Precipitation is the main axis of tropical plant phylogenetic turnover across space and time

Climatic niche lability but growth form conservatism in the African woody flora

(2022) Anaïs‐Pasiphaé Gorel et al.   ECOLOGY LETTERS

New segregates from the Neotropical genus Stryphnodendron (Leguminosae, Caesalpinioideae, mimosoid clade)

(2022) Alexandre G. de Lima et al.   PhytoKeys

Phylogenomic analysis of 997 nuclear genes reveals the need for extensive generic re-delimitation in Caesalpinioideae (Leguminosae)

(2022) Jens J. Ringelberg et al.   PhytoKeys

Disintegration of the genus Prosopis L. (Leguminosae, Caesalpinioideae, mimosoid clade)

(2022) Colin E. Hughes et al.   PhytoKeys

Dilemmas in generic delimitation of Senegalia and allies (Caesalpinioideae, mimosoid clade): how to reconcile phylogenomic evidence with morphology and taxonomy?

(2022) Vanessa Terra et al.   PhytoKeys

Re-circumscription of the mimosoid genus Entada including new combinations for all species of the phylogenetically nested Elephantorrhiza (Leguminosae, Caesalpinioideae, mimosoid clade)

(2022) Shawn A. O’Donnell et al.   PhytoKeys

Phylogeny and classification of the Australasian and Indomalayan mimosoid legumes Archidendron and Archidendropsis (Leguminosae, subfamily Caesalpinioideae, mimosoid clade)

(2022) Gillian K. Brown et al.   PhytoKeys

Re-establishment of the genus Pseudalbizzia (Leguminosae, Caesalpinioideae, mimosoid clade): the New World species formerly placed in Albizia

(2022) Gabriela Aviles Peraza et al.   PhytoKeys

Osodendron gen. nov. (Leguminosae, Caesalpinioideae), a new genus of mimosoid legumes of tropical Africa

(2022) Erik J. M. Koenen   PhytoKeys

Reinstatement of Ticanto (Leguminosae-Caesalpinioideae) – the final piece in the Caesalpinia group puzzle

(2022) Ruth P. Clark et al.   PhytoKeys

Phylogenomic assessment prompts recognition of the Serianthes clade and confirms the monophyly of Serianthes and its relationship with Falcataria and Wallaceodendron in the wider ingoid clade (Leguminosae, Caesalpinioideae)

(2022) Else Demeulenaere et al.   PhytoKeys

Boliviadendron, a new segregate genus of mimosoid legume (Leguminosae, Caesalpinioideae, mimosoid clade) narrowly endemic to the interior Andean valleys of Bolivia

(2022) Élvia Rodrigues de Souza et al.   PhytoKeys

A new generic circumscription of Hydrochorea (Leguminosae, Caesalpinioideae, mimosoid clade) with an amphi-Atlantic distribution

(2022) Marcos Vinicius Batista Soares et al.   PhytoKeys

Mezcala – a new segregate genus of mimosoid legume (Leguminosae, Caesalpinioideae, mimosoid clade) narrowly endemic to the Balsas Depression in Mexico

(2022) Colin E. Hughes et al.   PhytoKeys

Revisiting the phylogeny and taxonomy of the Pithecellobium clade (Leguminosae, Caesalpinioideae) with new generic circumscriptions

(2022) Iván Tamayo-Cen et al.   PhytoKeys

Misleading fruits: The non-monophyly of Pseudopiptadenia and Pityrocarpa supports generic re-circumscriptions and a new genus within mimosoid legumes

(2022) Leonardo M. Borges et al.   PhytoKeys

On the taxonomic affinity of Albizia carbonaria Britton (Leguminosae, Caesalpinioideae-mimosoid clade)

(2022) Erik J. M. Koenen   PhytoKeys

Extinction at the end-Cretaceous and the origin of modern Neotropical rainforests

