fish diversity

Scientists took a rare chance to prove we can quantify biodiversity by ‘testing the water’

Recent study conducted at a UK fishery farm provides new evidence that DNA from water samples can accurately determine fish abundance and biomass

Organisms excrete DNA in their surroundings through metabolic waste, sloughed skin cells or gametes, and this genetic material is referred to as environmental DNA (eDNA).

As eDNA can be collected directly from water, soil or air, and analysed using molecular tools with no need to capture the organisms themselves, this genetic information can be used to report biodiversity in bulk. For instance, the presence of many fish species can be identified simultaneously by sampling and sequencing eDNA from water, while avoiding harmful capture methods, such as netting, trapping or electrofishing, currently used for fish monitoring.

While the eDNA approach has already been applied in a number of studies concerning fish diversity in different types of aquatic habitats: rivers, lakes and marine systems, its efficiency in quantifying species abundance (number of individuals per species) is yet to be determined. Even though previous studies, conducted in controlled aquatic systems, such as aquaria, experimental tanks and artificial ponds, have reported positive correlation between the DNA quantity found in the water and the species abundance, it remains unclear how the results would fare in natural environments.

However, a research team from the University of Hull together with the Environment Agency (United Kingdom), took the rare opportunity to use an invasive species eradication programme carried out in a UK fishery farm as the ultimate case study to evaluate the success rate of eDNA sampling in identifying species abundance in natural aquatic habitats. Their findings were published in the open-access, peer-reviewed journal Metabarcoding and Metagenomics.

“Investigating the quantitative power of eDNA in natural aquatic habitats is difficult, as there is no way to ascertain the real species abundance and biomass (weight) in aquatic systems, unless catching all target organisms out of water and counting/measuring them all,”
explains Cristina Di Muri, PhD student at the University of Hull.

Drained pond after fish translocation.
Photo by Dr. Watson H.V.

During the eradication, the original fish ponds were drained and all fish, except the problematic invasive species: the topmouth gudgeon, were placed in a new pond, while the original ponds were treated with a piscicide to remove the invasive fish. After the eradication, the fish were returned to their original ponds. In the meantime, all individuals were counted, identified and weighed from experts, allowing for the precise estimation of fish abundance and biomass.

“We then carried out our water sampling and ran genetic analysis to assess the diversity and abundance of fish genetic sequences, and compared the results with the manually collected data. We found strong positive correlations between the amount of fish eDNA and the actual fish species biomass and abundance, demonstrating the existence of a strong association between the amount of fish DNA sequences in water and the actual fish abundance in natural aquatic environments,”
reports Di Muri.

Environmental DNA sampling using water collection bottles
Photo by Dr. Peirson G.

The scientists successfully identified all fish species in the ponds: from the most abundant (i.e. 293 carps of 852 kg total weight) to the least abundant ones (i.e. one chub of 0.7 kg), indicating the high accuracy of the non-invasive approach.

“Furthermore, we used different methods of eDNA capture and eDNA storage, and found that results of the genetic analysis were comparable across different eDNA approaches. This consistency allows for a certain flexibility of eDNA protocols, which is fundamental to maintain results comparable across studies and, at the same time, choose the most suitable strategy, based on location surveyed or resources available,”
elaborates Di Muri.

“The opportunity of using eDNA analysis to accurately assess species diversity and abundance in natural environments will drive a step change in future species monitoring programmes, as this non-invasive, flexible tool is adaptable to all aquatic environments and it allows quantitative biodiversity surveillance without hampering the organisms’ welfare.”

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Original publication:

Di Muri C, Lawson Handley L, Bean CW, Li J, Peirson G, Sellers GS, Walsh K, Watson HV, Winfield IJ, Hänfling B (2020) Read counts from environmental DNA (eDNA) metabarcoding reflect fish abundance and biomass in drained ponds. Metabarcoding and Metagenomics 4: e56959. https://doi.org/10.3897/mbmg.4.56959

Wakanda Forever! Scientific divers describe new purple species of “twilight zone” fish from Africa

Named for Black Panther’s mythical nation of Wakanda, a dazzling new “Vibranium” Fairy Wrasse enchants with purple scales and a preference for deep, little-known mesophotic reefs up to 260 feet below the surface

Africa has new purple-clad warriors more than 200 feet beneath the ocean’s surface. Deep-diving scientists from the California Academy of Sciences’ Hope for Reefs initiative and the University of Sydney spotted dazzling fairy wrasses—previously unknown to science—in the dimly lit mesophotic coral reefs of eastern Zanzibar, off the coast of Tanzania.

