Building a Robust, Densely-Sampled Spider Tree of Life for Ecosystem Research

Standardised inventories of spiders (Arachnida, Araneae) of Macaronesia II: The native forests and dry habitats of Madeira archipelago (Madeira and Porto Santo islands)

(2020) Jagoba Malumbres-Olarte et al.   Biodiversity Data Journal

Agriculturally dominated landscapes reduce bee phylogenetic diversity and pollination services

(2019) Heather Grab et al.   SCIENCE

Population structure and genetic differentiation of tea green leafhopper, Empoasca (Matsumurasca) onukii, in China based on microsatellite markers

(2019) Li Zhang et al.   Scientific Reports

Trophic interactions and abiotic factors drive functional and phylogenetic structure of vertebrate herbivore communities across the Arctic tundra biome

(2019) James D. M. Speed et al.   ECOGRAPHY

The use of DNA barcodes to estimate phylogenetic diversity in forest communities of southern China

(2019) Jiajia Liu et al.   Ecology and Evolution

For common community phylogenetic analyses, go ahead and use synthesis phylogenies

(2019) Daijiang Li et al.   ECOLOGY

Standardised inventories of spiders (Arachnida, Araneae) of Macaronesia I: The native forests of the Azores (Pico and Terceira islands)

(2019) Jagoba Malumbres-Olarte et al.   Biodiversity Data Journal

Effects of taxon sampling and tree reconstruction methods on phylodiversity metrics

(2019) Johanna R. Jantzen et al.   Ecology and Evolution

The fossil record of spiders revisited: implications for calibrating trees and evidence for a major faunal turnover since the Mesozoic

(2019) Ivan L. F. Magalhaes et al.   BIOLOGICAL REVIEWS

Taxonomic divergence and functional convergence in Iberian spider forest communities: Insights from beta diversity partitioning

(2019) José C. Carvalho et al.   JOURNAL OF BIOGEOGRAPHY

GenBank is a reliable resource for 21st century biodiversity research

(2019) Matthieu Leray et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenomics, Diversification Dynamics, and Comparative Transcriptomics across the Spider Tree of Life

(2018) Rosa Fernández et al.   CURRENT BIOLOGY

Choice between phylogram and chronogram can have a dramatic impact on the location of phylogenetic diversity hotspots

(2018) Meg J. Elliott et al.   JOURNAL OF BIOGEOGRAPHY

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

(2018) Daniel S. Park et al.   MOLECULAR ECOLOGY

PyPHLAWD: a python tool for phylogenetic dataset construction

(2018) Stephen A. Smith et al.   Methods in Ecology and Evolution

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

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

The spider tree of life: phylogeny of Araneae based on target-gene analyses from an extensive taxon sampling

(2016) Ward C. Wheeler et al.   CLADISTICS

Phylogenetic community structure metrics and null models: a review with new methods and software

(2016) Eliot T. Miller et al.   ECOGRAPHY

A combined field survey and molecular identification protocol for comparing forest arthropod biodiversity across spatial scales

(2016) Brent C. Emerson et al.   Molecular Ecology Resources

NCBIminer: sequences harvest from Genbank

(2015) Xiaoting Xu et al.   ECOGRAPHY

Influence of tree shape and evolutionary time-scale on phylogenetic diversity metrics

(2015) Florent Mazel et al.   ECOGRAPHY

Phylogenetic diversity-ecosystem function relationships are insensitive to phylogenetic edge lengths

(2015) Marc W. Cadotte   FUNCTIONAL ECOLOGY

Using phylogenetics in community assembly and ecosystem functioning research

(2015) Anita Narwani et al.   FUNCTIONAL ECOLOGY

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

(2015) Pille Gerhold et al.   FUNCTIONAL ECOLOGY

Fitting Linear Mixed-Effects Models Usinglme4

(2015) Douglas Bates et al.   Journal of Statistical Software

Untangling taxonomy: a DNA barcode reference library for Canadian spiders

(2015) Gergin A. Blagoev et al.   Molecular Ecology Resources

Synthesis of phylogeny and taxonomy into a comprehensive tree of life

(2015) Cody E. Hinchliff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ecological and evolutionary perspectives on community assembly

(2015) Gary G. Mittelbach et al.   TRENDS IN ECOLOGY & EVOLUTION

Are phylogenies derived from family-level supertrees robust for studies on macroecological patterns along environmental gradients?