(2021) Mónica R. Carvalho et al.   SCIENCE

The adaptive challenge of extreme conditions shapes evolutionary diversity of plant assemblages at continental scales

(2021) Danilo M. Neves et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Earth history events shaped the evolution of uneven biodiversity across tropical moist forests

(2021) Oskar Hagen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Multispecies Coalescent Model Outperforms Concatenation Across Diverse Phylogenomic Data Sets

(2020) Xiaodong Jiang et al.   SYSTEMATIC BIOLOGY

Evolutionary diversity in tropical tree communities peaks at intermediate precipitation

(2020) Danilo M. Neves et al.   Scientific Reports

The Global Museum: natural history collections and the future of evolutionary science and public education

(2020) Freek T. Bakker et al.   PeerJ

Biomes as evolutionary arenas: Convergence and conservatism in the trans‐continental succulent biome

(2020) Jens J. Ringelberg et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Extant timetrees are consistent with a myriad of diversification histories

(2020) Stilianos Louca et al.   NATURE

Fast diversification through a mosaic of evolutionary histories characterizes the endemic flora of ancient Neotropical mountains

(2020) Thais N. C. Vasconcelos et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Origin of the Legumes is a Complex Paleopolyploid Phylogenomic Tangle closely associated with the Cretaceous-Paleogene (K-Pg) Mass Extinction Event

(2020) Erik J M Koenen et al.   SYSTEMATIC BIOLOGY

Freezing and water availability structure the evolutionary diversity of trees across the Americas

(2020) Ricardo A. Segovia et al.   Science Advances

A New Species of Mimosa L. ser. Bipinnatae DC. (Leguminosae) from the Cerrado: Taxonomic and Phylogenetic Insights

(2020) Matías Morales et al.   Plants-Basel

Adaptation and coordinated evolution of plant hydraulic traits

(2020) Pablo Sanchez‐Martinez et al.   ECOLOGY LETTERS

An astronomically dated record of Earth’s climate and its predictability over the last 66 million years

(2020) Thomas Westerhold et al.   SCIENCE

Hybrid capture of 964 nuclear genes resolves evolutionary relationships in the mimosoid legumes and reveals the polytomous origins of a large pantropical radiation

(2020) Erik J. M. Koenen et al.   AMERICAN JOURNAL OF BOTANY

Environment and evolutionary history shape phylogenetic turnover in European tetrapods

(2019) Bianca Saladin et al.   Nature Communications

Eocene Fossil Legume Leaves Referable to the Extant Genus Arcoa (Caesalpinioideae, Leguminosae)

(2019) Patrick S. Herendeen et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Model clades are vital for comparative biology, and ascertainment bias is not a problem in practice: a response to Beaulieu and O'Meara (2018)

(2019) Michael J. Donoghue et al.   AMERICAN JOURNAL OF BOTANY

A preliminary phylogeny of Zapoteca (Fabaceae: Caesalpinioideae: Mimosoid clade)

(2019) Julia Ferm   PLANT SYSTEMATICS AND EVOLUTION

Cercis: A Non-polyploid Genomic Relic Within the Generally Polyploid Legume Family

(2019) Jacob S. Stai et al.   Frontiers in Plant Science

Quartet-based computations of internode certainty provide robust measures of phylogenetic incongruence

(2019) Xiaofan Zhou et al.   SYSTEMATIC BIOLOGY

Factors Affecting Targeted Sequencing of 353 Nuclear Genes From Herbarium Specimens Spanning the Diversity of Angiosperms

(2019) Grace E. Brewer et al.   Frontiers in Plant Science

Phylogeny of the Neotropical legume genera Zygia and Marmaroxylon and close relatives

(2019) Julia Ferm et al.   TAXON

Large‐scale genomic sequence data resolve the deepest divergences in the legume phylogeny and support a near‐simultaneous evolutionary origin of all six subfamilies

