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Tuesday 15 May 2012

Molecular Ecology special issue on Environmental DNA

TABERLET Pierre

This special issue on environmental DNA was edited by Pierre Taberlet, Eric Coissac, Mehrdad Hajibabaei, and Loren Rieseberg. It was published in April 2012, and contains many papers dealing with DNA metabarcoding. Several papers of this issue are "open access".

Molecular Ecology, Volume 21, Issue 8

Editorial

Environmental DNA (pages 1789–1793)
PIERRE TABERLET, ERIC COISSAC, MEHRDAD HAJIBABAEI and LOREN H. RIESEBERG

Methodological and Technical Advances

Next-generation sequencing technologies for environmental DNA research (pages 1794–1805, free access)
SHADI SHOKRALLA, JENNIFER L. SPALL, JOEL F. GIBSON and MEHRDAD HAJIBABAEI

Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA (pages 1806–1815)
SANNE BOESSENKOOL, LAURA S. EPP, JAMES HAILE, EVA BELLEMAIN, MARY EDWARDS, ERIC COISSAC, ESKE WILLERSLEV and CHRISTIAN BROCHMANN

Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies (pages 1816–1820)
PIERRE TABERLET, SOPHIE M. PRUD’HOMME, ETIENNE CAMPIONE, JULIEN ROY, CHRISTIAN MIQUEL, WASIM SHEHZAD, LUDOVIC GIELLY, DELPHINE RIOUX, PHILIPPE CHOLER, JEAN-CHRISTOPHE CLÉMENT, CHRISTELLE MELODELIMA, FRANÇOIS POMPANON and ERIC COISSAC

New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems (pages 1821–1833)
LAURA S. EPP, SANNE BOESSENKOOL, EVA P. BELLEMAIN, JAMES HAILE, ALFONSO ESPOSITO, TIAYYBA RIAZ, CHRISTER ERSÉUS, VLADIMIR I. GUSAROV, MARY E. EDWARDS, ARILD JOHNSEN, HANS K. STENØIEN, KRISTIAN HASSEL, HÅVARD KAUSERUD, NIGEL G. YOCCOZ, KARI ANNE BRÅTHEN, ESKE WILLERSLEV, PIERRE TABERLET, ERIC COISSAC and CHRISTIAN BROCHMANN

Bioinformatics Aspects

Bioinformatic challenges for DNA metabarcoding of plants and animals (pages 1834–1847, free access)
ERIC COISSAC, TIAYYBA RIAZ and NICOLAS PUILLANDRE

A fuzzy-set-theory-based approach to analyse species membership in DNA barcoding (pages 1848–1863)
A.-B. ZHANG, C. MUSTER, H.-B. LIANG, C.-D. ZHU, R. CROZIER, P. WAN, J. FENG and R. D. WARD

ABGD, Automatic Barcode Gap Discovery for primary species delimitation (pages 1864–1877)
N. PUILLANDRE, A. LAMBERT, S. BROUILLET and G. ACHAZ

Microbial Ecology

Two decades of describing the unseen majority of aquatic microbial diversity (pages 1878–1896, free access)
LUCIE ZINGER, ANGÉLIQUE GOBET and THOMAS POMMIER

Changes in the root-associated fungal communities along a primary succession gradient analysed by 454 pyrosequencing (pages 1897–1908)
RAKEL BLAALID, TOR CARLSEN, SURENDRA KUMAR, RUNE HALVORSEN, KARL INNE UGLAND, GIOVANNI FONTANA and HÅVARD KAUSERUD

Exploration of community traits as ecological markers in microbial metagenomes (pages 1909–1917)
ALBERT BARBERÁN, ANTONI FERNÁNDEZ-GUERRA, BRENDAN J. M. BOHANNAN and EMILIO O. CASAMAYOR

Hidden diversity in diatoms of Kenyan Lake Naivasha: a genetic approach detects temporal variation (pages 1918–1930)
KATHLEEN R. STOOF-LEICHSENRING, LAURA S. EPP, MARTIN H. TRAUTH and RALPH TIEDEMANN

Diet Analysis

Who is eating what: diet assessment using next generation sequencing (pages 1931–1950, free access)
FRANCOIS POMPANON, BRUCE E. DEAGLE, WILLIAM O. C. SYMONDSON, DAVID S. BROWN, SIMON N. JARMAN and PIERRE TABERLET

Carnivore diet analysis based on next-generation sequencing: application to the leopard cat (Prionailurus bengalensis) in Pakistan (pages 1951–1965)
WASIM SHEHZAD, TIAYYBA RIAZ, MUHAMMAD A. NAWAZ, CHRISTIAN MIQUEL, CAROLE POILLOT, SAFDAR A. SHAH, FRANÇOIS POMPANON, ERIC COISSAC and PIERRE TABERLET

