Tag: Japan

Simplified method to survey amphibians will aid conservation

Researchers developed a method to determine which amphibians inhabit a specific area. The new technique will resolve some of the issues with conventional methods, such as capture and observational surveys.

Ryukyu Sword Tailed Newt, or Firebellied Newt. *Photo by Neil Dalphin via Creative Commons CC0.*

An international collaborative research group of members from seven institutions has developed a method to determine which amphibians (frogs, newts and salamanders) inhabit a specific area. Their work was published in the open-access, peer-reviewed journal Metabarcoding and Metagenomics (MBMG).

To do so, the scientists amplified and analysed extra-organismal DNA (also known as environmental DNA or eDNA) found in the water. This DNA ends up in the water after being expelled from the amphibian’s body along with mucus and excrement.

The research group included Postdoctoral Researcher Sakata K. Masayuki and Professor Minamoto Toshifumi (Kobe University), Associate Professor Kurabayashi Atsushi (Nagahama Institute of Bio-Science and Technology), Nakamura Masatoshi (IDEA Consultants, Inc.) and Associate Professor Nishikawa Kanto (Kyoto University).

The newly developed technique will resolve some of the issues with conventional methods, such as capture and observational surveys, which require a specialist surveyor who can visually identify species. Conventional surveys are also prone to discrepancies due to environmental factors, such as climate and season.

The researchers hope that the new method will revolutionise species monitoring, as it will enable anyone to easily monitor the amphibians that inhabit an area by collecting water samples.

While monitoring in general is crucial to conserve the natural ecosystems, the importance of surveying amphibians is even more pressing, given the pace of their populations’ decline.

Amongst major obstacles to amphibian monitoring, however, are the facts that they are nocturnal; their young (e.g. tadpoles) and adults live in different habitats; and that specialist knowledge is required to capture individuals and identify their species. These issues make it particularly difficult to accurately survey amphibians in a standardised way, and results of individual efforts often contradict each other.

On the other hand, eDNA analysis techniques have already been established in programmes targeted at monitoring fish species, where they are already commonplace. So, the researchers behind the present study joined forces to contribute towards the development of a similar standardised analysis method for amphibians.

First of all, the researchers designed multiple methods for analysing the eDNA of amphibians and evaluated their performance to identify the most effective method. Next, they conducted parallel monitoring of 122 sites in 10 farmlands across Japan using the developed eDNA analysis along with the conventional methods (i.e. capture surveys using a net and observation surveys).

As a result, the newly developed method was able to detect all three orders of amphibians: Caudata (the newts and salamanders), Anura (the frogs), and Gymnophiona (the caecilians).

Furthermore, this novel eDNA analysis method was able to detect more species across all field study sites than the conventional method-based surveys, indicating its effectiveness.

Research Background

Amphibian biodiversity is continuing to decline worldwide and collecting basic information about their habitats and other aspects via monitoring is vital for conservation efforts. Traditional methods of monitoring amphibians include visual and auditory observations, and capture surveys.

However, amphibians tend to be small in size and many are nocturnal. The success of surveys varies greatly depending on the climate and season, and specialist knowledge is required to identify species. Consequently, it is difficult to monitor a wide area and assess habitats. The last decade has seen the significant development of environmental DNA analysis techniques, which can be used to investigate the distribution of a species by analysing external DNA (environmental DNA) that is released into the environment along with an organism’s excrement, mucus and other bodily fluids.

The fundamentals of this technique involve collecting water from the survey site and analysing the eDNA contained in it to find out which species inhabit the area. In recent years, the technique has gained attention as a supplement for conventional monitoring methods. Standardised methods of analysis have already been established for other species, especially fishes, and diversity monitoring using eDNA is becoming commonplace.

However, eDNA monitoring of amphibians is still at the development stage. One reason for this is that the proposed eDNA analysis method must be suitable for the target species or taxonomic group, and there are still issues with developing and implementing a comprehensive method for detecting amphibians. If such a method could be developed, this would make it possible for monitoring to be conducted even by people who do not have the specialised knowledge to identify species nor surveying experience.

