Rapid diversification rates in Amazonian Chrysobalanaceae inferred from plastid genome phylogenetics

Plastid phylogenomic insights into the evolution of Caryophyllales

(2019) Gang Yao et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Incongruence between gene trees and species trees and phylogenetic signal variation in plastid genes

(2019) Deise J.P. Gonçalves et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

(2019) Remco Bouckaert et al.   PLoS Computational Biology

Targeted Capture of Hundreds of Nuclear Genes Unravels Phylogenetic Relationships of the Diverse Neotropical Palm Tribe Geonomateae

(2019) Oriane Loiseau et al.   Frontiers in Plant Science

One thousand plant transcriptomes and the phylogenomics of green plants

(2019)   NATURE

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

Iriarteeae palms tracked the uplift of Andean Cordilleras

(2018) Christine D. Bacon et al.   JOURNAL OF BIOGEOGRAPHY

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

Is Amazonia a ‘museum’ for Neotropical trees? The evolution of the Brownea clade (Detarioideae, Leguminosae)

(2018) Rowan J. Schley et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Amazonia is the primary source of Neotropical biodiversity

(2018) Alexandre Antonelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2018) Charles Pouchon et al.   SYSTEMATIC BIOLOGY

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

(2018) Andrew Rambaut et al.   SYSTEMATIC BIOLOGY

Parallel diversifications of Cremastosperma and Mosannona (Annonaceae), tropical rainforest trees tracking Neogene upheaval of South America

(2018) Michael D. Pirie et al.   Royal Society Open Science

The Amazon at sea: Onset and stages of the Amazon River from a marine record, with special reference to Neogene plant turnover in the drainage basin

(2017) Carina Hoorn et al.   GLOBAL AND PLANETARY CHANGE

Hydroclimate changes across the Amazon lowlands over the past 45,000 years

(2017) Xianfeng Wang et al.   NATURE

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

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

Diversification of Rosaceae since the Late Cretaceous based on plastid phylogenomics

(2017) Shu-Dong Zhang et al.   NEW PHYTOLOGIST

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

Dispersal assembly of rain forest tree communities across the Amazon basin

(2017) Kyle G. Dexter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Miocene flooding events of western Amazonia

(2017) Carlos Jaramillo et al.   Science Advances

Unraveling the biogeographical history of Chrysobalanaceae from plastid genomes

(2016) Léa Bardon et al.   AMERICAN JOURNAL OF BOTANY

Fruits and wood of Parinari from the early Miocene of Panama and the fossil record of Chrysobalanaceae

(2016) N. A. Jud et al.   AMERICAN JOURNAL OF BOTANY

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

(2016) Laura P. Lagomarsino et al.   NEW PHYTOLOGIST

Towards a monophyletic Licania: a new generic classification of the polyphyletic Neotropical genus Licania (Chrysobalanaceae)

(2016) C. A. Sothers et al.   KEW BULLETIN

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

Confluence, synnovation, and depauperons in plant diversification

(2015) Michael J. Donoghue 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

A metacalibrated time-tree documents the early rise of flowering plant phylogenetic diversity

(2015) Susana Magallón et al.   NEW PHYTOLOGIST

Biome Shifts and Niche Evolution in Plants

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

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Resurrection of Angelesia, a Southeast Asian genus of Chrysobalanaceae

(2014) C.A. Sothers et al.   BLUMEA

From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes

(2014) Brad R Ruhfel et al.   BMC EVOLUTIONARY BIOLOGY

Drainage reversal of the Amazon River due to the coupling of surface and lithospheric processes

(2014) Victor Sacek   EARTH AND PLANETARY SCIENCE LETTERS

Fast demographic traits promote high diversification rates of Amazonian trees

(2014) Timothy R. Baker et al.   ECOLOGY LETTERS

INVESTIGATING PROCESSES OF NEOTROPICAL RAIN FOREST TREE DIVERSIFICATION BY EXAMINING THE EVOLUTION AND HISTORICAL BIOGEOGRAPHY OF THE PROTIEAE (BURSERACEAE)

(2014) Paul V. A. Fine et al.   EVOLUTION

Evidence for ecological divergence across a mosaic of soil types in an Amazonian tropical tree:Protium subserratum(Burseraceae)

