Fish DNA barcoding
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.
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.
[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.
Traditional methods are time-consuming and include destructive practices that can harm individuals of rare or protected species.
DNA barcoding is a relatively cost-effective and quick method for identifying fish species aquatic environments.
[9] Early detection is vital for control and removal of non-indigenous, ecologically harmful species (e.g. lion fish (Pteroissp.)
[10] Barcoding and metabarcoding approaches yield rigorous and extensive data on recruitment, ecology and geographic ranges of fisheries resources.
[12][13] Globalisation of food supply chains has led to an increased uncertainty of the origin and safety of fish-based products.
[14][15] A recent study from supermarkets in the state of New York found that 26.92% of seafood purchases with an identifiable barcode were mislabelled.
Free molecules, intestinal lining and skin cell debris are the main sources of fish eDNA.
The small size of ponds compared to other water bodies makes them more sensitive to environmental conditions such as exposure to UV light and changes in temperature and pH.
(2016) showed that the L1848/H1913 primer pair, which amplifies a region of 12S rRNA locus, was able to reach high taxonomical coverage and discrimination even with a short target fragment.
(2016) performed metabarcoding experiments focused on lake fish communities using 12S_F1/12S_R1 and CytB_L14841/CytB_H15149 primer pairs, whose targets were located in the mitochondrial 12S and cytochrome B regions respectively.
[23] In general, these studies summarize that special considerations about primer design and selection have to be taken according to the objectives and nature of the experiment.
The proper identification of fish specimens with DNA barcoding methods relies heavily on the quality and species coverage of available sequence databases.
For each classified specimen, the following information can be available: scientific name, picture, date, GPS coordinate, depth and method of capture, size, and Cytochrome Oxidase c Subunit 1 (CO1) DNA sequence.
eDNA can reduce the costs of fishing, transport of samples and time invested by taxonomists, and in most cases requires only small amounts of DNA from target species to reach reliable detection.
Although there are some cases in which quantification has been possible[33] there appears to be no consensus on how, or to what extent, molecular data can meet this aim for fish monitoring.