Preserved specimen of Vibranium fairy wrasse (*Cirrhilabrus wakanda*) retains its striking coloration.
Photo by Jon Fong © 2018 California Academy of Sciences.

The multicolored wrasses sport deep purple scales so pigmented, they even retain their color (which is typically lost) when preserved for research. The scientists name this “twilight zone” reef-dweller Cirrhilabrus wakanda (common name “Vibranium Fairy Wrasse”) in honor of the mythical nation of Wakanda from the Marvel Entertainment comics and movie Black Panther. The new fish is described in the open-access journal Zookeys.

Female specimen of Vibranium fairy wrasse (*Cirrhilabrus wakanda*) in its natural habitat (Zanzibar). Photo by Luiz Rocha © 2018 California Academy of Sciences.

Yi-Kai Tea, lead author and ichthyology PhD student from the University of Sydney, says:

“When we thought about the secretive and isolated nature of these unexplored African reefs, we knew we had to name this new species after Wakanda. We’ve known about other related fairy wrasses from the Indian Ocean, but always thought there was a missing species along the continent’s eastern edge. When I saw this amazing purple fish, I knew instantly we were dealing with the missing piece of the puzzle.”

The Academy scientists say Cirrhilabrus wakanda’s remote home in mesophotic coral reefs—below recreational diving limits—probably contributed to their long-hidden status in the shadows of the Indian Ocean.

A California Academy diver on an expedition in the Indian Ocean.
Photo by Bart Shepherd © 2018 California Academy of Sciences.

Therefore, Hope for Reefs’ scientific divers are highly trained for the dangerous process of researching in these deep, little-known mesophotic reefs, located 200 to 500 feet beneath the ocean’s surface. Accessing them requires technical equipment and physically intense training well beyond that of shallow-water diving. The team’s special diving gear (known as closed-circuit rebreathers) includes multiple tanks with custom gas blends and electronic monitoring equipment that allow the divers to explore deep reefs for mere minutes before a lengthy, hours-long ascent to the surface.

Dr. Luiz Rocha, Academy Curator of Fishes and co-leader of the Hope for Reefs, comments:

“Preparation for these deep dives is very intense and our dive gear often weighs more than us. When we reach these reefs and find unknown species as spectacular as this fairy wrasse, it feels like our hard work is paying off.”

California Academy’s “twilight zone” dive gear prepped for Zanzibar.
Photo by Luiz Rocha © 2018 California Academy of Sciences.

Using a microscope, the team examined the specimens’ scales, fin rays, and body structures. DNA and morphological analyses revealed the new fairy wrasse to be different from the other seven species in the western Indian Ocean as well as other relatives in the Pacific. The new species’ common name is inspired by the fictional metal vibranium, a rare, and, according to Rocha, “totally awesome” substance found in the nation of Wakanda. The Vibranium Fairy Wrasse’s purple chain-link scale pattern reminded the scientists of Black Panther’s super-strong suit and the fabric motifs worn by Wakandans in the hit film.

Precious life in deep reefs

In a recent landmark paper, the Academy team found that twilight zone reefs are unique ecosystems bursting with life and are just as vulnerable to human threats as their shallow counterparts. Their findings upended the long-standing assumption that species might avoid human-related stressors on those deeper reefs. The Hope for Reefs team will continue to visit and study twilight zone sites around the world to shed light on these often-overlooked ecosystems.

Newly described Pohnpei fish (*Liopropoma incandescens*). Photo by Luiz Rocha © 2018 California Academy of Sciences.

In addition to this new fish from Zanzibar, Rocha and his colleagues recently published descriptions of mesophotic fish from Rapa Nui (Easter Island) and Micronesia. Luzonichthys kiomeamea is an orange, white, and sunny yellow dwarf anthias endemic to Rapa Nui, and the basslet Liopropoma incandescens (another new species published today in Zookeys) inhabits Pohnpei’s deep reefs—a neon orange and yellow specimen collected from a rocky slope 426 feet beneath the ocean’s surface.