(2015) Hong Qian et al.   Journal of Systematics and Evolution

Investigating sensitivity of phylogenetic community structure metrics using North American desert bats

(2015) Lorelei E. Patrick et al.   JOURNAL OF MAMMALOGY

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 diversity, habitat loss and conservation in South American pitvipers (Crotalinae:BothropsandBothrocophias)

(2014) Jéssica Fenker et al.   DIVERSITY AND DISTRIBUTIONS

Phylogenetic approaches for studying diversification

(2014) Hélène Morlon   ECOLOGY LETTERS

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

Directional biases in phylogenetic structure quantification: a Mediterranean case study

(2013) Rafael Molina-Venegas et al.   ECOGRAPHY

Contrasting changes in taxonomic, phylogenetic and functional diversity during a long-term succession: insights into assembly processes

(2013) Oliver Purschke et al.   JOURNAL OF ECOLOGY

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

treePL: divergence time estimation using penalized likelihood for large phylogenies

(2012) Stephen A. Smith et al.   BIOINFORMATICS

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Ecophylogenetics: advances and perspectives

(2012) Nicolas Mouquet et al.   BIOLOGICAL REVIEWS

Gone with the plate: the opening of the Western Mediterranean basin drove the diversification of ground-dweller spiders

(2012) Leticia Bidegaray-Batista et al.   BMC EVOLUTIONARY BIOLOGY

Phylogenetic diversity and nature conservation: where are we?

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

A general and simple method for obtainingR2from generalized linear mixed-effects models

(2012) Shinichi Nakagawa et al.   Methods in Ecology and Evolution

Diversity and community assembly patterns of epigean vs. troglobiont spiders in the Iberian Peninsula

(2011) Pedro Cardoso   INTERNATIONAL JOURNAL OF SPELEOLOGY

Ecology’s cruel dilemma, phylogenetic trait evolution and the assembly of Serengeti plant communities

(2011) T. Michael Anderson et al.   JOURNAL OF ECOLOGY

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Phylogenetic diversity as a window into the evolutionary and biogeographic histories of present-day richness gradients for mammals

(2011) T. J. Davies et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Global Patterns of Guild Composition and Functional Diversity of Spiders

(2011) Pedro Cardoso et al.   PLoS One

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses

(2010) Ben C Stöver et al.   BMC BIOINFORMATICS

Determinants of beta diversity of spiders in coastal dunes along a gradient of mediterraneity

(2010) José C. Carvalho et al.   DIVERSITY AND DISTRIBUTIONS

Spatial mismatch and congruence between taxonomic, phylogenetic and functional diversity: the need for integrative conservation strategies in a changing world

(2010) Vincent Devictor et al.   ECOLOGY LETTERS

Trait similarity, shared ancestry and the structure of neighbourhood interactions in a subtropical wet forest: implications for community assembly

(2010) María Uriarte et al.   ECOLOGY LETTERS

Advances in the Use of DNA Barcodes to Build a Community Phylogeny for Tropical Trees in a Puerto Rican Forest Dynamics Plot

(2010) W. John Kress et al.   PLoS One

Species assortment or habitat filtering: a case study of spider communities on lake islands

(2009) Werner Ulrich et al.   ECOLOGICAL RESEARCH

Disentangling niche and neutral influences on community assembly: assessing the performance of community phylogenetic structure tests

(2009) Steven W. Kembel   ECOLOGY LETTERS

The merging of community ecology and phylogenetic biology

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

The Cladistic Basis for the Phylogenetic Diversity (PD) Measure Links Evolutionary Features to Environmental Gradients and Supports Broad Applications of Microbial Ecology’s “Phylogenetic Beta Diversity” Framework

(2009) Daniel Faith et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Phylogenetic Resolution and Quantifying the Phylogenetic Diversity and Dispersion of Communities

(2009) Nathan G. Swenson   PLoS One

Testing the spatial phylogenetic structure of local communities: statistical performances of different null models and test statistics on a locally neutral community

(2008) Olivier J. Hardy   JOURNAL OF ECOLOGY

Emerging patterns in the comparative analysis of phylogenetic community structure

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

A comparative test of phylogenetic diversity indices

(2008) Oliver Schweiger et al.   OECOLOGIA