Biodiversity Assessment of Plants and Animals

Meta-barcoding of ‘dirt’ DNA from soil reflects vertebrate biodiversity (pages 1966–1979)
KENNETH ANDERSEN, KAREN LISE BIRD, MORTEN RASMUSSEN, JAMES HAILE, HENRIK BREUNING-MADSEN, KURT H. KJÆR, LUDOVIC ORLANDO, M. THOMAS P. GILBERT and ESKE WILLERSLEV

Islands in the ice: detecting past vegetation on Greenlandic nunataks using historical records and sedimentary ancient DNA Meta-barcoding (pages 1980–1988)
TINA JØRGENSEN, KURT H. KJÆR, JAMES HAILE, MORTEN RASMUSSEN, SANNE BOESSENKOOL, KENNETH ANDERSEN, ERIC COISSAC, PIERRE TABERLET, CHRISTIAN BROCHMANN, LUDOVIC ORLANDO, M. THOMAS P. GILBERT and ESKE WILLERSLEV

A comparative study of ancient sedimentary DNA, pollen and macrofossils from permafrost sediments of northern Siberia reveals long-term vegetational stability (pages 1989–2003)
TINA JØRGENSEN, JAMES HAILE, PER MÖLLER, ANDREI ANDREEV, SANNE BOESSENKOOL, MORTEN RASMUSSEN, FRANK KIENAST, ERIC COISSAC, PIERRE TABERLET, CHRISTIAN BROCHMANN, NANCY H. BIGELOW, KENNETH ANDERSEN, LUDOVIC ORLANDO, M. THOMAS P. GILBERT and ESKE WILLERSLEV

Plant species richness belowground: higher richness and new patterns revealed by next-generation sequencing (pages 2004–2016)
INGA HIIESALU, MAARJA ÖPIK, MADIS METSIS, LIISA LILJE, JOHN DAVISON, MARTTI VASAR, MARI MOORA, MARTIN ZOBEL, SCOTT D. WILSON and MEELIS PÄRTEL

Tracking earthworm communities from soil DNA (pages 2017–2030)
FRIEDERIKE BIENERT, SÉBASTIEN DE DANIELI, CHRISTIAN MIQUEL, ERIC COISSAC, CAROLE POILLOT, JEAN-JACQUES BRUN and PIERRE TABERLET

Perspectives

The future of environmental DNA in ecology (pages 2031–2038)
NIGEL G. YOCCOZ

Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing (pages 2039–2044, free access)
DONALD J. BAIRD and MEHRDAD HAJIBABAEI

Towards next-generation biodiversity assessment using DNA metabarcoding (pages 2045–2050)
PIERRE TABERLET, ERIC COISSAC, FRANÇOIS POMPANON, CHRISTIAN BROCHMANN and ESKE WILLERSLEV

Twitter : @Metabarcoding
Editorial board
  • BRANDNER Melissa
    • University of Nordland
    • Bodø (Norway)
  • BROCHMANN Christian
    • National Centre for Biosystematics
    • Oslo (Norway)
  • CHARITON Anthony
    • CSIRO Land and Water
    • Lucas Heights NA (Australia)
  • DEAGLE Bruce
    • University of Victoria
    • Victoria (Canada)
  • Eric Coissac
    • LECA
    • Grenoble (France)
  • KASAPIDIS Panagiotis
    • Hellenic Center for Marine Research
    • Irakleion, Crete (Greece)
  • PAWLOWSKI Jan
    • Université de Genève
    • Genève 4 (Switzerland)
  • TABERLET Pierre
    • LECA,
    • Grenoble (France)
  • WILLERSLEV Eske
    • Centre for GeoGenetics
    • Copenhagen (Denmark)
Editorial
  • Vodka, Bison and Metabarcoding

    31 July 2015, by BRANDNER Melissa

    The start of last month saw the occurrence of the Fifth Metabarcoding Spring School held in Białowieża National Park , Poland. A variety of scientists attended from all over the globe to learn, share and inspire with unique stories of metabarcoding.
    The scientists at the Mammal Research Institute PAS in Białowieża National Park hosted this year’s workshop. And our hats go off to them for the organizational skills, warmth and hospitality. During the week, experienced metabarcoders gave lectures on their trials and tribulations in the field of metabarcoding, sparking conversations between the attendees. The end of the first day saw flash talks from all participants of the event, creating an icebreaker and showing the wide variety of applications for metabarcoding, including, dietary studies, environmental health, fundamental ecology and exploration of rare and ancient habitats.
    Pierre Taberlet (who is rumoured to run 8000 PCR a day!) taught technical aspects such as DNA extraction in (...)

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