• Corpus ID: 4661002

eDNA-based metabarcoding as a monitoring tool for fish in large lakes

  title={eDNA-based metabarcoding as a monitoring tool for fish in large lakes},
  • Published 2016
  • Environmental Science


How will the ‘molecular revolution’ contribute to biological recording?
It is argued that eDNA surveys offer exciting new opportunities to engage the public in biological recording and that molecular approaches will complement conventional surveys, enabling unprecedented insights into species distributions and there is a need to rapidly establish ways of managing molecular records.
Monitoring the fish populations
  • Windermere,
  • 2014
Trimmomatic: a flexible trimmer for Illumina sequence data
Timmomatic is developed as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data and is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested.
Using Environmental DNA to Census Marine Fishes in a Large Mesocosm
Estimating the vertebrate fauna in a 4.5-million-liter mesocosm aquarium tank at the Monterey Bay Aquarium and sequencing the eDNA from its constituent seawater concludes that eDNA has substantial potential to become a core tool for environmental monitoring, but that a variety of challenges remain before reliable quantitative assessments of ecological communities in the field become possible.
Detection of a Diverse Marine Fish Fauna Using Environmental DNA from Seawater Samples
It is demonstrated that even small samples of seawater contain eDNA from a wide range of local fish species, which indicates the potential of using metabarcoding of environmental DNA (eDNA) obtained directly from seawater samples to account for marine fish biodiversity.
Monitoring endangered freshwater biodiversity using environmental DNA.
It is demonstrated that entire faunas of amphibians and fish can be detected by high-throughput sequencing of DNA extracted from pond water, underpin the ubiquitous nature of DNA traces in the environment and establish environmental DNA as a tool for monitoring rare and threatened species across a wide range of taxonomic groups.
FLASH: fast length adjustment of short reads to improve genome assemblies
FLASH is a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short and when FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds.
An In silico approach for the evaluation of DNA barcodes
A standard method for evaluating barcode quality is presented, based on the use of a new bioinformatic tool that performs in silico PCR over large databases, and shows a strong variation of taxonomic coverage: barcodes based on highly degenerated primers and those corresponding to the conserved region of the Cyt-b showed the highest coverage.
Universal primer cocktails for fish DNA barcoding
The results show that M13-tailed primer cocktails are more effective than conventional degenerate primers, allowing barcode work on taxonomically diverse samples to be carried out in a high-throughput fashion.