(2014) Tracy M. Misiewicz et al.   MOLECULAR ECOLOGY

Phylogenetic signal detection from an ancient rapid radiation: Effects of noise reduction, long-branch attraction, and model selection in crown clade Apocynaceae

(2014) Shannon C.K. Straub et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The drivers of tropical speciation

(2014) Brian Tilston Smith et al.   NATURE

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

(2014) Daniel L. Rabosky   PLoS One

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

(2014) Nicholas J. Matzke   SYSTEMATIC BIOLOGY

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

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

Taxonomic novelties in Neotropical Chrysobalanaceae: towards a monophyletic Couepia

(2014) Cynthia Sothers et al.   Phytotaxa

Resolving ancient radiations: can complete plastid gene sets elucidate deep relationships among the tropical gingers (Zingiberales)?

(2013) Craig F. Barrett et al.   ANNALS OF BOTANY

Hyperdominance in the Amazonian Tree Flora

(2013) H. ter Steege et al.   SCIENCE

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

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

Can phylogenetic signal, character displacement, or random phenotypic drift explain the morphological variation in the genus Geonoma (Arecaceae)?

(2012) JULISSA RONCAL et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Origin and evolution of Chrysobalanaceae: insights into the evolution of plants in the Neotropics

(2012) Léa Bardon et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Cenozoic colonization and diversification patterns of tropical American palms: evidence fromAstrocaryum(Arecaceae)

(2012) Julissa Roncal et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Neotropical Plant Evolution: Assembling the Big Picture

(2012) Colin E. Hughes et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Global biogeography and diversification of palms sheds light on the evolution of tropical lineages. II. Diversification history and origin of regional assemblages

(2012) William J. Baker et al.   JOURNAL OF BIOGEOGRAPHY

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Phylogenomics and a posteriori data partitioning resolve the Cretaceous angiosperm radiation Malpighiales

(2012) Z. Xi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Permineralized fruits from the late Eocene of Panama give clues of the composition of forests established early in the uplift of Central America

(2012) Fabiany Herrera et al.   REVIEW OF PALAEOBOTANY AND PALYNOLOGY

Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics

(2011) Shannon C. K. Straub et al.   AMERICAN JOURNAL OF BOTANY

Best Practices for Justifying Fossil Calibrations

(2011) James F. Parham et al.   SYSTEMATIC BIOLOGY

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

Phylogenetic Relationships of the Chrysobalanaceae Inferred from Chloroplast, Nuclear, and Morphological Data1

(2010) Deepthi Yakandawala et al.   ANNALS OF THE MISSOURI BOTANICAL GARDEN

Assembling the Tree of the Monocotyledons: Plastome Sequence Phylogeny and Evolution of Poales1

(2010) Thomas J. Givnish et al.   ANNALS OF THE MISSOURI BOTANICAL GARDEN

A Floristic Study of the White-Sand Forests of Peru1

(2010) Paul V. A. Fine et al.   ANNALS OF THE MISSOURI BOTANICAL GARDEN

Why does biparental plastid inheritance revive in angiosperms?

(2010) Quan Zhang et al.   JOURNAL OF PLANT RESEARCH

Amazonia Through Time: Andean Uplift, Climate Change, Landscape Evolution, and Biodiversity

(2010) C. Hoorn et al.   SCIENCE

CSA: An efficient algorithm to improve circular DNA multiple alignment

(2009) Francisco Fernandes et al.   BMC BIOINFORMATICS

Hypotheses to explain the origin of species in Amazonia

(2009) J. Haffer   BRAZILIAN JOURNAL OF BIOLOGY

Late Miocene onset of the Amazon River and the Amazon deep-sea fan: Evidence from the Foz do Amazonas Basin

(2009) J. Figueiredo et al.   GEOLOGY

The evolution of antiherbivore defenses and their contribution to species coexistence in the tropical tree genus Inga

(2009) T. A. Kursar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Antarctic subglacial topography and ice-sheet evolution

(2008) Martin J. Siegert   EARTH SURFACE PROCESSES AND LANDFORMS

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

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