(2019) Erik J. M. Koenen et al.   NEW PHYTOLOGIST

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

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees

(2018) Uyen Mai et al.   BMC GENOMICS

Tropical savannas and dry forests

(2018) R. Toby Pennington et al.   CURRENT BIOLOGY

Phylogenetic scale in ecology and evolution

(2018) Catherine H. Graham et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

So many genes, so little time: A practical approach to divergence-time estimation in the genomic era

(2018) Stephen A. Smith et al.   PLoS One

Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis

(2018) Maximilian Griesmann et al.   SCIENCE

Modeling the ecology and evolution of biodiversity: Biogeographical cradles, museums, and graves

(2018) Thiago F. Rangel et al.   SCIENCE

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

(2018) Andrew Rambaut et al.   SYSTEMATIC BIOLOGY

Characterization of the chloroplast genome of Erythrophleum fordii (Fabaceae)

(2018) Songyi Huang et al.   Conservation Genetics Resources

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

(2018) Daniel L. Rabosky   EVOLUTION

A sharp floristic discontinuity revealed by the biogeographic regionalization of African savannas

(2018) Adeline Fayolle et al.   JOURNAL OF BIOGEOGRAPHY

Global Succulent Biome phylogenetic conservatism across the pantropical Caesalpinia Group (Leguminosae)

(2018) Edeline Gagnon et al.   NEW PHYTOLOGIST

Dissimilarity measures affected by richness differences yield biased delimitations of biogeographic realms

(2018) Adrián Castro-Insua et al.   Nature Communications

Environmental niche conservatism explains the accumulation of species richness in Mediterranean-hotspot plant genera

(2017) Alexander Skeels et al.   EVOLUTION

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

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

Global patterns of β-diversity along the phylogenetic time-scale: The role of climate and plate tectonics

(2017) Florent Mazel et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Geographical patterns of phylogenetic beta-diversity components in terrestrial mammals

(2017) F. P. Peixoto et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Plant phylogeny as a window on the evolution of hyperdiversity in the tropical rainforest biome

(2017) Wolf L. Eiserhardt et al.   NEW PHYTOLOGIST

Amazon plant diversity revealed by a taxonomically verified species list

(2017) Domingos Cardoso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Is BAMM Flawed? Theoretical and Practical Concerns in the Analysis of Multi-Rate Diversification Models

(2017) Daniel L. Rabosky et al.   SYSTEMATIC BIOLOGY

The Past Sure is Tense: On Interpreting Phylogenetic Divergence Time Estimates

(2017) Joseph W Brown et al.   SYSTEMATIC BIOLOGY

Phylogenetic Relationships in Senegalia (Leguminosae-Mimosoideae) Emphasizing the South American Lineages

(2017) Vanessa Terra et al.   SYSTEMATIC BOTANY

A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny – The Legume Phylogeny Working Group (LPWG)

(2017) Nasim Azani et al.   TAXON

Understanding the Processes Underpinning Patterns of Phylogenetic Regionalization

(2017) Barnabas H. Daru et al.   TRENDS IN ECOLOGY & EVOLUTION

Climatologies at high resolution for the earth’s land surface areas

(2017) Dirk Nikolaus Karger et al.   Scientific Data

Multidimensional biases, gaps and uncertainties in global plant occurrence information

(2016) Carsten Meyer et al.   ECOLOGY LETTERS

Defining functional biomes and monitoring their change globally

(2016) Steven I. Higgins et al.   GLOBAL CHANGE BIOLOGY

Dissecting global turnover in vascular plants

(2016) Christian König et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Molecular Phylogeny of Stryphnodendron (Mimosoideae, Leguminosae) and Generic Delimitations in the Piptadenia Group

(2016) Marcelo F. Simon et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Revising the biome concept for understanding and predicting global change impacts

(2016) Glenn R. Moncrieff et al.   JOURNAL OF BIOGEOGRAPHY

The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut

(2016) David John Bertioli et al.   NATURE GENETICS

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

Plant diversity patterns in neotropical dry forests and their conservation implications

