Finding flies in the mushroom soup: Host specificity of fungus-associated communities revisited with a novel molecular method

Host genetic variation strongly influences the microbiome structure and function in fungal fruiting-bodies

(2018) Mari Pent et al.   ENVIRONMENTAL MICROBIOLOGY

Agriculture shapes the trophic niche of a bat preying on multiple pest arthropods across Europe: Evidence from DNA metabarcoding

(2018) Ostaizka Aizpurua et al.   MOLECULAR ECOLOGY

The choice of universal primers and the characteristics of the species mixture determine when DNA metabarcoding can be quantitative

(2018) Josep Piñol et al.   MOLECULAR ECOLOGY

Performance of DNA metabarcoding, standard barcoding, and morphological approach in the identification of host–parasitoid interactions

(2017) Martin Šigut et al.   PLoS One

Pellets of proof: First glimpse of the dietary composition of adult odonates as revealed by metabarcoding of feces

(2017) Kari M. Kaunisto et al.   Ecology and Evolution

Polyphagy on unpredictable resources does not exclude host specialization: insects feeding on mushrooms

(2016) Kadri Põldmaa et al.   ECOLOGY

The use of DNA barcodes in food web construction—terrestrial and aquatic ecologists unite!

(2016) Tomas Roslin et al.   GENOME

Structure of insect community in the fungusInonotus radiatusin riparian boreal forests

(2016) Mats Jonsell et al.   JOURNAL OF NATURAL HISTORY

What you need is what you eat? Prey selection by the bat Myotis daubentonii

(2016) Eero J. Vesterinen et al.   MOLECULAR ECOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Dissecting host-associated communities with DNA barcodes

(2016) Christopher C. M. Baker et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Host diversity and trophic status as determinants of species richness and community composition of fungus gnats

(2015) Kadri Põldmaa et al.   BASIC AND APPLIED ECOLOGY

Error filtering, pair assembly and error correction for next-generation sequencing reads

(2015) Robert C. Edgar et al.   BIOINFORMATICS

Host abundance, durability, basidiome form and phylogenetic isolation determine fungivore species richness

(2015) Simon Thorn et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Food web structure of the fungivorous insect community on bracket fungi in a Bornean tropical rain forest

(2015) SATOSHI YAMASHITA et al.   ECOLOGICAL ENTOMOLOGY

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

(2015) Pille Gerhold et al.   FUNCTIONAL ECOLOGY

Tree genotype mediates covariance among communities from microbes to lichens and arthropods

(2015) Louis J. Lamit et al.   JOURNAL OF ECOLOGY

Not all are free-living: high-throughput DNA metabarcoding reveals a diverse community of protists parasitizing soil metazoa

(2015) S. Geisen et al.   MOLECULAR ECOLOGY

Establishing a community-wide DNA barcode library as a new tool for arctic research

(2015) H. Wirta et al.   Molecular Ecology Resources

The Mycetophila ruficollis Meigen (Diptera, Mycetophilidae) group in Europe: elucidating species delimitation with COI and ITS2 sequence data

(2015) Siiri Jürgenstein et al.   ZooKeys

Exposing the structure of an Arctic food web

(2015) Helena K. Wirta et al.   Ecology and Evolution

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

(2015) Shadi Shokralla et al.   Scientific Reports

Molecular detection of trophic interactions: emerging trends, distinct advantages, significant considerations and conservation applications

(2014) Elizabeth L. Clare   Evolutionary Applications

Complementary molecular information changes our perception of food web structure

(2014) Helena K. Wirta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global diversity and geography of soil fungi

(2014) L. Tedersoo et al.   SCIENCE

Antagonistic interaction networks are structured independently of latitude and host guild

(2013) Rebecca J. Morris et al.   ECOLOGY LETTERS

The ecology of differences: assessing community assembly with trait and evolutionary distances

(2013) Marc Cadotte et al.   ECOLOGY LETTERS

DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet

(2013) M. De Barba et al.   Molecular Ecology Resources

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System

(2013) Sujeevan Ratnasingham et al.   PLoS One

Ecophylogenetics: advances and perspectives

(2012) Nicolas Mouquet et al.   BIOLOGICAL REVIEWS

Methodology A rapid and inexpensive method for isolation of total DNA from Trichoderma spp (Hypocreaceae)

(2012) J.C. Vazquez-Angulo et al.   GENETICS AND MOLECULAR RESEARCH

Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture

(2012) N. Rohland et al.   GENOME RESEARCH

Towards next-generation biodiversity assessment using DNA metabarcoding

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

High-Coverage ITS Primers for the DNA-Based Identification of Ascomycetes and Basidiomycetes in Environmental Samples

(2012) Hirokazu Toju et al.   PLoS One

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

(2012) C. L. Schoch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Description and DNA barcoding of Tipula (Pterelachisus) recondita sp. n. from the Palaearctic region (Diptera, Tipulidae)

(2012) Jukka Salmela et al.   ZooKeys

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

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

Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea

(2011) Daniel PR Herlemann et al.   ISME Journal

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

(2011) Albert Barberán et al.   ISME Journal

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Taxon-specific PCR for DNA barcoding arthropod prey in bat faeces

(2010) MATT R. K. ZEALE et al.   Molecular Ecology Resources

Diversity, abundance and community network structure in sporocarp-associated beetle communities of the central Appalachian Mountains

(2010) Mary Jane Epps et al.   MYCOLOGIA

Progress towards DNA barcoding of fungi

(2009) KEITH A. SEIFERT   Molecular Ecology Resources