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

/ Maarten De Brauwer / Leave a comment

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.

 

H subelongatus

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.

H breviceps (1)

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.

H subelongatus_Dave

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

/ Maarten De Brauwer / 2 Comments

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.

Hippocampus nalu - South African pygmy seahorse, Sodwana Bay

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.

Juvenile Hippocampus nalu - South African pygmy seahorse, Sodwan

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.

CT_Hippocampus_nalu

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

Ambon and Halmahera fieldwork: Mini-blog 3 – Surveying Ambon’s reefs

/ Maarten De Brauwer / 1 Comment

In the previous fieldwork blog I wrote that we were about to leave on the boat to survey coral reefs around Ambon. So let me walk you through how our first week went.

Leaving Ambon took a bit more effort than expected, getting the necessary pre-departure paperwork signed off took 6 hours instead of 10 minutes, but we finally managed to leave late afternoon. We left under a rather gloomy sky, with grey clouds and scattered rain showers seeing us out of the bay instead of the bright sunshine we hoped for. But with an overnight boat trip ahead of us to get to the first sites, we could maybe wake up to blue skies.

That, unfortunately, was not meant to be…

Leaving Ambon

Gloomy Ambon skies

When I mention “dive expedition in Indonesia”, most people tend not to imagine grey skies and unrelenting rain, but the lush tropics wouldn’t be quite as lush without lots and lots of rain! Throughout the week we had plenty of rain, sometimes so much we had to postpone dives because of the limited visibility at the surface: the boat driver needs to be able to see the divers at the surface to pick them up when surveys are done.

 

Rainy days
Maria and Gino

But we had come to Ambon to study coral reefs, so (mostly) undeterred by the rain, we hopped in and started our work! The first thing we noticed was a conspicuous lack of…coral. We started surveys in an area with a lot of human fishing activity, and it showed, big time. We did not hear any blasts while diving, but there was a lot of evidence of dynamite fishing. Entire reefs were reduced to rubble, some places even had large bomb craters, something I had never seen before. I dread to think about the size of the bomb and the immediate impacts of its blast. A lot of explosive power is required to leave a 40cm deep, 1.5m wide crater underwater!

It wasn’t all bad news though, some places were showing slow signs of recovery, which could mean they hadn’t been bombed for a while. There were still some large fish left, nowhere near as many as there should be, but I did spot a few large groupers and emperors, and even a few adult blacktip reef sharks. We saw encrusting algae and small coral slowly starting to take hold in some places, although they were still a long way from becoming a real coral reef again. I would estimate it could easily take another 50-100 years for these sites to become a fully functional reef, even if they were left in peace and there were no other impacts.

 

Crater caused by dynamite fishing
Dynamited reef, now a rubble field

After a couple of days of rain and survey dives that made our hearts ache, the team’s morale (or at least mine) had seen better days. Luckily, two things happened: we moved on to sites that had less fishing pressure and the sun started shining!

This part of the trip brought home just how rich coral reefs can be if you just use them in a less destructive way. Sites with very high and diverse coral cover, big schools of fish, lots of invertebrates, funky critters, everything you could want in a dive. This time our only regret was that the tight schedule didn’t give us time to explore each site more thoroughly. Between trying to count and identify large schools of mixed fish species, processing eDNA samples and entering data, little time was left to do anything else than eat and prepare for the next dive. Not that I’m complaining though, being able to work on reefs like this is a privilege that never gets old.

We were also privileged to see some of Ambon’s funky critters. During quite a few dives we came across ghostpipefish (Solenostomus paradoxus and S. cyanopterus), a rare sight on standard coral reef surveys. Our invertebrate expert had his work cut out counting a variety of nudibranchs, shrimp, cowries, and anything in between. Even the algae crew got more fish than they bargained for when a giant frogfish (Antennarius commersoni) decided to swim by and say hello.

 

Counting and identifying the fish on a reef can be a challenge
Coral reef near Nusa Laut

Despite some adverse weather and a slow start, we finished surveys within the planned time and arrived back in Ambon Bay two days ago. Our two days on land were put to good use, catching up on data entry and admin, meetings, and even catching a movie last night (Joker, pretty good actually). Tomorrow we leave at first light for a longer trip. We are headed to Halmahera, an area where precious little information exists on the health of coral reefs. If all goes according to plan, I should be able to write an update from Ternate in about 6 days!