Guestblog: Environmental DNA allows for the detection of cryptic seahorse species

I’m very proud to publish this guestblog by Georgia Nester. Georgia is a PhD-candidate at Curtin University, where she focuses on the use of environmental DNA on species that are otherwise hard to study. She has just published her first paper, which could be a game changer on how we detect and study seahorses and their relatives in the future.


Seahorses (members of the Syngnathidae family) have never been detected using environmental DNA (eDNA), despite the fact that globally there are 14 species classified as “Threatened” by the IUCN. We compared the ability to detect a wide range of fish including Syngnathidae of two existing fish metabarcoding assays (= methods to detect eDNA and two new fish metabarcoding assays which we developed. With our new assays, we detected three Syngnathidae species in eDNA survey of the Perth metropolitan area (Western Australia), while the existing assays did not detect any Syngnathidae. These detections include the seahorse species Hippocampus subelongatus and Hippocampus breviceps, which represents the first time a seahorse has been detected using eDNA.

 

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The West Australian Seahorse (Hippocampus subelongatus). Photo credit: Maarten De Brauwer

With increasing human pressures and climate change resulting in a continuous decline of global biodiversity, there is a growing demand for rapid and sensitive conservation and monitoring programs. Using traditional methods, accurate data on species presence/absence and distribution is often difficult to obtain in aquatic environments. Environmental DNA metabarcoding is an increasingly popular solution. eDNA metabarcoding is capable of revealing what species are present in an environment by detecting traces of DNA they leave behind in the environment (e.g. shed skin cells, scales, blood, faeces etc). While eDNA metabarcoding surveys have been applied to a wide range of aquatic environments, no one has reported the detection of a seahorse to the best of our knowledge.

Many Syngnathidae species are considered threatened, however many more species (over 30%) lack the data necessary to assess their extinction risk. With the risk of a ‘silent extinction’ for many Syngnathidae species, the design of a non-invasive method for monitoring and managing these cryptic species may be critical to their survival. False negatives (failure to detect a species when they are in fact present) are significant in conservation management. For this reason, we aimed to determine if the Syngnathidae family (seahorses, seadragons and pipefish) were being inadvertently missed in current eDNA surveys.

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Camouflaged species such as the shorthead seahorse (Hippocampus breviceps) can be hard to detect with the naked eye. Photo credit: Maarten De Brauwer

Australia is home to 128 species of Syngnathidae in 40 genera, 65 of which are found in Western Australian waters. The Perth metropolitan area in Western Australia was chosen as our study site as it encompasses several habitat types, including brackish and salt water. We sampled from five locations across the Perth metropolitan area and processed the samples back at the TrEnD Laboratory in Curtin University. The results of this study have recently been published in the scientific journal environmental DNA.

In total, we detected four species of Syngnathidae using our newly developed metabarcoding assays “16S_FishSyn_Short” and “16S_FishSyn_Long”. The Syngnathidae species we detected were the Western Australian seahorse (Hippocampus subelongatus), the shorthead seahorse (Hippocampus breviceps), the spotted pipefish (Stigmatopora argus) and the tiger pipefish (Filicampus tigris). With Syngnathidae populations declining due to exploitation for the aquarium trade and habitat degradation, we have shown that eDNA methodologies are capable of detecting Syngnathidae taxa in the environment. This will help inform conservation and management strategies by providing a much-needed non-invasive method for monitoring these populations. Importantly, our study represents the first time a seahorse species has been detected using eDNA methodologies.

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The Western Australia seahorse (Hippocampus subelongatus, one of the first seahorse species to be detected with eDNA. Photo credit: David Harasti

The discovery of the Sodwana seahorse (Hippocampus nalu), Africa’s first pygmy seahorse

I am beyond excited to share the news that with a fantastic team of colleagues, we described a new species of pygmy seahorse!!! Hippocampus nalu, or the Sodwana pygmy seahorse in normal language, is the 45th seahorse species to be described, and the first pygmy seahorse species found in African coastal waters. It’s gorgeous and cute and very tiny.

To explain the story of how such a discovery happens, we wrote an explainer in The Conversation. Just so you wouldn’t have to do effort of clicking the link, I am also sharing the article below, which was co-written by myself, Louw Claassens, Graham Short, and David Harasti. All pictures provided are by Richard Smith.


Before you read this article, pause for a moment and look at the nail on your little finger. That’s about the size of a new species of seahorse discovered in the waters of Sodwana Bay, South Africa, which falls within the iSimangaliso Wetland Park, a World Heritage Site, in KwaZulu-Natal province.

