A global research team collects seawater from all over the globe to determine which tropical reef fish are found where. The residual DNA of the animals in the water was used to identify species and families. However, not all fish can be traced this way.
Coral reefs in tropical corals are beautiful, colorful, and abundant with species. Researchers estimate that coral reefs may be home to as many 8,000 species of fish in the world.
However, coral reefs are disappearing at alarming rates due to global warming and human activity. Unfortunately, it is still not known how many species and distributions of these reef fish exist.
Many fish species live very secretive lives and are often very similar to one another. The majority of biodiversity research relies on visual observations and catching fish to record the presence of fish in an area.
A new approach to ecology is now available: environmental DNA (eDNA). This new approach suggests that organisms leave part or all of their genetic material in the environment.
Researchers can use this approach to collect water samples at a single location, isolate DNA fragments and sequence them. The order of DNA building block components can be determined. The sequences can then be compared with reference DNA sequences taken from well-identified specimens. This will allow them to determine whether the species is found at the location.
This is the method that an international team of researchers led by researchers at the University of Montpellier and ETH Zurich used to study the occurrence of fish reefs.
The researchers collected 226 samples of water at 26 locations in 5 tropical marine areas between 2017-2019. They then analysed the DNA and assigned it to the appropriate species or families.
One-sixth more diversity detected
The researchers discovered a 16 percent greater diversity of reef fishes using eDNA than conventional survey methods like visual observations during dives. “Thanks to the eDNA method, we can detect many fish species and families much faster than with observations alone,” says Loïc Pellissier, Professor of Ecosystems and Landscape Evolution at ETH Zurich. He is one of two authors in a study that was published in the scientific journal. Proceedings of the Royal Society. Although the DNA analysis was completed in two years, the visual observations that supported the study were made by countless observers over 13 years.
Researchers discovered more species living in open water (pelagic), in reef-bound species (cryptobenthic), and in caves and crevices of reefs (cryptobenthic). These fish are less frequently seen or identified by divers.
Many of the documented pelagic species prefer open seas or deeper depths. Some belong to families that don’t live permanently in coral reefs or avoid divers, like mackerel or tuna in this family. ScombridaeAs well as sharks from within the family Carcharhinidae (requiem sharks, e.g. The blacktip reef shark
These species are important because they play an active role in coral reef function via their pelagic larval stages and nocturnal migrations to it. This is why it is often overlooked the importance of these fishes in the ecosystem.
Visual observations are still necessary
However, not all species can easily be recorded using eDNA.Labridae) or blennies (Blenniidae). Pellissier claims that only a portion of these species-rich family members are covered by the reference databases. These gaps have meant that a significant portion of the eDNA in the water samples has yet to be assigned.
The researchers are currently sequencing DNA from more fish species to improve the approach and feeding the data into the reference database. However, divers will still be required to record species not easily detected by eDNA. They also need to collect additional information such as fish sizes and biomass which cannot yet be recovered by eDNA.
Extraordinary diversity in Coral Triangle
The researchers also confirmed previous findings that the compositions of species vary widely between marine bioregions. The “Coral Triangle”, which includes Borneo, Papua New Guinea, and the Philippines, has a remarkable fish diversity. It is five times greater than the Caribbean. There are many species of herbivores and coral-eating fish.
Pellissier explains that this is due to the fact the Coral Triangle was (and continues to be) very tectonically dynamic, resulting in a wide range habitats. This marine area’s surface temperature was also more stable during the Ice Ages, which was why it was able to support a high degree of diversity.
The Caribbean, however, was more affected by the ice ages and its coral reefs, fish stocks, and other natural phenomena, shrank during cold periods. Additionally, the Isthmus of Panama formed over 2.7 million years ago. This, among other things changed the Caribbean’s ocean currents. Both of these events resulted in higher extinctions.
International cooperation
Monaco Explorations, an organization of the Prince of Monaco, was the sponsor for this study. The organization provided a research vessel to the scientists for the first part, which allowed them to collect water samples off the Colombian coast and in the Caribbean. Additional samples were also collected on separate trips that were also funded by Monaco’s government.
Pellissier says, “It was very important for me as a Swiss researcher to be part of international collaboration.” He would not have been capable of carrying out this study without the connections to his French and Indonesian partners. He says, “We cannot do isolated research at this level of Switzerland.”
Another expedition to collect water samples has been planned for later in the year. The researchers plan to sample the Indian Ocean’s tropical waters between South Africa, and the Seychelles. The coronavirus forced the cancellation of the expedition, which will be in addition to the previous years.