High-Throughput Sequencing: A Roadmap Toward Community Ecology

MicrobeDB: a locally maintainable database of microbial genomic sequences

(2012) M. G. I. Langille et al.   BIOINFORMATICS

Ecophylogenetics: advances and perspectives

(2012) Nicolas Mouquet et al.   BIOLOGICAL REVIEWS

Conservation biogeography: what's hot and what's not?

(2012) David M. Richardson   DIVERSITY AND DISTRIBUTIONS

Microbial community phylogenetic and trait diversity declines with depth in a marine oxygen minimum zone

(2012) Jessica A. Bryant et al.   ECOLOGY

Accounting for dispersal and biotic interactions to disentangle the drivers of species distributions and their abundances

(2012) Isabelle Boulangeat et al.   ECOLOGY LETTERS

Does phylogeny matter? Assessing the impact of phylogenetic information in ecological meta-analysis

(2012) Scott A. Chamberlain et al.   ECOLOGY LETTERS

The dissimilarity of species interaction networks

(2012) Timothée Poisot et al.   ECOLOGY LETTERS

Molecular phylogenetics: principles and practice

(2012) Ziheng Yang et al.   NATURE REVIEWS GENETICS

Novel communities from climate change

(2012) M. Lurgi et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Pyrosequencing the Bemisia tabaci Transcriptome Reveals a Highly Diverse Bacterial Community and a Robust System for Insecticide Resistance

(2012) Wen Xie et al.   PLoS One

Distance Decay of Similarity in Neotropical Diatom Communities

(2012) Carlos E. Wetzel et al.   PLoS One

Linking genes to communities and ecosystems: Daphnia as an ecogenomic model

(2012) B. E. Miner et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Trait diversity promotes stability of community dynamics

(2012) Lai Zhang et al.   Theoretical Ecology

‘Ecosystomics’: ecology by sequencer

(2012) Anthony M. Poole et al.   TRENDS IN ECOLOGY & EVOLUTION

Sequencing our way towards understanding global eukaryotic biodiversity

(2012) Holly M. Bik et al.   TRENDS IN ECOLOGY & EVOLUTION

Phage–bacteria infection networks

(2012) Joshua S. Weitz et al.   TRENDS IN MICROBIOLOGY

Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring

(2012) Douglas W. Yu et al.   Methods in Ecology and Evolution

Intraspecific variability in the response of bloom-forming marine microalgae to changed climate conditions

(2012) Anke Kremp et al.   Ecology and Evolution

Microbes in High Arctic Snow and Implications for the Cold Biosphere

(2011) Tommy Harding et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Gulf of Mexico Oil Blowout Increases Risks to Globally Threatened Species

(2011) Claudio Campagna et al.   BIOSCIENCE

From diversity indices to community assembly processes: a test with simulated data

(2011) T. Münkemüller et al.   ECOGRAPHY

Using species co-occurrence networks to assess the impacts of climate change

(2011) Miguel B. Araújo et al.   ECOGRAPHY

The community effects of phenotypic and genetic variation within a predator population

(2011) Sebastian J. Schreiber et al.   ECOLOGY

The ecological causes of individual specialisation

(2011) Márcio S. Araújo et al.   ECOLOGY LETTERS

Combining Conservation Value, Vulnerability, and Effectiveness of Mitigation Actions in Spatial Conservation Decisions: An Application to Coastal Oil Spill Combating

(2011) Taina Ihaksi et al.   ENVIRONMENTAL MANAGEMENT

Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes

(2011) Thomas M. Gihring et al.   ENVIRONMENTAL MICROBIOLOGY

Beyond taxonomic diversity patterns: how do α, β and γ components of bird functional and phylogenetic diversity respond to environmental gradients across France?

(2011) Christine N. Meynard et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Co-occurrence patterns for abundant marine archaeal and bacterial lineages in the deep chlorophyll maximum of coastal California

(2011) J Michael Beman et al.   ISME Journal

Illumina-based analysis of microbial community diversity

(2011) Patrick H Degnan et al.   ISME Journal

Using network analysis to explore co-occurrence patterns in soil microbial communities

(2011) Albert Barberán et al.   ISME Journal

Towards novel approaches to modelling biotic interactions in multispecies assemblages at large spatial extents

(2011) W. D. Kissling et al.   JOURNAL OF BIOGEOGRAPHY

Joint consequences of dispersal and niche overlap on local diversity and resource use

(2011) Benjamin Gilbert   JOURNAL OF ECOLOGY

The Microbial Phyllogeography of the Carnivorous Plant Sarracenia alata

(2011) Margaret M. Koopman et al.   MICROBIAL ECOLOGY

Commentary: do we have a consistent terminology for species diversity? Yes, if we choose to use it

(2011) Hanna Tuomisto   OECOLOGIA

On the importance of intraspecific variability for the quantification of functional diversity

(2011) Cécile H. Albert et al.   OIKOS

Persistence Increases with Diversity and Connectance in Trophic Metacommunities

(2011) Dominique Gravel et al.   PLoS One

Microbial Biogeography of Public Restroom Surfaces

(2011) Gilberto E. Flores et al.   PLoS One

Arctic Ocean Microbial Community Structure before and after the 2007 Record Sea Ice Minimum

