Fish DNA barcoding

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DNA barcoding methods for fish are used to identify groups of fish based on DNA sequences within selected regions of a genome. These methods can be used to study fish, as genetic material, in the form of environmental DNA (eDNA) or cells, is freely diffused in the water. This allows researchers to identify which species are present in a body of water by collecting a water sample, extracting DNA from the sample and isolating DNA sequences that are specific for the species of interest.[1] Barcoding methods can also be used for biomonitoring and food safety validation, animal diet assessment, assessment of food webs and species distribution, and for detection of invasive species.[1]

In fish research, barcoding can be used as an alternative to traditional sampling methods. Barcoding methods can often provide information without damage to the studied animal.[2]

Aquatic environments have unique properties that affect how genetic material from organisms is distributed. DNA material diffuses rapidly in aquatic environments, which makes it possible to detect organisms from a large area when sampling a specific spot.[1] Due to rapid degradation of DNA in aquatic environments, detected species represent contemporary presence, without confounding signals from the past.[3]

DNA-based identification is fast, reliable and accurate in its characterization across life stages and species.[4] Reference libraries are used to connect barcode sequences to single species and can be used to identify the species present in DNA samples. Libraries of reference sequences are also useful in identifying species in cases of morphological ambiguity, such as with larval stages.[4]

eDNA samples and barcoding methods are used in water management, as species composition can be used as an indicator of ecosystem health.[5] Barcoding and metabarcoding methods are particularly useful in studying endangered or elusive fish, as species can be detected without catching or harming the animals.[6]

  1. ^ a b c Rees, Helen C.; Maddison, Ben C.; Middleditch, David J.; Patmore, James R.M.; Gough, Kevin C. (2014). Crispo, Erika (ed.). "REVIEW: The detection of aquatic animal species using environmental DNA - a review of eDNA as a survey tool in ecology" (PDF). Journal of Applied Ecology. 51 (5): 1450–1459. Bibcode:2014JApEc..51.1450R. doi:10.1111/1365-2664.12306. Archived from the original (PDF) on 2018-07-22. Retrieved 2019-11-16.
  2. ^ Goldberg, Caren S.; Turner, Cameron R.; Deiner, Kristy; Klymus, Katy E.; Thomsen, Philip Francis; Murphy, Melanie A.; Spear, Stephen F.; McKee, Anna; Oyler-McCance, Sara J. (2016). Gilbert, M. (ed.). "Critical considerations for the application of environmental DNA methods to detect aquatic species". Methods in Ecology and Evolution. 7 (11): 1299–1307. Bibcode:2016MEcEv...7.1299G. doi:10.1111/2041-210X.12595. hdl:20.500.11850/502281.
  3. ^ Thomsen, Philip Francis; Willerslev, Eske (2015). "Environmental DNA – An emerging tool in conservation for monitoring past and present biodiversity". Biological Conservation. 183: 4–18. doi:10.1016/j.biocon.2014.11.019.
  4. ^ a b "FISH-BOL". www.fishbol.org. Archived from the original on 2019-04-12. Retrieved 2019-03-28.
  5. ^ Hänfling, Bernd; Lawson Handley, Lori; Read, Daniel S.; Hahn, Christoph; Li, Jianlong; Nichols, Paul; Blackman, Rosetta C.; Oliver, Anna; Winfield, Ian J. (2016). "Environmental DNA metabarcoding of lake fish communities reflects long-term data from established survey methods" (PDF). Molecular Ecology. 25 (13): 3101–3119. doi:10.1111/mec.13660. PMID 27095076. S2CID 21984641.
  6. ^ Jerde, Christopher L.; Mahon, Andrew R.; Chadderton, W. Lindsay; Lodge, David M. (2011). ""Sight-unseen" detection of rare aquatic species using environmental DNA: eDNA surveillance of rare aquatic species". Conservation Letters. 4 (2): 150–157. doi:10.1111/j.1755-263X.2010.00158.x. S2CID 39849851.