Building megaphylogenies for macroecology: taking up the challenge

Tectonic calibrations in molecular dating

(2016) Ullasa Kodandaramaiah   Current Zoology

RAxML-Light: a tool for computing terabyte phylogenies

(2012) A. Stamatakis et al.   BIOINFORMATICS

Ecophylogenetics: advances and perspectives

(2012) Nicolas Mouquet et al.   BIOLOGICAL REVIEWS

Understanding angiosperm diversification using small and large phylogenetic trees

(2011) S. A. Smith et al.   AMERICAN JOURNAL OF BOTANY

Testing Darwin’s naturalization hypothesis in the Azores

(2011) Hanno Schaefer et al.   ECOLOGY LETTERS

Consequences of climate change on the tree of life in Europe

(2011) Wilfried Thuiller et al.   NATURE

Terraces in Phylogenetic Tree Space

(2011) M. J. Sanderson et al.   SCIENCE

Testing the Impact of Calibration on Molecular Divergence Times Using a Fossil-Rich Group: The Case of Nothofagus (Fagales)

(2011) Hervé Sauquet et al.   SYSTEMATIC BIOLOGY

SATé-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees

(2011) Kevin Liu et al.   SYSTEMATIC BIOLOGY

Space, time, form: viewing the Tree of Life

(2011) Roderic D.M. Page   TRENDS IN ECOLOGY & EVOLUTION

A simple polytomy resolver for dated phylogenies

(2011) Tyler S. Kuhn et al.   Methods in Ecology and Evolution

Biodiversity and Climate Change: Integrating Evolutionary and Ecological Responses of Species and Communities

(2010) Sébastien Lavergne et al.   Annual Review of Ecology Evolution and Systematics

webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser

(2010) Ari Löytynoja et al.   BMC BIOINFORMATICS

Phylogenomics with incomplete taxon coverage: the limits to inference

(2010) Michael J Sanderson et al.   BMC EVOLUTIONARY BIOLOGY

Phylogenetic patterns differ for native and exotic plant communities across a richness gradient in Northern California

(2010) Marc W. Cadotte et al.   DIVERSITY AND DISTRIBUTIONS

Resolving Darwin’s naturalization conundrum: a quest for evidence

(2010) Wilfried Thuiller et al.   DIVERSITY AND DISTRIBUTIONS

Hidden patterns of phylogenetic non-stationarity overwhelm comparative analyses of niche conservatism and divergence

(2010) José Alexandre Felizola Diniz-Filho et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

How Many Bootstrap Replicates Are Necessary?

(2010) Nicholas D. Pattengale et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

FASconCAT: Convenient handling of data matrices

(2010) Patrick Kück et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Canopy phylogenetic, chemical and spectral assembly in a lowland Amazonian forest

(2010) Gregory P. Asner et al.   NEW PHYTOLOGIST

GenBank

(2010) D. A. Benson et al.   NUCLEIC ACIDS RESEARCH

Combining Historical Biogeography with Niche Modeling in the Caprifolium Clade of Lonicera (Caprifoliaceae, Dipsacales)

(2010) Stephen A. Smith et al.   SYSTEMATIC BIOLOGY

Comparative Performance of Supertree Algorithms in Large Data Sets Using the Soapberry Family (Sapindaceae) as a Case Study

(2010) Sven Buerki et al.   SYSTEMATIC BIOLOGY

Calibrating the Tree of Life: fossils, molecules and evolutionary timescales

(2009) Félix Forest   ANNALS OF BOTANY

Richness gradients of stream invertebrates across the USA: taxonomy- and trait-based approaches

(2009) Leah A. Bêche et al.   BIODIVERSITY AND CONSERVATION

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Evolution of climate niches in European mammals?

(2009) C. F. Dormann et al.   Biology Letters

Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches

(2009) Stephen A Smith et al.   BMC EVOLUTIONARY BIOLOGY

The merging of community ecology and phylogenetic biology

(2009) Jeannine Cavender-Bares et al.   ECOLOGY LETTERS

Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama

(2009) W. J. Kress et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees

(2009) K. Liu et al.   SCIENCE

Sparse Supermatrices for Phylogenetic Inference: Taxonomy, Alignment, Rogue Taxa, and the Phylogeny of Living Turtles

(2009) Robert C. Thomson et al.   SYSTEMATIC BIOLOGY

Phylocom: software for the analysis of phylogenetic community structure and trait evolution

(2008) Campbell O. Webb et al.   BIOINFORMATICS

Phyutility: a phyloinformatics tool for trees, alignments and molecular data

(2008) S. A. Smith et al.   BIOINFORMATICS

Hybridization-prone plant families do not generate more invasive species

(2008) Kenneth D. Whitney et al.   BIOLOGICAL INVASIONS

Darwin’s naturalization conundrum: dissecting taxonomic patterns of species invasions

(2008) Jeffrey M. Diez et al.   ECOLOGY LETTERS

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE

Evolutionary history and the effect of biodiversity on plant productivity

(2008) M. W. Cadotte et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenetic trees and the future of mammalian biodiversity

(2008) T. J. Davies et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenetic distributions of British birds of conservation concern

(2008) G. H Thomas   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Rise of the Andes

(2008) C. N. Garzione et al.   SCIENCE

A Phylogenomic Study of Birds Reveals Their Evolutionary History

(2008) S. J. Hackett et al.   SCIENCE

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

(2008) A. Loytynoja et al.   SCIENCE

The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains

(2008) Pablo Yarza et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

The PhyLoTA Browser: Processing GenBank for Molecular Phylogenetics Research

(2008) Michael J. Sanderson et al.   SYSTEMATIC BIOLOGY

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY