archive-org.com » ORG » M » METABARCODING.ORG

Total: 246

Choose link from "Titles, links and description words view":

Or switch to "Titles and links view".
  • Diet analysis of the Mediterranean shag (Phalacrocorax aristotelis desmarestii) using conventional techniques and next generation sequencing - metabarcoding.org
    is carried out using both conventional prey identification methods and next generation sequencing Regurgitates undigested prey remains and faeces have been collected from a large colony of the species in the N Aegean Sea A conventional prey analysis has been carried out by identifying indigestible part remains mainly fish otoliths from regurgitates The latter as well as faecal samples will be subjected to amplicon sequencing using the 454 GS FLX platform following the protocol of Deagle et al 2009 By analyzing the same samples i e regurgitates both by conventional and molecular techniques we will be able to check whether molecular approaches perform better for prey identification at the species level and if they can give reliable quantitative estimations Moreover the analysis of faecal samples will show whether there are prey items that are not detected in the regurgitates Finally we will estimate which approach is more cost effective for determining the diet of the Mediterranean shag 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

    Original URL path: http://metabarcoding.org/spip.php?article18 (2016-04-26)
    Open archived version from archive


  • Diet analysis using NGS - metabarcoding.org
    identification Initially this involved sequencing clones from PCR products and studies were limited in scale because of the costs and effort required The recent development of next generation sequencing NGS has made this approach much more powerful by allowing the direct characterization of dozens of samples with several thousand sequences per PCR product and has the potential to reveal many consumed species simultaneously DNA metabarcoding Continual improvement of NGS technologies on going decreases in costs and current massive expansion of reference databases make this approach promising Here we review the power and pitfalls of NGS diet methods We present the critical factors to take into account when choosing or designing a suitable barcode Then we consider both technical and analytical aspects of NGS diet studies Finally we discuss the validation of data accuracy including the viability of producing quantitative data open access paper Pompanon et al 2012 Mol Ecol doi 10 1111 j 1365 294X 2011 05403 x 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

    Original URL path: http://metabarcoding.org/spip.php?article10 (2016-04-26)
    Open archived version from archive

  • DNA barcoding at the Museum Koenig - metabarcoding.org
    of the DNA barcoding activities at the Zoologisches Forschungsmuseum A Koenig ZFMK Bonn Germany that I am involved in Most of these focus on Sanger sequencing but NGS of environmental samples is and will be included as well A personal taxon oriented focus in barcoding lies on weevils and spiders while the ZFMK is embarking as the speaker of the project in a large project to barcode the national biotas the German Barcode of Life GBOL project 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

    Original URL path: http://metabarcoding.org/spip.php?article21 (2016-04-26)
    Open archived version from archive

  • Exploring the Role of Land snails in Ecosystems - metabarcoding.org
    is work intensive and the lowest taxonomic levels usually cannot be separated by eye One step up the food chain the literature on the predators and diseases of land snails is largely anecdotal Visual analyses of feces or stomach contents of predators would generally overlook slugs and often snails whose soft bodies are digested quickly It should be possible to answer important questions in invasion and conservation biology by performing metabarcoding on the feces of land snails and their potential predators Another possible use of genetic approaches is in surveying land snails Weather and other environmental factors can strongly affect traditional surveying methods for slugs or rare snails Biodiversity surveys and population genetics studies could be greatly aided if mucus and other land snail residues could be genotyped rather than the animals themselves which are so frequently hidden and inaccessible 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

    Original URL path: http://metabarcoding.org/spip.php?article26 (2016-04-26)
    Open archived version from archive

  • Human Identification through Analysis of the Salivary Microbiome - metabarcoding.org
    be used in a new method for human identification and evaluating its robustness Illumina high throughput sequencing is the chosen technique to analyse the bacterial composition of saliva followed by a Bayesian based statistical analysis to calculate the forensic value of the data Three different targets 16S RNA RpoB Streptococcus and RpoB Gram negative have been chosen to maximise coverage of the salivary microbiome and combined they should increase the power of identification 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

    Original URL path: http://metabarcoding.org/spip.php?article16 (2016-04-26)
    Open archived version from archive

  • Investigating fish abundance through quantification of aqueous environmental DNA - metabarcoding.org
    can provide evidence that a given organism is present and may also provide information about population or biomass density As one part of my PhD research University of Notre Dame USA on genetic monitoring of aquatic macrofauna using eDNA I am investigating the relationship between fish abundance and eDNA abundance In this presentation I will discuss some findings and some methods for optimizing this relatively new approach to genetic monitoring I will additionally discuss some new aquatic eDNA work just beginning in our research group that will utilize a metagenetic metabarcoding approach with next generation sequencing 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

    Original URL path: http://metabarcoding.org/spip.php?article32 (2016-04-26)
    Open archived version from archive

  • Is orchid distribution limited by their mycorrhizal associations? - metabarcoding.org
    diverse trophic strategies within habitats as they could be pathogens endophytes or mycorrhizal with other plant species or only saprobes My PhD generally focuses on influence of distribution of the mycorrhizal fungi on ecology and distribution of the orchids in landscape Furthermore the presence of many endophytic fungi in orchid roots allows to study potential interactions via common mycelial networks with surrounding plants within habitats High throughput sequencing with metabarcoding could provide a comprehensive environmental context by showing complete fungal species pool in the soil plant selectivity patterns on the fungal associates and potential mycelial networking among plants which could have strong impact on a species presence and coexistence 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

    Original URL path: http://metabarcoding.org/spip.php?article24 (2016-04-26)
    Open archived version from archive

  • Molecular and morphological approaches to biodiversity assessment of soft bottom assemblages - metabarcoding.org
    to be used as tags Our first idea is to work with COI and rDNA 18s barcodes and compare the information gleaned from both genes We will also compare DNA extractions with RNA extractions in duplicate samples total vs living DNA Our project includes comparisons of soft bottom communities in submarine canyons bathyal assemblages vs continental shelf circalittoral assemblages and well preserved habitats vs contaminated sites We will work in close collaboration with a team that will analyse the same samples through conventional methods of sorting and identification We also want to explore the capabilities of the method to obtain quantitative rather than merely qualitative information To this end we plan to work with artificial samples with known numbers of individuals and species to assess the reliability of the use of number of reads as a proxy for abundance of taxa 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

    Original URL path: http://metabarcoding.org/spip.php?article11 (2016-04-26)
    Open archived version from archive



  •