers in Genetics

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

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

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

The rise of the Himalaya enforced the diversification of SE Asian ferns by altering the monsoon regimes

(2012) Li Wang et al.   BMC PLANT BIOLOGY

EXPLOSIVE RADIATION OF A BACTERIAL SPECIES GROUP

(2012) Hélène Morlon et al.   EVOLUTION

Spatio-temporal evolution ofFosterella(Bromeliaceae) in the Central Andean biodiversity hotspot

(2012) Natascha Wagner et al.   JOURNAL OF BIOGEOGRAPHY

Multiple Continental Radiations and Correlates of Diversification in Lupinus (Leguminosae): Testing for Key Innovation with Incomplete Taxon Sampling

(2012) Christopher S. Drummond et al.   SYSTEMATIC BIOLOGY

Diversitree: comparative phylogenetic analyses of diversification in R

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

Centres of plant endemism in China: places for survival or for speciation?

(2011) Jordi López-Pujol et al.   JOURNAL OF BIOGEOGRAPHY

Phylogeny of iguanian lizards inferred from 29 nuclear loci, and a comparison of concatenated and species-tree approaches for an ancient, rapid radiation

(2011) Ted M. Townsend et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Applications of next-generation sequencing to phylogeography and phylogenetics

(2011) John E. McCormack et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

PALEOGENE EVOLUTION OF PRECIPITATION IN NORTHEASTERN CHINA SUPPORTING THE MIDDLE EOCENE INTENSIFICATION OF THE EAST ASIAN MONSOON

(2011) C. QUAN et al.   PALAIOS

Orographic Controls on Climate and Paleoclimate of Asia: Thermal and Mechanical Roles for the Tibetan Plateau

(2010) Peter Molnar et al.   Annual Review of Earth and Planetary Sciences

Phylogenetic Insights on Adaptive Radiation

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

The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell

(2010) T. Junier et al.   BIOINFORMATICS

Biodiverse, a tool for the spatial analysis of biological and related diversity

(2010) Shawn W. Laffan et al.   ECOGRAPHY

Ecological opportunity and the origin of adaptive radiations

(2010) J. B. YODER et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Multilocus phylogeny and rapid radiations in Neotropical cichlid fishes (Perciformes: Cichlidae: Cichlinae)

(2010) Hernán López-Fernández et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Diversification and biogeography of Juniperus (Cupressaceae): variable diversification rates and multiple intercontinental dispersals

(2010) Kangshan Mao et al.   NEW PHYTOLOGIST

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

Unparalleled rates of species diversification in Europe

(2010) L. M. Valente et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Ecological limits and diversification rate: alternative paradigms to explain the variation in species richness among clades and regions

(2009) Daniel L. Rabosky   ECOLOGY LETTERS

Rapid radiation of Impatiens (Balsaminaceae) during Pliocene and Pleistocene: Result of a global climate change

(2009) Steven B. Janssens et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Adaptive Radiation: Contrasting Theory with Data

(2009) S. Gavrilets et al.   SCIENCE

The Red Queen and the Court Jester: Species Diversity and the Role of Biotic and Abiotic Factors Through Time

(2009) M. J. Benton   SCIENCE

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

Resolving Species Phylogenies of Recent Evolutionary Radiations1

(2008) L. Lacey Knowles et al.   ANNALS OF THE MISSOURI BOTANICAL GARDEN

ON PHYLOGENETIC TESTS OF IRREVERSIBLE EVOLUTION

(2008) Emma E. Goldberg et al.   EVOLUTION

An early Cenozoic perspective on greenhouse warming and carbon-cycle dynamics

(2008) James C. Zachos et al.   NATURE

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

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

Density-Dependent Cladogenesis in Birds

(2008) Albert B Phillimore et al.   PLOS BIOLOGY