Taxon sampling effects on the quantification and comparison of community phylogenetic diversity

A guide to phylogenetic metrics for conservation, community ecology and macroecology

(2016) Caroline M. Tucker et al.   BIOLOGICAL REVIEWS

Relationships among taxonomic, functional, and phylogenetic ant diversity across the biogeographic regions of Europe

(2016) Xavier Arnan et al.   ECOGRAPHY

Ecological and evolutionary variation in community nitrogen use traits during tropical dry forest secondary succession

(2016) Radika Bhaskar et al.   ECOLOGY

Testing the trait-based community framework: Do functional traits predict competitive outcomes?

(2016) Jennifer L. Funk et al.   ECOLOGY

Phylogenetic diversity is maintained despite richness losses over time in restored tallgrass prairie plant communities

(2016) Nicholas A. Barber et al.   JOURNAL OF APPLIED ECOLOGY

Effects of landscape configuration and composition on phylogenetic diversity of trees in a highly fragmented tropical forest

(2016) Fabio Antonio R. Matos et al.   JOURNAL OF ECOLOGY

Is phylogenetic diversity a good proxy for functional diversity of plant communities? A case study from urban habitats

(2016) Zdeňka Lososová et al.   JOURNAL OF VEGETATION SCIENCE

Contribution of co-occurring shrub species to community richness and phylogenetic diversity along an environmental gradient

(2016) Nuria Pistón et al.   PERSPECTIVES IN PLANT ECOLOGY EVOLUTION AND SYSTEMATICS

Tree phylogenetic diversity promotes host–parasitoid interactions

(2016) Michael Staab et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Restoring phylogenetic diversity through facilitation

(2016) Jose A. Navarro-Cano et al.   RESTORATION ECOLOGY

Soil phosphorus heterogeneity promotes tree species diversity and phylogenetic clustering in a tropical seasonal rainforest

(2016) Wumei Xu et al.   Ecology and Evolution

Stochastic assembly in a subtropical forest chronosequence: evidence from contrasting changes of species, phylogenetic and functional dissimilarity over succession

(2016) Xiangcheng Mi et al.   Scientific Reports

The evolutionary history of ferns inferred from 25 low-copy nuclear genes

(2015) C. J. Rothfels et al.   AMERICAN JOURNAL OF BOTANY

Phylogenetics, divergence times and diversification from three genomic partitions in monocots

(2015) Kate L. Hertweck et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Deconstructing Darwin's Naturalization Conundrum in the San Juan Islands using community phylogenetics and functional traits

(2015) Hannah E. Marx et al.   DIVERSITY AND DISTRIBUTIONS

Phylogenetic patterns are not proxies of community assembly mechanisms (they are far better)

(2015) Pille Gerhold et al.   FUNCTIONAL ECOLOGY

A reciprocal test of Darwin's naturalization hypothesis in two mediterranean-climate regions

(2015) Daniel S. Park et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Why close relatives make bad neighbours: phylogenetic conservatism in niche preferences and dispersal disproves Darwin's naturalization hypothesis in the thistle tribe

(2015) Daniel S. Park et al.   MOLECULAR ECOLOGY

Do missing data influence the accuracy of divergence-time estimation with BEAST?

(2015) Yuchi Zheng et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2015) Susana Magallón et al.   NEW PHYTOLOGIST

Phylogenetic diversity meets conservation policy: small areas are key to preserving eucalypt lineages

(2015) L. J. Pollock et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Revised Time Tree of the Asterids: Establishing a Temporal Framework For Evolutionary Studies of the Coffee Family (Rubiaceae)

(2015) Niklas Wikström et al.   PLoS One

Phylodiversity to inform conservation policy: An Australian example

(2015) Tania Laity et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Community Phylogenetics: Assessing Tree Reconstruction Methods and the Utility of DNA Barcodes

(2015) Elizabeth E. Boyle et al.   PLoS One

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Phylogenetic relatedness and the determinants of competitive outcomes

(2014) Oscar Godoy et al.   ECOLOGY LETTERS

Two New Fern Chloroplasts and Decelerated Evolution Linked to the Long Generation Time in Tree Ferns

(2014) B. Zhong et al.   Genome Biology and Evolution

Contrasting effects of phylogenetic relatedness on plant invader success in experimental grassland communities

(2014) Shao-peng Li et al.   JOURNAL OF APPLIED ECOLOGY

BAT - Biodiversity Assessment Tools, an R package for the measurement and estimation of alpha and beta taxon, phylogenetic and functional diversity

(2014) Pedro Cardoso et al.   Methods in Ecology and Evolution

Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: a mega-phylogeny approach

(2014) David L. Erickson et al.   Frontiers in Genetics

Turnover of plant lineages shapes herbivore phylogenetic beta diversity along ecological gradients

(2013) Loïc Pellissier et al.   ECOLOGY LETTERS

Partitioning taxon, phylogenetic and functional beta diversity into replacement and richness difference components

(2013) Pedro Cardoso et al.   JOURNAL OF BIOGEOGRAPHY

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

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

A test of Darwin's naturalization hypothesis in the thistle tribe shows that close relatives make bad neighbors

(2013) D. S. Park et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Species distributions in response to individual soil nutrients and seasonal drought across a community of tropical trees

(2013) R. Condit et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenetic diversity promotes ecosystem stability

(2012) Marc W. Cadotte et al.   ECOLOGY

Phylogenetic diversity and nature conservation: where are we?

(2012) Marten Winter et al.   TRENDS IN ECOLOGY & EVOLUTION

Seeing the Forest for the Trees: The Limitations of Phylogenies in Comparative Biology

(2011) Jonathan B. Losos   AMERICAN NATURALIST

Incompletely resolved phylogenetic trees inflate estimates of phylogenetic conservatism

(2011) T. Jonathan Davies et al.   ECOLOGY

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

Improved Phylogenomic Taxon Sampling Noticeably Affects Nonbilaterian Relationships

(2010) K. S. Pick et al.   MOLECULAR BIOLOGY AND EVOLUTION

Increasing taxon sampling using both unidentified environmental sequences and identified cultures improves phylogenetic inference in the Prorodontida (Ciliophora, Prostomatea)

(2010) Zhenzhen Yi et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life

(2010) Laura Wegener Parfrey et al.   SYSTEMATIC BIOLOGY

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

Taking into account phylogenetic and divergence-time uncertainty in a parametric biogeographical analysis of the Northern Hemisphere plant clade Caprifolieae

(2009) Stephen A. Smith   JOURNAL OF BIOGEOGRAPHY

Phylogenetic Resolution and Quantifying the Phylogenetic Diversity and Dispersion of Communities

(2009) Nathan G. Swenson   PLoS One

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

Biogeographic diversification inNolana(Solanaceae), a ubiquitous member of the Atacama and Peruvian Deserts along the western coast of South America

(2009) Michael O. DILLON et al.   Journal of Systematics and Evolution

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

(2008) Campbell O. Webb et al.   BIOINFORMATICS

Emerging patterns in the comparative analysis of phylogenetic community structure

(2008) S. M. VAMOSI et al.   MOLECULAR ECOLOGY

Phylogenetic analysis of community assembly and structure over space and time

(2008) Brent C. Emerson et al.   TRENDS IN ECOLOGY & EVOLUTION