(2016) et al.   SCIENCE

Retrieval of hundreds of nuclear loci from herbarium specimens

(2016) Michelle L. Hart et al.   TAXON

RPANDA: an R package for macroevolutionary analyses on phylogenetic trees

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

Remotely Sensed High-Resolution Global Cloud Dynamics for Predicting Ecosystem and Biodiversity Distributions

(2016) Adam M. Wilson et al.   PLOS BIOLOGY

HybPiper: Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using Target Enrichment

(2016) Matthew G. Johnson et al.   Applications in Plant Sciences

A new generic system for the pantropical Caesalpinia group (Leguminosae)

(2016) Edeline Gagnon et al.   PhytoKeys

Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants

(2015) Stephen A Smith et al.   BMC EVOLUTIONARY BIOLOGY

Phylogenetic position of Madagascan species ofAcacia s.l.and new combinations inSenegaliaandVachellia(Fabaceae, Mimosoideae, Acacieae)

(2015) James S. Boatwright et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Confluence, synnovation, and depauperons in plant diversification

(2015) Michael J. Donoghue et al.   NEW PHYTOLOGIST

The contrasting nature of woody plant species in different neotropical forest biomes reflects differences in ecological stability

(2015) R. Toby Pennington et al.   NEW PHYTOLOGIST

Recently evolved diversity and convergent radiations of rainforest mahoganies (Meliaceae) shed new light on the origins of rainforest hyperdiversity

(2015) Erik J. M. Koenen et al.   NEW PHYTOLOGIST

Mimosoid legume plastome evolution: IR expansion, tandem repeat expansions, and accelerated rate of evolution in clpP

(2015) Diana V. Dugas et al.   Scientific Reports

Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae)

(2015) James A. Nicholls et al.   Frontiers in Plant Science

Biome Shifts and Niche Evolution in Plants

(2014) Michael J. Donoghue et al.   Annual Review of Ecology Evolution and Systematics

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

FOSSILS AND A LARGE MOLECULAR PHYLOGENY SHOW THAT THE EVOLUTION OF SPECIES RICHNESS, GENERIC DIVERSITY, AND TURNOVER RATES ARE DISCONNECTED

(2014) Yaowu Xing et al.   EVOLUTION

Multiple Polyploidy Events in the Early Radiation of Nodulating and Nonnodulating Legumes

(2014) Steven B. Cannon et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

(2014) Daniel L. Rabosky   PLoS One

C4 Photosynthesis Promoted Species Diversification during the Miocene Grassland Expansion

(2014) Elizabeth L. Spriggs et al.   PLoS One

The latitudinal species richness gradient in New World woody angiosperms is consistent with the tropical conservatism hypothesis

(2014) A. J. Kerkhoff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Model Selection in Historical Biogeography Reveals that Founder-Event Speciation Is a Crucial Process in Island Clades

(2014) Nicholas J. Matzke   SYSTEMATIC BIOLOGY

Phylogeny of Calliandra (Leguminosae: Mimosoideae) based on nuclear and plastid molecular markers

(2014) Élvia Rodrigues de Souza et al.   TAXON

Mistaking geography for biology: inferring processes from species distributions

(2014) Dan. L. Warren et al.   TRENDS IN ECOLOGY & EVOLUTION

Phylogenetic measures of biodiversity and neo- and paleo-endemism in Australian Acacia

(2014) Brent D. Mishler et al.   Nature Communications

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

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

Comparative dating of Acacia: combining fossils and multiple phylogenies to infer ages of clades with poor fossil records

(2013) Joseph T. Miller et al.   AUSTRALIAN JOURNAL OF BOTANY

Phylogenetic generalised dissimilarity modelling: a new approach to analysing and predicting spatial turnover in the phylogenetic composition of communities