Hippocampus nalu grows to a maximum size of just 2cm. It is the first pygmy seahorse ever discovered in African waters. Our team has conclusively demonstrated that Hippocampus nalu is physically and genetically distinct from the seven known species of pygmy seahorses. Its nearest relatives are found more than 8,000 km away in the Pacific Ocean.

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An adult male Sodwana seahorse (Hippocampus nalu). Credit: Richard Smith

Seahorses are threatened all around the world. Many species are at risk of becoming extinct because of human activities such as bottom trawling, over-fishing, and habitat destruction. As a result, several species are listed on the IUCN Red List of Threatened Species. However, to date no pygmy seahorses are considered threatened – because we simply do not know enough about them. By discovering more species, and learning more about these tiny creatures, scientists can offer advice on how best to protect them.

Pygmy seahorses can also provide an important boost for tourism: scuba divers love these small species and are willing to travel far and wide for a chance to see them. If coastal communities and scuba divers alike are taught about the best ways to protect these species and others in the oceans, there can be huge economic and social benefits.

The most astonishing part of this discovery is that it didn’t start in a laboratory, or with keen scientific minds assessing the likelihood of finding a pygmy seahorse in African waters. Instead, it began with a photograph.

Tracking the seahorse

Dr Louw Claassens and Dr Dave Harasti arrived in Sodwana in early 2018 looking for an entirely different animal: a seahorse-like species called a pygmy pipehorse. But then a local dive guide named Savannah Olivier showed them a photograph of a very small seahorse. The scientists recognised it as a pygmy seahorse, which are supposed to live an entire ocean away. South Africa is home to four other seahorse species, but this was the first time a pygmy seahorse had been observed in South Africa, let alone Africa.

Nine months later Louw returned to Sodwana Bay, this time accompanied by Dr Richard Smith, a pygmy seahorse expert. They, with Olivier, found a pair of the tiny pygmy seahorses along a rock face at about 15m depth. The little creatures were grasping on to slivers of algae amid raging surging seas. The reefs of Sodwana Bay are exposed to the swells of the Indian Ocean, very unlike the more sheltered coral reef settings in the tropical Pacific where the other known pygmy seahorses are found.

Later they even found a tiny juvenile measuring just a centimetre in length, which was dwarfed by a diver’s finger.

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Juvenile Hippocampus nalu – South African pygmy seahorse, Sodwana Bay. Credit: Richard Smith

Finding the seahorses was only the first step in describing the new species. The rest of the team now got to work. Graham Short, a researcher at the Australian Museum and California Academy of Sciences, compared the mystery seahorses with other pygmy seahorse species by looking at their characteristics under a microscope, as well as a powerful CT scanner. Dr Mike Stat, a geneticist from Australia, used genetic methods to test how distinct it was from other species. Through combined team efforts, we confirmed that the Sodwana pygmy seahorse was a new species and could give it an official scientific name.

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CT scan of the Sodwana seahorse (Hippocampus nalu). Credit: Graham Short

The name “nalu” has three layers of meaning. In the local isiXhosa and isiZulu languages it means “here it is”, to show that the species had been there all along until its discovery. “Nalu” is also the diver Savannah Olivier’s middle name. Finally, “nalu” means “surging surf, wave” in Hawaiian, which hints at the habitat the species lives in.

More to learn

The discovery of the Sodwana pygmy seahorse is exciting for more than just its scientific value. It provides new insights into the global distribution of these tiny fish and paves the way for further exploration in other locations. Only a handful of research publications focused on the ecology of pygmy seahorses exist, so anything we can learn more about these critters will help the future conservation of this unique group.

Finding a species like Hippocampus nalu also shows how little we know about Africa’s marine biodiversity, and how much more is left to discover. It highlights how important the observations of keen amateurs are to help scientists. If a keen fisherman did not consider a strange looking fish caught off the south coast of South Africa worth sharing with Marjory Courtney-Latimer in 1938, the discovery of the coelacanth, a living fossil, might never have happened.

Similarly, without a diver’s sharp eyes and an expert’s initial questions, the world would still not know that the Sodwana pygmy seahorse exists. As scientists, being open to questions from the general public not only helps inform non-scientists, but can also help us make new discoveries.

Hippocampus nalu - South African pygmy seahorse, Sodwana Bay

 A female Hippocampus nalu. Credit: Richard Smith

Finding the Knysna Seahorse: Mini-blog 6

I feel like I only just arrived in South Africa to look for endangered seahorses, but instead I am flying to Johannesburg where I will catch a connecting flight to Perth. This trip was no different than other fieldwork trips in that regard: what looks like a long time of sampling at the planning stage just flies by before you know it.