(2011) André M. Comeau et al.   PLoS One

Bacterial community assembly based on functional genes rather than species

(2011) C. Burke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Why intraspecific trait variation matters in community ecology

(2011) Daniel I. Bolnick et al.   TRENDS IN ECOLOGY & EVOLUTION

Time to change how we describe biodiversity

(2011) Andrew R. Deans et al.   TRENDS IN ECOLOGY & EVOLUTION

Evolutionary informatics: unifying knowledge about the diversity of life

(2011) Cynthia S. Parr et al.   TRENDS IN ECOLOGY & EVOLUTION

Phylogenetic Metrics of Community Similarity

(2010) Anthony R. Ives et al.   AMERICAN NATURALIST

Picante: R tools for integrating phylogenies and ecology

(2010) S. W. Kembel et al.   BIOINFORMATICS

Gut Microbiota: Metagenomics to Study Complex Ecology

(2010) A. Vacharaksa et al.   CURRENT BIOLOGY

Metacommunity phylogenetics: separating the roles of environmental filters and historical biogeography

(2010) Mathew A. Leibold et al.   ECOLOGY LETTERS

Spatial patterns of phylogenetic diversity

(2010) Hélène Morlon et al.   ECOLOGY LETTERS

A global network of coexisting microbes from environmental and whole-genome sequence data

(2010) S. Chaffron et al.   GENOME RESEARCH

Using presence-only and presence-absence data to estimate the current and potential distributions of established invasive species

(2010) Andrew M. Gormley et al.   JOURNAL OF APPLIED ECOLOGY

Microbial eukaryotic distribution in a dynamic Beaufort Sea and the Arctic Ocean

(2010) C. Lovejoy et al.   JOURNAL OF PLANKTON RESEARCH

Quantifying microbial communities with 454 pyrosequencing: does read abundance count?

(2010) ANTHONY S. AMEND et al.   MOLECULAR ECOLOGY

Antagonistic coevolution accelerates molecular evolution

(2010) Steve Paterson et al.   NATURE

454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases

(2010) Leho Tedersoo et al.   NEW PHYTOLOGIST

GenBank

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

Unlocking Short Read Sequencing for Metagenomics

(2010) Sébastien Rodrigue et al.   PLoS One

The Taxonomic and Functional Diversity of Microbes at a Temperate Coastal Site: A ‘Multi-Omic’ Study of Seasonal and Diel Temporal Variation

(2010) Jack A. Gilbert et al.   PLoS One

Scenarios for Global Biodiversity in the 21st Century

(2010) H. M. Pereira et al.   SCIENCE

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

Field theory for biogeography: a spatially explicit model for predicting patterns of biodiversity

(2009) James P. O'Dwyer et al.   ECOLOGY LETTERS

Phylogenetic diversity metrics for ecological communities: integrating species richness, abundance and evolutionary history

(2009) Marc W. Cadotte et al.   ECOLOGY LETTERS

Functional diversity in arbuscular mycorrhiza – the role of gene expression, phosphorous nutrition and symbiotic efficiency

(2009) Nadja Feddermann et al.   Fungal Ecology

Microbial community structure in the North Pacific ocean

(2009) Mark V Brown et al.   ISME Journal

Defining and measuring ecological specialization

(2009) Vincent Devictor et al.   JOURNAL OF APPLIED ECOLOGY

Biodiversity in microbial communities: system scale patterns and mechanisms

(2009) J. JACOB PARNELL et al.   MOLECULAR ECOLOGY

The Beagle in a bottle

(2009) Angus Buckling et al.   NATURE

Large-scale parallel 454 sequencing reveals host ecological group specificity of arbuscular mycorrhizal fungi in a boreonemoral forest

(2009) M. Öpik et al.   NEW PHYTOLOGIST

Ecology of the rare microbial biosphere of the Arctic Ocean

(2009) Pierre E. Galand et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Competition promotes the evolution of host generalists in obligate parasites

(2009) K. P. Johnson et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Emerging horizons in biodiversity and ecosystem functioning research

(2009) Julia Reiss et al.   TRENDS IN ECOLOGY & EVOLUTION

CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment

(2008) Svetlin A Manavski et al.   BMC BIOINFORMATICS

Survey of bacterial diversity in chronic wounds using Pyrosequencing, DGGE, and full ribosome shotgun sequencing

(2008) Scot E Dowd et al.   BMC MICROBIOLOGY

New tools for discovering and characterizing microbial diversity

(2008) Erick Cardenas et al.   CURRENT OPINION IN BIOTECHNOLOGY

PARTITIONING THE FACTORS OF SPATIAL VARIATION IN REGENERATION DENSITY OF SHADE-TOLERANT TREE SPECIES

(2008) Dominique Gravel et al.   ECOLOGY

A general framework for the distance-decay of similarity in ecological communities

(2008) Hélène Morlon et al.   ECOLOGY LETTERS

Influence of rare species on beta diversity estimates in marine benthic assemblages

(2008) Giovanni Fontana et al.   JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY

Microbial Biogeography: From Taxonomy to Traits

(2008) J. L. Green et al.   SCIENCE

The evolutionary ecology of metacommunities

(2008) M URBAN et al.   TRENDS IN ECOLOGY & EVOLUTION