High-throughput monitoring of wild bee diversity and abundance via mitogenomics

$1 DNA barcodes for reconstructing complex phenomes and finding rare species in specimen-rich samples

(2015) Rudolf Meier et al.   CLADISTICS

Soup to Tree: The Phylogeny of Beetles Inferred by Mitochondrial Metagenomics of a Bornean Rainforest Sample

(2015) Alex Crampton-Platt et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics

(2015) Carmelo Andújar et al.   MOLECULAR ECOLOGY

Detection and decay rates of prey and prey symbionts in the gut of a predator through metagenomics

(2015) Débora P. Paula et al.   Molecular Ecology Resources

DNA barcoding largely supports 250 years of classical taxonomy: identifications for Central European bees (Hymenoptera, Apoideapartim)

(2015) Stefan Schmidt et al.   Molecular Ecology Resources

Bee declines driven by combined stress from parasites, pesticides, and lack of flowers

(2015) D. Goulson et al.   SCIENCE

Validating the power of mitochondrial metagenomics for community ecology and phylogenetics of complex assemblages

(2015) Carola Gómez-Rodríguez et al.   Methods in Ecology and Evolution

Use of Droplet Digital PCR for Estimation of Fish Abundance and Biomass in Environmental DNA Surveys

(2015) Hideyuki Doi et al.   PLoS One

Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform

(2015) Shadi Shokralla et al.   Scientific Reports

Blue: correcting sequencing errors using consensus and context

(2014) Paul Greenfield et al.   BIOINFORMATICS

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

(2014) Y. Xie et al.   BIOINFORMATICS

Bulk De Novo Mitogenome Assembly from Pooled Total DNA Elucidates the Phylogeny of Weevils (Coleoptera: Curculionoidea)

(2014) Conrad P.D.T. Gillett et al.   MOLECULAR BIOLOGY AND EVOLUTION

Universal and blocking primer mismatches limit the use of high-throughput DNA sequencing for the quantitative metabarcoding of arthropods

(2014) J. Piñol et al.   Molecular Ecology Resources

Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data

(2014) Gentile F. Ficetola et al.   Molecular Ecology Resources

Comparing the effectiveness of metagenomics and metabarcoding for diet analysis of a leaf-feeding monkey (Pygathrix nemaeus)

(2014) Amrita Srivathsan et al.   Molecular Ecology Resources

‘Life on Earth’ project gets under way

(2014) Natasha Gilbert   NATURE

Multiplex sequencing of pooled mitochondrial genomes—a crucial step toward biodiversity analysis using mito-metagenomics

(2014) Min Tang et al.   NUCLEIC ACIDS RESEARCH

Extinctions of aculeate pollinators in Britain and the role of large-scale agricultural changes

(2014) J. Ollerton et al.   SCIENCE

An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform

(2014) Douglas W Fadrosh et al.   Microbiome

Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding

(2013) Yinqiu Ji et al.   ECOLOGY LETTERS

A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents

(2013) Matthieu Leray et al.   Frontiers in Zoology

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Plant-Pollinator Interactions over 120 Years: Loss of Species, Co-Occurrence, and Function

(2013) L. A. Burkle et al.   SCIENCE

Wild Pollinators Enhance Fruit Set of Crops Regardless of Honey Bee Abundance

(2013) L. A. Garibaldi et al.   SCIENCE

Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification

(2013) Xin Zhou et al.   GigaScience

Detecting Insect Pollinator Declines on Regional and Global Scales

(2012) Gretchen Lebuhn et al.   CONSERVATION BIOLOGY

DNA from soil mirrors plant taxonomic and growth form diversity

(2012) N. G. YOCCOZ et al.   MOLECULAR ECOLOGY

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

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

Pollination services in the UK: How important are honeybees?

(2011) T.D. Breeze et al.   AGRICULTURE ECOSYSTEMS & ENVIRONMENT

Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering

(2011) Xiaolin Hao et al.   BIOINFORMATICS

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Patterns of widespread decline in North American bumble bees

(2011) S. A. Cameron et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA

(2011) María C. Ávila-Arcos et al.   Scientific Reports

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

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

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

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Global pollinator declines: trends, impacts and drivers

(2010) Simon G. Potts et al.   TRENDS IN ECOLOGY & EVOLUTION

Second-generation environmental sequencing unmasks marine metazoan biodiversity

(2010) Vera G. Fonseca et al.   Nature Communications

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

MEASURING BEE DIVERSITY IN DIFFERENT EUROPEAN HABITATS AND BIOGEOGRAPHICAL REGIONS

(2008) Catrin Westphal et al.   ECOLOGICAL MONOGRAPHS