Louw and me have been busy since the last mini-blog. Most importantly, we successfully finished sampling! The last locations were less explored areas than the first ones, which is very exciting. Even if we do not find seahorses in these spots, they give inspiration to come back for new research projects.

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Cormorant in Jongensfontein

After wrapping up the sampling we visited Stellenbosch University. The university is the home to the von der Heyden Lab, which specialises on genetic research for conservation and biodiversity planning. They also have an eDNA project which investigates fish diversity in South Africa. During our visit I gave a talk about my own research to the marine students in the university. It was great to share my love for strange critters, especially since the students had some very relevant questions at the end of the talk. As much as I enjoy talking (or writing) about my research, it’s even more fun to have a conversation about it and getting a fresh look through someone else’s eyes.

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South African penguins (Spheniscus demersus) taking a stroll

In the last two days of the trip we relaxed, caught up with friends, and explored Cape Town and False Bay. The highlights were definitely diving in the kelp forests of Simonstown and visiting the nearby African penguin (Spheniscus demersus) colony. While I have dived in cold water before, I never had the pleasure of seeing this particular ecosystem. If you ever have the opportunity, I can highly recommend it!

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Kelp diving

If a coral reef dive is like swimming through an underwater flower garden, kelp diving would be the equivalent of walking through a forest. There’s something very special about weaving your way through underwater plants that reach from he bottom all the way to the surface. The sunlight is filtered and the canopy above creates shadows you just do not get in other kinds of diving. On top of that, the bottom is very rich with all kinds of life. There are plenty of invertebrates like sea urchins, featherstars and nudibranchs. The fish life is very different than what I am used to, the small pufadder shysharks (Haploblepharus edwardsii) only live in South Africa area and are the cutest little things. To top it off, two southern right whales passe by close to shore as we were exiting the water. Louw even managed to snorkel out and catch a glimpse of them!

I guess it’s safe to say that this trip has been a successful one. It will be another few months before we will have all the results, but I am very excited to discover in which places we found the elusive Knysna seahorse!

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Not a bad spot for a dive…

 

Finding the Knysna Seahorse: Mini-blog 5

It’s already been a week since I arrived in South Africa to study the endangered Knysna seahorse with Dr. Louw Claassens from the Knysna Basin Project. Together we are testing if environmental DNA (eDNA) can be used to find rare seahorses and pipefishes.

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eDNA filtering in progress

To do this, we have been travelling along the southern coast of South Africa, taking water samples along the way in estuaries where our focal species lives, where it used to live, or where it might live. Yesterday we left Knysna to sample water in Klein Brak and Groot Brak. We are especially interested in the Klein Brak estuary, since there are multiple anecdotes that the Knysna seahorse (Hippocampus capensis) used to live here. Nobody has checked recently if it really was the Knysna seahorses and it seems that the most recent sighting has been many years ago. Because of this, it is usually assumed that there are no more Knysna seahorses in Klein Brak.

This brings me to a very important (maybe the most important?) question about this whole endeavour: WHY are we actually doing this? It’s all good an well to say that we want to help these endangered animals, but what exactly are we hoping to achieve? What will our results mean for managing the endangered Knysna seahorse, the critically endangered Estuarine pipefish, or any other endangered small fish for that matter?

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Knysna estuary, just imagine all the seahorses down there!

What we are hoping to achieve can be summarised in three main points.

  1. We want to test if the eDNA method can really be used to find small, endangered fishes (particularly seahorses and their relatives). So far, previous research has shown that eDNA work on large fishes such as sawfish, but it is not sure yet if this will work for seahorses, which are obviously much smaller.
  2. The best case scenario would be that we could also find seahorses in estuaries where it was thought to have disappeared. This would be great news for the conservation status for the species, as it would mean that it occurs in a wider area than we thought, which would mean that it is less likely to go extinct.
  3. If this would happen, it would mean two things. First of all, the new locations would have to be studied, so we can find out how many live in these estuaries. It would also mean that those new places need extra protection and monitoring to ensure the species do not disappear from their newly discovered homes.

Ultimately, if the eDNA method works for small, endangered seahorses (or their relatives), it could be used to monitor small fishes worldwide. This would help solving one of the biggest problems with studying small species, especially those that are rare or hard to find.

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Louw looking for Knysna seahorses in the Thesen Island Marina (she found 3!)