In an article recently published in Methods in ecology and evolution, researchers from the Conservation Forensics Lab at the University of Hong Kong have described a powerful new tool to monitor the trade of rare and endangered fish species in Hong Kong’s wet markets. Using environmental DNA (eDNA) found in runoff from fish markets, researchers were able to extract and sequence enough DNA to identify more than 100 species of fish that passed through the market.
Various kinds of vulnerable or endangered species were detected by eDNA method in the study, including Epinephelus fuscoguttatusa type of brown marbled grouper listed as vulnerable and declining by the International Union for Conservation of Nature (IUCN), and three species of eel including Anguilla japonica and Anguilla rostratawhich are listed as threatened by the IUCN, as well as the European eel listed by CITES (Convention on International Trade in Endangered Species of Wild Fauna and Flora), Anguilla anguilla. Two types of bream were detected including the golden thread bream (Nemipterus virgatus) classified as vulnerable by the IUCN, and the Okinawa sea bream (Acanthopagus sivicolus), listed as vulnerable and declining by the IUCN.
Metabarcoding allows the identification of species both
Barcoding is a common method of species identification, in which certain regions of an organism’s genome are sequenced and used to identify the organism in question. Each species has its own unique “barcode”, which can provide a more reliable form of identification than traditional morphology-based methods. This technique can be extended to identify multiple species at once (known as metabarcoding) using advanced high-throughput sequencing technology. Even small amounts of DNA released from plants and animals into the environment (eDNA) are sufficient for metabarcoding that allows the identification of mixed communities of species that may have been present in the region.
In this study, Conservation Forensics Lab researchers aimed to develop a method of identifying fish species traded in Hong Kong markets that does not rely on experts in fish taxonomy spending hours visually identifying each fish for sale. Additionally, many fish sellers are often reluctant to allow lengthy inspections of their goods, as endangered fish species can often be found for sale in Hong Kong markets.
The method described in the article compared the two most common types of eDNA capture: filtration and precipitation. In the filtration method, a liter of water collected from the sewers of three wet markets was collected and passed through a fine filter, which captured tissue, blood and other cellular debris containing enough DNA to identify the species of fish that reject it. . The precipitation method used even less water, allowing identification of fish species present by chemical precipitation of eDNA present in cell debris from 45 mL of drain runoff. Once the drainage water was collected, the eDNA was extracted and sequenced and the fish species present in the three wet markets studied over a period of 5 days were identified. To confirm the results, an expert fish taxonomist performed a visual survey and the overlap of species detections was compared.
High reliability and easy to adapt
Although it is impossible to be 100% certain in the identification of every species present with either method, the advantages of a DNA-based survey method are numerous. Primarily, DNA-based identifications can be more reliable than morphological identifications, and this is especially true when fish are sold slaughtered or belong to certain genera and families of similar appearance. The DNA extraction method described in the article is also very simple and can easily be performed by anyone with a basic molecular laboratory training of several hours. Visual surveys require hours and hours of in-depth work by several expert taxonomists, which has been a factor that has held back the rollout of regular surveys in Hong Kong.
“We hope that our method will not only encourage local authorities to adopt more high-tech solutions to monitor and combat illegal wildlife trade in Hong Kong, but also help expand the use of eDNA and metabarcoding. further in urban contexts,” said John L. RICHARDS, co-author of the journal article.