DNA analysis reveals the presence of endangered species in fishery catch and bycatch

Over half of the rays and skates caught in Brazil belong to protected species, a DNA barcoding study shows.

By André Julião  |  Agência FAPESP – Rays have low commercial value but are often accidentally caught in large numbers by becoming entangled in the nets of fishing expeditions that set out to catch more valuable species. A new study shows the impact of this unintentional fishing of rays on marine biodiversity.

The genetic analysis of 228 rays caught as bycatch by artisanal and small industrial fishing vessels in the Southeast Region of Brazil between 2012 and 2018 showed that 101 specimens were listed as globally endangered species, while 131 specimens were on Brazil’s list of species that must not be caught or sold.

The study, conducted by researchers at the Federal University of São Paulo (UNIFESP), Santa Cecília University (UNISANTA) and São Paulo State University (UNESP), is published in the journal Genes.

The study warns of the need for more effective surveillance of fisheries in Brazil and demonstrates the potential for the application of genetic techniques to produce accurate and high-quality fishing statistics.

Many species look similar or are cut up or processed by trawler crews before offloading; therefore, catch identification based solely on external characteristics is impossible.

“Rays and skates are neglected by the scientific research community. Few studies have shown the fragility of these populations. In addition, surveillance and law enforcement are scant, and fraud is very frequent,” said Fernando Fernandes Mendonça, a professor in UNIFESP’s Sea Institute and the principal investigator for the study.

The material was collected, and the analysis was performed as part of a project supported by FAPESP. The original goal was to create a genetic database of Elasmobranchii in Brazil. Elasmobranch species comprise sharks, rays, skates, guitarfish and sawfish. “We went further and now have samples from practically everywhere in the world,” Mendonça said.

Samples were collected during the offloading of artisanal and small- to medium-sized industrial fishing vessels that operate along the coast of São Paulo state. The researchers removed small pieces of muscle and fin tissue from the bycatch specimens to analyze their DNA.

“Many of the animals had already been cut up. This practice serves to facilitate conservation on the vessel but also helps deceive inspectors,” said Bruno Lopes da Silva Ferrette, the first author of the article and currently a postdoctoral fellow at UNISANTA in Santos, São Paulo state.

At least 90% of the elasmobranch species worldwide are currently on the IUCN Red List of Threatened Species, the global benchmark in this field.

To identify the species, the researchers used DNA barcoding based on the cytochrome C oxidase subunit I (COI) mitochondrial gene, the marker of choice for this purpose. The generated sequences were compared with a reference library in the Barcode of Life Data System (BOLD), an online genetic database.

The comparison led to the identification of at least 17 species, four of which were the most representative, accounting for 46.49% of the samples: the Rio skate (Rioraja agassizii), Bullnose ray (Myliobatis freminvillei), Spiny butterfly ray (Gymnura altavela), and Brazilian cownose ray (Rhinoptera brasiliensis). The Brazilian cownose ray is an endemic species similar to another cownose ray (Rhinoptera bonasus), of which there were 15 specimens.

In addition, 44.3% of the identified samples belonged to species on the IUCN Red List, while 57.47% were protected in Brazil under Ordinance 445 issued in December 2014 by the Environment Ministry (MMA). One of the specimens was a Brazilian guitarfish (Pseudobatos horkelii), a species that is found only in Brazil and has lost 80% of its population owing to human activity.

Targeted species

The researchers also collected three specimens of the bentfin devil ray (Mobula thurstoni), which has a pair of horn-like extensions and can be as long as 2 meters in length. Sought after in Asia for its high-value gill plates, this species is protected under Appendix II of the Convention on International Trade in Endangered Species (CITES), which Brazil signed in 1975.

In addition to the high proportion of threatened species, 21.5% of the specimens belonged to species classed by the IUCN as “data-deficient” (DD) because insufficient information is available for a proper assessment of their conservation status or extinction risk; it was impossible to accurately identify the species of 39 specimens belonging to the genus Dasyatis.

“There are several possible reasons for this. The species concerned may not have been formally described yet. They may not have been properly deposited in genetic databases. A number of species may be so similar genetically that DNA barcoding alone cannot differentiate them, as it uses only one gene,” Ferrette explained.

For the researchers, the results demonstrate the need for more effective surveillance and a proper system for fishery statistics using modern techniques for data collection and analysis. Only then will it be possible to know details of the catch and bycatch in Brazilian waters.

Brazil has not had a standardized national fishery statistics system for at least ten years. While some states, including São Paulo, have monitoring programs, the data are often generic (dogfish, ray, hake, etc.) and there is insufficient data at the species level. “This severely jeopardizes efforts to establish a sustainable fishery management system,” Ferrette said.

The authors propose the use of lower-cost genetic tools such as multiplex polymerase chain reaction (PCR) and real-time or quantitative PCR (qPCR), as well as next-generation techniques such as DNA metabarcoding, to analyze artisanal or factory-ship catch and bycatch samples from the Brazilian coast in order to learn more about the impact of fisheries, improve data quality and make good fishery management possible.

The article “DNA barcoding reveals the bycatch of endangered batoid species in the Southwest Atlantic: implications for sustainable fisheries management and conservation efforts” (doi: https://doi.org/10.3390/genes10040304) by Bruno Lopes da Silva Ferrette, Rodrigo Rodrigues Domingues, Matheus Marcos Rotundo, Marina Provetti Miranda, Ingrid Vasconcellos Bunholi, Juliana Beltramin De Biasi, Claudio Oliveira, Fausto Foresti and Fernando Fernandes Mendonça is published at: www.mdpi.com/2073-4425/10/4/304/htm.