Hopefully, this would be established as a unified standard for large-scale monitoring surveys, such as those on a national scale. This research group’s efforts to develop and evaluate analysis methods will hopefully lay the foundations for eDNA analysis to become a common tool for monitoring amphibians, as well as fish.

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Follow Metabarcoding and Metagenomics (MBMG) journal on Twitter and Facebook.

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Research article:

Sakata MK, Kawata MU, Kurabayashi A, Kurita T, Nakamura M, Shirako T, Kakehashi R, Nishikawa K, Hossman MY, Nishijima T, Kabamoto J, Miya M, Minamoto T (2022) Development and evaluation of PCR primers for environmental DNA (eDNA) metabarcoding of Amphibia. Metabarcoding and Metagenomics 6: e76534. https://doi.org/10.3897/mbmg.6.76534

World’s largest campodeid dipluran named after the mythological giant Daidarabotchi

*The giant newly described species Pacificampa daidarabotchi, discovered in the Mejiro-do cave, Kyushu, Japan. Photo by Rodrigo Lopes Ferreira.*

The insect-like animal is also the first subterranean representative of its family in Japan

Amongst the fauna thriving in the subterranean spaces below the surface of the earth’s crust, the insect-like diplurans and, precisely, those in the campodeid family are one of the best-known groups, currently comprising almost 150 species. However, not a single subterranean member of the family had been known from Japan until very recently.

As part of a project at the National Council of Technological and Scientific Development, the research team of Dr. Rodrigo Lopes Ferreira, Universidade Federal de Lavras, Brasil, and Dr. Kazunori Yoshizawa, Hokkaido University, Japan, conducted an expedition to a total of 11 carbonate caves in the southern Japanese islands of Kyushu and Shikoku. Out of these, they managed to collect dipluran specimens from three touristic sites and sent them to Dr. Alberto Sendra from the Research group in Soil Biology and Subterranean Ecosystems at Alcala University, Spain, for identification.

*The Mejiro-do cave, Kyushu Island, Japan: the type locality of the newly discovered record-breaking species Pacificampa daidarabotchi. Photo by Rodrigo Lopes Ferreira.*

To the amazement of the scientists, it turned out that they had collected specimens of two previously unrecognised species of well-adapted subterranean campodeid diplurans.

Moreover, one of the new species (Pacificampa daidarabotchi), identified exclusively from the Mejiro-do cave located near an active quarry in Kyushu, proved to be the largest known dipluran in the family Campodeidae. Measuring about 10 mm in length, the creature looks gigantic next to any other campodeid, which, most often, are only half as big.

Inspired by the peculiar size of the former, the researchers decided to name it after the giant yökai creature Daidarabotchi, known from Japanese mythology. According to one of the legends, Daidarabotchi once lifted up the mountains of Fuji and Tsukuba in order to weigh them. By accident, he split the peak of Tsukuba in the process.

Another remarkable finding from the same study is that the genus, where both new species were assigned – Pacificampa – serves as yet another example of the former physical connection between Asia and America some millennia ago. In their paper, the scientists note that the genus demonstrates close affinities with a genus known from North America.

“We hope that this discovery could stop the destruction of the land nearby and preserve for the future the subterranean habitat of these remarkable gigantic species,” say the researchers in conclusion.

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Last year, lead author Dr. Alberto Sendra and his colleagues Prof. Boris Sket, University of Ljubljana, and Prof. Pavel Stoev, National Museum of Natural History, Bulgaria, described another cave-dwelling campodeid dipluran to the world’s amazement.

Discovered in Eastern Turkmenistan, the species, whose name (Turkmenocampa mirabilis) refers to its wondrous peculiarity, was the first of in the order Diplura found in Central Asia. Further, it was the first strictly subterranean terrestrial creature recorded in the country.

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Original source:

Sendra A, Yoshizawa K, Ferreira RL (2018) New oversize troglobitic species of Campodeidae in Japan (Diplura). Subterranean Biology 27: 53-73. https://doi.org/10.3897/subtbiol.27.28575

Plants cheat too: A new species of fungus-parasitizing orchid

Plants usually produce their own nutrients by using sun energy, but not all of them. A new ‘cheater’ species of orchid from Japan, lives off nutrients obtained via a special kind of symbiosis with fungi. The study was published in the open access journal PhytoKeys.

The new orchid species, named Lecanorchis tabugawaensis, is by far not on its own in its strange feeding habits. The so called mycoheterotrophic plants are found among all plant species groups.

Mycoheterotrophy is a term derived from Greek to describe the bizarre symbiotic relationship between some plants and fungi, where the plant gets nutrients parasitizing upon fungi, rather than using photosynthesis.

Considered a kind of a cheating relationship, these plants are sometimes informally referred to as “mycorrhizal cheaters”.

Having long attracted the curiosity of botanists and mycologists, a common feature of most mycoheterotrophic plants is their extreme scarcity and small size. In addition, most species are hiding in the dark understory of forests, only discoverable during the flowering and fruiting period when aboveground organs appear through the leaf litter.

Despite it seems like these ‘cheating’ plants have it all easy for themselves, in reality they are highly dependent on the activities of both the fungi and the trees that sustain them. Such a strong dependency makes this fascinating plant group particularly sensitive to environmental destruction.

“Due to the sensitivity of mycoheterotrophic plants it has long been suggested that their species richness provides a useful indicator of the overall floral diversity of forest habitats. A detailed record of the distribution of these vulnerable plants therefore provides crucial data for the conservation of primary forests,” explains leading author Dr Kenji Suetsugu, Kobe University.

Just discovered, the new orchid species has been already assessed with an IUCN status – Critically Endangered. With a distribution restricted to only two locations along the Tabu and Onna Rivers, Yakushima Island, this fungus-eating cheater might need some conservation attention.

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Original Source:

Suetsugu K, Fukunaga H (2016) Lecanorchis tabugawaensis (Orchidaceae, Vanilloideae), a new mycoheterotrophic plant from Yakushima Island, Japan. PhytoKeys 73: 125-135. doi: 10.3897/phytokeys.73.10019

Living together in mud: New bivalve species dwelling on a sea cucumber discovered in Japan

Most bivalves live in sand or mud or attached to rock surface. However, a new bivalve species described from Japan lives on a sea cucumber.

Ryutaro Goto, postdoctoral fellow in Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, and Hiroshi Ishikawa, amateur malacologist in Japan, have their paper, describing the new species, published in the open access journal ZooKeys.

The new species, named Borniopsis mortoni(Galeommatoidea), was discovered in mudflats at the mouth of the Souzu River, southwestern Shikoku Island, Japan.

This bivalve has tiny brownish shells (up to 4.1 mm in length). The species lives attached by both its foot and byssal threads to the body surface of the earthworm-like sea cucumberPatinapta ooplax (Synaptidae). Individuals of B. mortoni are often found on the same host, yet sometimes there could be more than 10 individuals existing side-by-side.

The new species is dedicated to a famous British malacologist Brian Morton, emeritus professor of University of Hong Kong. He has described many interesting Pseudopythina species from mudflats in Hong Kong, now assigned to the genus Borniopsis.

Host sea cucumbers burrow in mudflats. Most likely, the B. mortoni bivalve uses the host burrows as shelter from predators.

The new species is one of the smallest species in this genus. With the burrow of the host sea cucumber being very narrow, the small body size of B. mortoni is probably a corresponding adaptation.

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Original source:

Goto R, Ishikawa H (2016) Borniopsis mortoni sp. n. (Heterodonta, Galeommatoidea, Galeommatidae sensu lato), a new bivalve commensal with a synaptid sea cucumber from Japan. ZooKeys 615: 33-45. doi: 10.3897/zookeys.615.8125

Unusual new zoantharian species is the first described solitary species in over 100 years

A very unusual new species of zoantharian surprised Drs Takuma Fujii and James Davis Reimer, affiliated with Kagoshima University and University of the Ryukyus.

The scientists stumbled upon a solitary individual polyp while conducting SCUBA surveys around the southern Japanese island of Okinawa. They noticed that the creatures were buried almost completely in the soft sediment of the seafloor. It was only their oral disks and tentacles that were protruding above the surface.

Generally, most known zoantharians are colonial (hence their common name of ‘colonial anemones’), and many dwell in shallow waters of subtropical and tropical regions, where their large colonies can be found on coral reefs.

However, these newly discovered polyps were not only leading solitary lives. They were also found to lack zooxanthellae, single-celled organisms that coexist in symbiosis with certain marine invertebrates, also typical for the majority of zoantharians.

The discovery of this unusual new species is reported in the open access journal ZooKeys.

Solitary zoantharian species, such as this one, are known from scant few reports, and only three species are described, all reported more than 100 years ago from the Indo-Pacific region. Overall, very little is known about the hereby studied genus Sphenopus.

The new species, named Sphenopus exilis, is much smaller than the other three Sphenopus species, with its polyps measuring approximately 3 cm in length. It is currently only known from two bays on the east coast of Okinawa Island.

Both of the bays where Sphenopus exilis is found are threatened by development, with one of the bays currently the center of controversy over a proposed American military base expansion and landfill.

“This report demonstrates how much more research is needed on these understudied ecosystems”, stated lead author Dr. Takuma Fujii.

“The only reason this species was discovered was that the right person was in the right place at the right time”, added co-author Dr. James Reimer.

“Such research also shows how important it is to have specialist researchers participate in surveys — otherwise, we might be missing a lot of the biodiversity present in the marine realm simply because we don’t know what we are looking at,” he concluded.

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Original source:

Fujii T, Reimer JD (2016) A new solitary free-living species of the genus Sphenopus (Cnidaria, Anthozoa, Zoantharia, Sphenopidae) from Okinawa-jima Island, Japan. ZooKeys 606: 11-24. doi: 10.3897/zookeys.606.9310

Undergraduate student takes to Twitter to expose illegal release of alien fish in Japan

Posing a significant threat to the native biodiversity in Japan, specifically that of threatened aquatic insects, some alien fishes, such as the bluegill, have become the reason for strict prohibitions. All activities potentially capable of introducing the species into the wild are currently punishable by either a fine of up to 3 million yen for a person (100 million yen for corporations), or a prison sentence of up to 3 years.

Recently, ten years after the law has been adopted, illegal release of bluegill fish has been reported for the first time with the help of a post on Twitter from Akinori Teramura, undergraduate student at the Tokyo University of Marine Science and Technology and second author of the present study. The case is reported and discussed by him and two scientists, affiliated with Kanagawa Prefectural Museum of Natural History, Japan, in the open-access journal ZooKeys.

In June 2015, Akinori Teramura tweeted two photographs of the invasive bluegill fish, both adults and juveniles, along with two young goldfish, which do not belong to the local fauna, either. In his post he identified the species and shared his surprise at the irresponsibility of the people who had released the fish. When lead author Dr Yusuke Miyazaki saw the tweet, he signalled his colleagues with the idea to publish the information as a scientific report.

The student found them in an outdoor public pool in Yokohama city, Japan, while it was being cleaned before being opened ahead of the summer. Usually, these facilities are closed to the public during the colder seasons and it is then when native aquatic insect species, such as dragonflies and diving beetles, find spawning and nursery habitats in them. Curiously enough, though, the pool had been isolated from natural waters since its construction.

Therefore, the researchers conclude that the alien fishes have most likely been released from an aquarium from a local shop or an aquarist who no longer wanted them. However, the authors note that according to the law, keeping bluegill fish in a home aquarium is illegal as well.

“Our report demonstrates an example of web data mining in the discipline of Citizen Science,” say the authors. “Web data mining has been rapidly developing over recent years, and its potential continues to expand.”

“Community awareness of this issue needs to be improved, and widespread reporting of cases such as this one will help,” they conclude.

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Original source:

Miyazaki Y, Teramura A, Senou H (2016) Biodiversity data mining from Argus-eyed citizens: the first illegal introduction record of Lepomis macrochirus macrochirus Rafinesque, 1819 in Japan based on Twitter information. ZooKeys 569: 123-133. doi: 10.3897/zookeys.569.7577