“It’s a time of global crisis for coral reefs, and exploring little-known habitats and the life they support is now more important than ever,” concludes Rocha. “Because they are out of sight, these deeper reefs are often left out of marine reserves, so we hope our discoveries inspire their protection.”

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(Text by the California Academy of Sciences, USA)

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Research articles:

Tea YK, Pinheiro HT, Shepherd B, Rocha LA (2019) Cirrhilabrus wakanda, a new species of fairy wrasse from mesophotic ecosystems of Zanzibar, Tanzania, Africa (Teleostei, Labridae). ZooKeys 863: 85–96. https://doi.org/10.3897/zookeys.863.35580.

Pinheiro HT, Shepherd B, Greene BD, Rocha LA (2019) Liopropoma incandescens sp. nov. (Epinephelidae, Liopropominae), a new species of basslet from mesophotic coral ecosystems of Pohnpei, Micronesia. ZooKeys 863: 97–106. https://doi.org/10.3897/zookeys.863.33778.

‘Hidden fish’ genus described for 2 new weakly electric mormyrid species from Gabon

A new weakly electric mormyrid fish genus of two new species has been described from only three specimens collected over a period of 13 years in the rivers of the Central African country of Gabon. The genus has been named Cryptomyrus, meaning ‘hidden fish’ in Greek, and is the first new genus to be described within the family Mormyridae since 1977.

The study, authored by Dr. John Sullivan and Prof. Carl Hopkins of Cornell University, Ithaca, New York, and Sebastien Lavoue of the Institute of Oceanography at the National Taiwan University in Taipei, Taiwan, is published in the open-access journal ZooKeys.

“It’s odd we have only three specimens, given how much fish collection effort there’s been in Gabon over the past years,” says lead author Dr. John Sullivan. “Not having more made the descriptions difficult, but it was important to bring this discovery to light without further delay.” Sullivan added that he does not know if these fish are rare throughout their range or if specialists simply have not sampled localities or habitats where they are common, yet. “It shows that we still have a very incomplete picture of fish diversity in Gabon,” says Dr. Sullivan.

The last of the three specimens was found on an expedition to Gabon’s Ogooue River in September 2014, jointly sponsored by CENAREST and The Nature Conservancy. It was after nightfall on the Ogooue, beside Doume Falls, when Sullivan and the other team members caught the one odd fish in a plastic fish trap baited with earthworms. Reflecting its river of origin, the species now bares the name Cryptomyrus ogoouensis, while the second – Cryptomyrus ona, is named after Gabonese environmental activist Marc Ona Essangui.

Puzzled over the identity of the fish, back home at the Cornell University Museum of Vertebrates Dr. Sullivan remembered two somewhat similar specimens collected in Gabon and sent to him for identification by his colleagues Sebastien Lavoue and Yves Fermon, 11 years apart. “This is why we need natural history collections,” said Dr. Sullivan, “to keep these specimens and their DNA samples in good condition, because it can take years or even decades to connect the dots.”

Analyses of the DNA from the three specimens conducted at Cornell University showed they were close relatives and did not belong within any recognized genus. “That left us no choice but to describe them as a new genus, and Cryptomyrus, which means “hidden fish,” seemed an appropriate name given how hard they are to find,” said Dr. Sullivan.

Over 200 species of mormyrid fish live in fresh waters across Africa where they orient to their environment and communicate using electric pulses, too weak to be felt by humans, in combination with highly sensitive electroreceptor cells embedded in their skin.

The Nature Conservancy, a global conservation organization that works in more than 35 countries around the world, funded the 2014 expedition of the Ogooue. “We were thrilled to have contributed to this discovery,” said Marie-Claire Paiz, Gabon Program Director for The Nature Conservancy. “Our goal is to help Gabon acquire better baseline knowledge about the state of their fish and rivers which will enable them make science-guided choices about where and how to use their resources wisely for both people and nature.”

“The Nature Conservancy deserves a lot of credit,” commented Sullivan. “It’s a great example of how a conservation organization can promote the discovery of biodiversity by partnering with taxonomists and natural history museums.”

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Original Source:

Citation: Sullivan JP, Lavoue S, Hopkins CD (2016) Cryptomyrus: a new genus of Mormyridae (Teleostei, Osteoglossomorpha) with two new species from Gabon, West-Central Africa.ZooKeys 561: 117-150. doi: 10.3897/zookeys.561.7137