Nick Dunn tells the story behind his most recent eDNA publication
In September 2019, before the world changed forever, I had the opportunity to join an expedition to Diego Garcia, Chagos Archipelago in the Indian Ocean. Led by Dr. David Curnick (ZSL) and joined by Dr. Sam Weber (University of Exeter) and Dr. Sammy Andrzejaczek (Stanford University), our primary aim was to tag yellowfin tuna, a task that was hampered by bad weather preventing us from getting out to sea most of the trip. My aim was to take water samples from around the outside of the atoll and from its lagoon and use environmental DNA (eDNA) in the samples to identify the diversity of elasmobranchs (sharks and rays) in the water. Environmental DNA can be thought of as parts of an animal (skin cells, faeces, blood, saliva etc.) that have been left in its wake and contains genetic material that we can use to identify species from.
Example of the spring closing mechanism of the Niskin video, allowing us to take samples from a given depth.
We took 32 water samples from 20 sites around the atoll, at 12 sites we took samples from the surface water and from 40m, at the other 8 sites we just took surface water samples. We used a Niskin bottle to take these samples, allowing us to lower it into the water to a depth of 40m and, using a spring mechanism, close the bottle at that depth (see video). We would take trips out each morning and afternoon (weather dependent), coming back to land in between so that I could filter the samples we’d taken. Filtration allows us to isolate all the DNA and other organic matter out of the sample so, rather than keeping the whole water sample, I was left with a small filter containing the DNA from each water sample which I then preserved for travel back to the UK. Back in the laboratory in the UK, I extracted the DNA from the filter capsules and used a process called metabarcoding to identify fish and elasmobranch DNA in the sample. This involves using the Polymerase Chain Reaction (PCR) to make millions of copies of all the target DNA in a sample, followed by sequencing to identify what species each bit of DNA came from.
A silvertip shark comes to investigate the boat during a sampling trip.
From our 32 samples, we identified ten elasmobranch species: six shark species and 4 ray species. Almost every sample contained eDNA from grey reef sharks and silvertip sharks, suggesting that these two species are common and abundant in the habitat. Other notable species that we detected included the spinetail devilray, a first scientific record for the species in the region, and the critically endangered scalloped hammerhead shark. We found that the elasmobranch communities detected were different between the surface and 40m samples, a phenomenon likely to be driven by the fact that most stingray species were detected inside the lagoon, where the habitat is sandy compared to the coral reefs on the outside of the lagoon. We also detected eDNA from blue shark which despite being commonly caught as by-catch before the establishment of the large marine protected area (MPA) that surrounds the archipelago, has never been recorded in scientific surveys in the area since MPA establishment.
Although our results showed that biodiversity sampling using eDNA can be incredibly useful, identifying species that are rarely seen using conventional monitoring methods, we did note the absence of two common species from our samples. Given the historical relative abundance of whitetip reef sharks and tawny nurse sharks, we would have expected to detect them in our samples, but we didn’t. It’s possible that communities have shifted and they simply weren’t there, or that the methods we used weren’t suitable to detect these species. We conclude that although eDNA metabarcoding is a highly efficient methods to gather of biodiversity data quickly and easily, it is not without its limitations. To best protect and study sharks and rays in our oceans, continued monitoring using multiple methods is essential and we show eDNA can be an integral part of this.
If you would like the read further, our open access paper in the Zoological Journal of the Linnean Society can be viewed here.
If you have any issues accessing the article or would like to discuss our work further, please feel free to get in touch with us.
Blog by Nick Dunn