(2013) Dan F. Rosauer et al.   ECOGRAPHY

Phylogenetic beta diversity of angiosperms in North America

(2013) Hong Qian et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

A biogeographical regionalization of AustralianAcaciaspecies

(2013) Carlos E. González-Orozco et al.   JOURNAL OF BIOGEOGRAPHY

Three keys to the radiation of angiosperms into freezing environments

(2013) Amy E. Zanne et al.   NATURE

Hyperdominance in the Amazonian Tree Flora

(2013) H. ter Steege et al.   SCIENCE

Stability structures tropical woody plant diversity more than seasonality: Insights into the ecology of high legume-succulent-plant biodiversity

(2013) A.T. Oliveira-Filho et al.   SOUTH AFRICAN JOURNAL OF BOTANY

PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment

(2013) Nicolas Lartillot et al.   SYSTEMATIC BIOLOGY

Dispersal and niche evolution jointly shape the geographic turnover of phylogenetic clades across continents

(2013) Wolf L. Eiserhardt et al.   Scientific Reports

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Modeling Protein Evolution with Several Amino Acid Replacement Matrices Depending on Site Rates

(2012) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

Correction: Quantifying Phylogenetic Beta Diversity: Distinguishing between ‘True’ Turnover of Lineages and Phylogenetic Diversity Gradients

(2012) Fabien Leprieur et al.   PLoS One

FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads

(2012) Haibin Xu et al.   PLoS One

Cenozoic imprints on the phylogenetic structure of palm species assemblages worldwide

(2012) W. D. Kissling et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Update of Wallace's Zoogeographic Regions of the World

(2012) B. G. Holt et al.   SCIENCE

Pruning Rogue Taxa Improves Phylogenetic Accuracy: An Efficient Algorithm and Webservice

(2012) Andre J. Aberer et al.   SYSTEMATIC BIOLOGY

The evolutionary history of Mimosa (Leguminosae): Toward a phylogeny of the sensitive plants

(2011) Marcelo F. Simon et al.   AMERICAN JOURNAL OF BOTANY

The complex evolutionary dynamics of ancient and recent polyploidy in Leucaena (Leguminosae; Mimosoideae)

(2011) Rajanikanth Govindarajulu et al.   AMERICAN JOURNAL OF BOTANY

The Medicago genome provides insight into the evolution of rhizobial symbioses

(2011) Nevin D. Young et al.   NATURE

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

(2011) Vincent Ranwez et al.   PLoS One

Contemporaneous and recent radiations of the world's major succulent plant lineages

(2011) M. Arakaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

(2010) Alexis Criscuolo et al.   BMC EVOLUTIONARY BIOLOGY

A framework for delineating biogeographical regions based on species distributions

(2010) Holger Kreft et al.   JOURNAL OF BIOGEOGRAPHY

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

EXTINCTION RATES SHOULD NOT BE ESTIMATED FROM MOLECULAR PHYLOGENIES

(2009) Daniel L. Rabosky   EVOLUTION

Partitioning the turnover and nestedness components of beta diversity

(2009) Andrés Baselga   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Phylogenetic biome conservatism on a global scale

(2009) Michael D. Crisp et al.   NATURE

Recent assembly of the Cerrado, a neotropical plant diversity hotspot, by in situ evolution of adaptations to fire

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

Late Paleocene fossils from the Cerrejon Formation, Colombia, are the earliest record of Neotropical rainforest

(2009) S. L. Wing et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenetic patterns and diversification in the caesalpinioid legumesThis paper is one of a selection of papers published in the Special Issue on Systematics Research.

(2008) Anne Bruneau et al.   Botany

Phylogenetic beta diversity: linking ecological and evolutionary processes across space in time

(2008) Catherine H. Graham et al.   ECOLOGY LETTERS

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

(2008) James C. Zachos et al.   NATURE

A phylogenetic perspective on the distribution of plant diversity

(2008) M. J. Donoghue   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA