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

Revolutionary method could bring us much closer to the description of hyperdiverse faunas

A novel approach relying on a short sequence of mitochondrial DNA in conjunction with a lateral image of the holotype specimen was proposed to greatly accelerate species identification and description, especially when it comes to hyperdiverse taxa, such as parasitic wasps.

At today’s rate, it could take another two millennia for science to document all currently existing species of multicellular life

Two hundred and sixty-one years ago, Linnaeus formalized binomial nomenclature and the modern system of naming organisms. Since the time of his first publication, taxonomists have managed to describe 1.8 million of the estimated 8 to 25 million extant species of multicellular life, somewhere between 7% and 22%. At this rate, the task of treating all species would be accomplished sometime before the year 4,000. In an age of alarming environmental crises, where taking measures for the preservation of our planet’s ecosystems through efficient knowledge is becoming increasingly urgent, humanity cannot afford such dawdling.

“Clearly something needs to change to accelerate this rate, and in this publication we propose a novel approach that employs only a short sequence of mitochondrial DNA in conjunction with a lateral image of the holotype specimen,”

explain the researchers behind a new study, published in the open-access journal Deutsche Entomologische Zeitschrift (DEZ).
Description rate of parasitic wasps species (superfamily
Ichneumonoidea).
Data from Taxapad (Yu et al. 2016).

In standardized practices, it is required that experts conduct plenty of time- and labor-consuming analyses, in order to provide thorough descriptions of both the morphology and genetics of individual species, as well as a long list of characteristic features found to differentiate each from any previously known ones. However, the scientists argue, at this stage, it is impossible to pinpoint distinct morphological characters setting apart all currently known species from the numerous ones not yet encountered. To make matters worse, finding human and financial resources for performing this kind of detailed research is increasingly problematic.

This holds especially true when it comes to hyperdiverse groups, such as ichneumonoid parasitoid wasps: a group of tiny insects believed to comprise up to 1,000,000 species, of which only 44,000 were recognised as valid, according to 2016 data. In their role of parasitoids, these wasps have a key impact on ecosystem stability and diversity. Additionally, many species parasitise the larvae of commercially important pests, so understanding their diversity could help resolve essential issues in agriculture.

Meanwhile, providing a specific species-unique snippet of DNA alongside an image of the specimen used for the description of the species (i.e. holotype) could significantly accelerate the process. By providing a name for a species through a formal description, researchers would allow for their successors to easily build on their discoveries and eventually reach crucial scientific conclusions.

“If this style were to be adopted by a large portion of the taxonomic community, the mission of documenting Earth’s multicellular life could be accomplished in a few generations, provided these organisms are still here,”

say the authors of the study.

To exemplify their revolutionary approach, the scientists use their paper to also describe a total of 18 new species of wasps in two genera (Zelomorpha and Hemichoma) known from Área de Conservación Guanacaste, Costa Rica. Currently, the team works on the treatment of related species, which still comprise only a portion of the hundreds of thousands that remain unnamed.

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Original source:

Meierotto S, Sharkey MJ, Janzen DH, Hallwachs W, Hebert PDN, Chapman EG, Smith MA (2019) A revolutionary protocol to describe understudied hyperdiverse taxa and overcome the taxonomic impediment. Deutsche Entomologische Zeitschrift 66(2): 119-145. https://doi.org/10.3897/dez.66.34683

Living room conservation: Gaming & virtual reality for insect and ecosystem conservation

Gaming and virtual reality could bridge the gap between urban societies and nature, thereby paving the way to insect conservation by the means of education and participation. This is what an interdisciplinary team at Florida International University strive to achieve by developing a virtual reality game (desktop version also available) dedicated to insect and plant species. Focused on imperiled butterflies, their innovative idea: Butterfly World 1.0, is described in the open-access journal Rethinking Ecology.

Participant playing the virtual reality version of Butterfly World 1.0.
Photo by Jaeson Clayborn.

Players explore and search for butterflies using knowledge gained through gameplay

Gaming and virtual reality (VR) could bridge the gap between urban societies and nature, thereby paving the way to insect conservation by the means of education, curiosity and life-like participation.

This is what Florida International University‘s team of computer scientist Alban Delamarre and biologist Dr Jaeson Clayborn strive to achieve by developing a VR game (desktop version also available) dedicated to insect and plant species. Focused on imperiled butterflies, their innovative idea: Butterfly World 1.0, is described in the open-access journal Rethinking Ecology.


When playing, information about each butterfly species is accessed on the player’s game tablet. Image by
Alban Delamarre and Dr Jaeson Clayborn.

Butterfly World 1.0 is an adventure game designed to engage its users in simulated exploration and education. Set in the subtropical dry forest of the Florida Keys (an archipelago situated off the southern coast of Florida, USA), Butterfly World draws the players into an immersive virtual environment where they learn about relationships between butterflies, plants, and invasive species. While exploring the set, they interact with and learn about the federally endangered Schaus’ swallowtail butterfly, the invasive graceful twig ant, native and exotic plants, and several other butterflies inhabiting the dry forest ecosystem. Other nature-related VR experiences, including conservation awareness and educational programs, rely on passive observations with minimal direct interactions between participants and the virtual environment.

According to the authors, virtual reality and serious gaming are “the new frontiers in environmental education” and “present a unique opportunity to interact with and learn about different species and ecosystems”.


In the real world, Spanish needles (Bidens alba) is considered a weed in South Florida. However, it is an excellent nectar source for butterflies.
Photo by Alban Delamarre.

The major advantage is that this type of interactive, computer-generated experience allows for people to observe phenomena otherwise impossible or difficult to witness, such as forest succession over long periods of time, rare butterflies in tropical dry forests, or the effects of invasive species against native wildlife.

“Imagine if, instead of opening a textbook, students could open their eyes to a virtual world. We live in a time where experiential learning and stories about different species matter, because how we feel about and connect with these species will determine their continued existence in the present and future. While technology cannot replace actual exposure to the environment, it can provide similar, near-realistic experiences when appropriately implemented,” say the scientists.

In conclusion, Delamarre and Clayborn note that the purpose of Butterfly World is to build knowledge, reawaken latent curiosity, and cultivate empathy for insect and ecosystem conservation.

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The game is accessible online at: http://ocelot.aul.fiu.edu/~adela177/ButterflyWorld/.

Original source:

Clayborn J, Delamarre A (2019) Living room conservation: a virtual way to engage participants in insect conservation. Rethinking Ecology 4: 31-43. https://doi.org/10.3897/rethinkingecology.4.32763

New commentary on the famous ‘Warning to Humanity’ paper brings up global inequalities

Dubbed as ‘the most talked about paper’, the cautionary publication is suggested to have omitted a non-western view on inequality that impedes global sustainability

By pointing out the western lifestyle is not “the norm and end goal of societal evolution”, the research team of Dr Mohsen Kayal (University of Perpignan, France) contributes to the debate on the urgency of achieving sustainability, as ignited by the largely publicised article “World Scientists’ Warning to Humanity: A Second Notice” published in BioScience in 2017. Their Response paper in the open-access journal Rethinking Ecology emphasizes that societies in developing countries are often more dependent on natural resources, while least responsible for the ecological crisis.

While expressing explicit support and endorsement for the call made in the original paper, the team argue that several of its recommendations “address symptoms rather than root causes”, while steering away from historical patterns and underlying drivers of the global socio-economic system, namely those relating to wealth inequality, human demography, and food production.

According to the researchers, the desired universal sustainability cannot be achieved in a situation of inequitable wealth distribution. They highlight the link between the consumerism and neocolonialism in the western society and the environmental declines. Meanwhile, communities in the developing world are much more vulnerable to ecological disasters and their homelands are being overexploited and compromised for the production of a major part of the commodities sold around the world.

Inequitable distribution is also evident in the ecological footprint of the western world as opposed to poorer regions. The team of Dr Mohsen Kayal question the appeal made in the Warning to Humanity paper that restricting birth rates is of primary concern when it comes to mitigating the anthropogenic effect on the planet. Rather, they argue that it is the excessive resource consumption and ecosystem-destructive practices observed in the western lifestyle that need to be prioritized.

Citing the 2017 data from the Food and Agriculture Organization of the United Nations, the authors note that there is indeed enough food being produced to meet the needs of even more people on Earth than there currently are. However, it is again the unequal distribution of resources that results in both hunger and obesity. In the meantime, the replacement of the current industrial model of agriculture with a suite of environmentally friendly practices (e.g. cover crops, diverse crop rotations), the adoption of ecologically-based farming and well-managed grazing could preserve soils and their properties, while also increasing yields, resilience to climate change and socio-economic development.

“Sustainability can only be achieved through prioritizing global ethics, including universal equality and respect for all forms of life,” conclude the authors of the Response paper. “Sustainable solutions to Earth’s socio-ecological crisis already exist, however humanity still needs to realize that pursuing the same practices that created these problems is not going to solve them.”

Global Resource Trade

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Original source:

Kayal M, Lewis H, Ballard J, Kayal E (2019) Humanity and the 21st century’s resource gauntlet: a commentary on Ripple et al.’s article “World scientists’ warning to humanity: a second notice”. Rethinking Ecology 4: 21-30. https://doi.org/10.3897/rethinkingecology.4.32116

‘Insectageddon’ is ‘alarmist by bad design’: Scientists point out the study’s major flaws

Many insects species require pristine environments, including old-growth forests. Photo by Atte Komonen.

Earlier this year, a research article triggered a media frenzy by predicting that as a result of an ongoing rapid decline, nearly half of the world’s insects will be no more pretty soon

Amidst worldwide publicity and talks about ‘Insectageddon’: the extinction of 40% of the world’s insects, as estimated in a recent scientific reviewa critical response was published in the open-access journal Rethinking Ecology.

Query- and geographically-biased summaries; mismatch between objectives and cited literature; and misuse of existing conservation data have all been identified in the alarming study, according to Drs Atte Komonen, Panu Halme and Janne Kotiaho of the University of Jyväskylä (Finland). Despite the claims of the review paper’s authors that their work serves as a wake-up call for the wider community, the Finnish team explain that it could rather compromise the credibility of conservation science.

The first problem about the paper, titled “Worldwide decline of the entomofauna: A review of its drivers” and published in the journal Biological Conservation, is that its authors have queried the Web of Science database specifically using the keywords “insect”, “decline” and “survey”.

“If you search for declines, you will find declines. We are not questioning the conclusion that insects are declining,” Komonen and his team point out, “but we do question the rate and extent of declines.”

Many butterflies have declined globally. Scolitantides orion, for example, is an endangered species in Finland. Photo by Atte Komonen.

The Finnish research team also note that there are mismatches between methods and literature, and misuse of IUCN Red List categories. The review is criticised for grouping together species, whose conservation status according to the International Union for Conservation of Nature (IUCN) is Data Deficient with those deemed Vulnerable. By definition, there are no data for Data Deficient species to assess their declines.

In addition, the review paper is seen to use “unusually forceful terms for a peer-reviewed scientific paper,” as the Finnish researchers quote a recent news story published in The Guardian. Having given the words dramatic, compelling, extensive, shocking, drastic, dreadful, devastating as examples, they add that that such strong intensifiers “should not be acceptable” in research articles.

“As actively popularising conservation scientists, we are concerned that such development is eroding the importance of the biodiversity crisis, making the work of conservationists harder, and undermining the credibility of conservation science,” the researchers explain the motivation behind their response.

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Original source:

Komonen A, Halme P, Kotiaho JS (2019) Alarmist by bad design: Strongly popularized unsubstantiated claims undermine credibility of conservation science. Rethinking Ecology 4: 17-19. https://doi.org/10.3897/rethinkingecology.4.34440